text:
|UFDC Home
|myUFDC Home | Help
This item has the following downloads:
|Full Text
Copyright 2007
Hong Yu
To my daughter, Elaine Rogers
I would like foremost to thank my parents, Shunyang Yu and Huaizhen Yan, who always
put their children's wellbeing first, and believed in me and encouraged me to be my best, as well
as my sister, Qiong Yu for her friendship. I also would like to thank my husband, James Rogers,
for his guidance and help in my adjustment to life in a new country and in learning English, and
for his companionship through my graduate career. I would like to thank all my other family
members, who gave me support and love throughout my life.
Many thanks are given to the friends I have met along my graduate career, who have
helped me in my personal life as well as my graduate life in chemistry: Dr. Rong Jiang, Dr. Chia
Pooput, Dr. Yi'an Zhai, Dr. Lin Wang, and Dr. Hui Tao.
I also sincerely thank Dr. James Yang and Yanrong Wu, who helped making part of my
research possible by synthesizing aptamers whenever I need them. I would like to thank Dr.
Weihong Tan for encouraging the collaboration between our group and his group. I would like
to thank Lin Yuan for sharing her hood with me for the carboxylation reaction. I would like to
thank Dr. Gary Cunningham and Nancy Liu for providing the access to the UV-vis
I am very grateful for the help Michael Napolitano and Daniel Magparangalan gave me
for correcting my dissertation. My thanks also are extended to other former and present group
members: Dr. Timothy Garrett, Dr. Alisha Mitchell-Roberts, Dr. Samaret Otero-Santos, Dr.
Mike Belford, Christopher Hilton, Frank Kero, Dodge Baluya, and Rachelle Landgraf.
I would like to thank Dr. David Powell and Dr. Ken Wagener for their helpful discussion
about my research proj ect.
I want to thank my advisor, Professor Richard Yost, for giving me the opportunity to
obtain my doctorate under his direction. He offered me the freedom of choosing the proj ect I
was interested in, and gave me guidance and perspective for the research along the way. I would
also like to thank my first graduate advisor, Professor Timothy Patrick at Southern Illinois
University, where I received a Master of Science in Chemistry. His belief in my abilities
inspired me to continue my education at the University of Florida. There are many teachers and
instructors I would like to thank over the years, all of whom have encouraged me and supported
me to continue my stated goals.
Introduction to Mass Spectrometry: 3-D And 2-D Quadrupole lon Trap Mass
Spectrometry .............. ........................1
Introduction to Mass Spectrometry .............. ......... .............1
Introduction to 3-D Quadrupole lon Trap Mass Spectrometry ................... ...............15
Introduction to 2-D Quadrupole lon Trap Mass Spectrometry ................. .. .................16
Development of Ionization Methods for MS Analysis: from LD to MALDI and from
MALDI to SELDI ............ ...... .__ ...............17...
Introduction to Aptamers ........._._.. ..... .... ...............22...
Definition and Synthesis of Aptamers ........._................ ._.. .. ........ ...........2
The Advantages of Using Aptamers vs. Antibody and the Applications in
Bioanalysis............... ..............2
Overview of Dissertation ............ ...... .. ...............30.
Problems Associated with MALDI-MS Sample Preparation Methods ............... .... ........._..47
Background Interference from Matrix Molecules in MALDI-MS...................... ........._..47
The Uneven Distribution of Analyte Molecules with the Traditional MALDI-MS
Sample Preparation Methods .............. ...............50....
Introduction to the RF Polym er ..................... ..... .. ......... ... .. ..... ... .......5
Systematic Investigation in Preparation of the RF and Matrix-Derived RF Polymers ..........54
Analysis of the Spiperone on the CHCA Derived RF Polymer for Lower Background
Interference from Matrix Molecules ............. ..... .....__ ... ..._ ..... ........5
Analysis of the Spiperone on the CHCA-Derived RF Polymer vs. Analysis of the
Spiperone on the Stainless Steel Using CHCA as Matrix for More Uniform Analyte
Signal Intensity Across the Sample .............. ...............61....
Conclusion ............ ..... ._ ...............64...
Aptamers Used for RF Polymer Surface Modification .............. ...............89....
Direct Surface Modification of the RF Polymer with Aptamer ................. ..........___.......92
Surface Modification of the RF Polymer with Aptamers via Surface Modification of the
RF Polymer with Carboxylic Groups...................... ... ...............9
Characterization of the Carboxylic Group-Modified RF Polymer .............. .. ..........___...93
Affinity Capture of RG 19 with RG 19-Retaining Aptamer-Modified RF Polymer and
Characterization of the Modified RF Polymer .............. ....... ._ ...... ..___..........9
Affinity Capture of Cocaine with Direct and Indirect Cocaine-Retaining Aptamer-
M odified RF Polymer .............. ...............96....
Conclusion ............ ............ ...............99...
Table page
2-1 RF polymers with acetone as solvent and Na2CO3 aS catalyst .............. ....................8
2-2 RF polymers with ethanol as solvent and Na2CO3 as catalyst .............. ....................84
2-3 RF polymers with water as solvent and Na2CO3 Or HC1, or HCIO4 aS catalyst.................85
2-4 RF polymers with acetone as solvent and HCI as catalyst ................. ......._ ..........86
Figure page
1-1 Parts of the 3 -D quadrupole ion trap ............ ..... ._ ...............31
1-2 Stability diagram in (az qz) space for the region of simultaneous stability. .....................32
1-3 Basic design of the two-dimensional linear ion trap ................. ................ ......... .3 3
1-4 Application of DC, RF trapping, and AC excitation voltages for 2-D ion trap. ................34
1-5 Electron ionization schematic ................. ...............35................
1-6 Chemical ionization schematic .............. ...............36....
1-7 Illustration of FAB ............ ..... ._ ...............37...
1-8 Electrospray ionization schematic .............. ...............38....
1-9 Most commonly used MALDI matrices .............. ...............39....
1-10 Mechanism of MALDI ................. ...............40................
1-11 The chemical and biochemical surfaces for SELDI .............. ...............41....
1-12 The bulge and stem structure of aptamers .............. ...............42....
1-13 The hairpin structure of aptamer ................. ...............43...............
1-14 The pseduknot structure of aptamer ................. ...............44...............
1-15 The G-quartet structure of an aptamer ................. ...............45........... ..
1-16 Generalized scheme indicating the key steps in the SELEX process .............. .... ........._..46
2-1 The mechanism of the TEOS sol-gel reaction ......... ................ .............. ....6
2-2 Illustration of incorporation of the matrix molecules in the TEOS gel ................. ...........66
2-3 Microscope pictures of sample surfaces of manually prepared samples .........._................67
2-4 MALDI ion images showing intensities for selected peptides using............... ................68
2-5 Mechanism of the polymerization of RF polymer proposed by Lin and Ritter.. ...............69
2-6 Base catalyzed RF polymerization............... .............7
2-7 Cross-section of the ion trap mass spectrometer ................. ...............71..............
2-8 Illustration of the path of laser and ions in mass spectrometer............_ .. ......._.._.. ....72
2-9 Fragment path of spiperone .............. ...............73....
2-10 UV absorbances of the matrices-embedded RF polymers ......____ .... ... ..__............74
2-11 UV absorbances of the RF polymer, CHCA embedded RF polymer, and CHCA
soluti on ........... __..... ._ ...............75....
2-12 Mass spectrum of the 100 ppm spiperone on CHCA embedded RF polymer and
stainless steel............... ...............76.
2-13 CHCA embedded in the RF polymer structure ................. ...............77..............
2-14 LTQ with vMALDI ion source from ThermoFinnigan .............. ...............78....
2-15 The microscopic image of the sample well of dry droplet sample preparation ................79
2-16 The distribution of the spiperone using dry droplet method on stainless steel. .................80
2-17 The microscopic image of the RF-16 polymer pellet after the deposition of spiperone....81
2-18 The distribution of the spiperone using dry droplet method on RF-16 polymer. .............82
3-1 The structure of the RF polymer. ........... ..... ._ ...............100
3-2 Chemical structure of reactive green 19. ................ ................ ......... ........ 101
3-3 The 27-mer oligodeoxyribonucleotide sequence. .............. ...............102....
3-4 The two cocaine isomers: a) pseudococaine and b) cocaine............... .................0
3-5 Anti-cocaine aptamer MNS-4.1 bound to cocaine .............. ...............104....
3-6 The picture of a Applied Biosystems 3400 DNA Synthesizer .............. .....................105
3-7 Scheme of the indirect surface modification of the RF polymer via the carboxylation ..106
3-8 Chemical structure of PDAM .....___................ ................. ..............._107
3-9 Fluorescent emission intensity of PDAM-bond and noncarboxylated RF polymer........108
3-10 Structure of Toluidine blue O .............. .....................109
3-11 UV absorbance of toluidine blue O desorbed from the carboxylated and
noncarboxylated RF polymer. ..........._ ..... ._ ...............110..
3-12 UV of the toluidine blue O solutions of different concentration ................ ...............11 1
3-13 Calibration curve of the concentration of the toluidine blue O solution ................... .......1 12
3-14 UV absorbance of reactive green 19 desorbed from aptamer attached RF polymer
and RF polymer ................. ...............113................
3-15 Calibration curve of the concentration of the reactive green 19 solution ................... .....1 14
3-16 Cocaine displaces diethylthiatricarbocyanine iodide completed with aptamer MNS-
4.1............... ...............115..
3-17 A microscopic image of the indirectly cocaine retaining-aptamer modified RF
polym er. .............. .. ...............116......... ......
3-18 MS spectrum of the cocaine on the unmodified RF polymer and on the cocaine
retaining aptamer attached RF polymer ................. ...............117........... ...
3-19 The 2-D and 3-D image of the cocaine signal intensity across the indirect cocaine
retaining-aptamer modified RF polymer ................. ...............118...............
3-20 The image of the direct cocaine retaining-aptamer modified RF polymer ................... ...1 19
3-21 MS spectrum of the cocaine on the direct cocaine retaining-aptamer modified RF
polym er ................. ...............120......... ......
3 -22 The 2-D and 3-D image of the cocaine signal intensity across the direct cocaine
retaining-aptamer modified RF polymer .............. ...............121....
Abstract of Dissertation Presented to the Graduate School
of the University of Florida in Partial Fulfillment of the
Requirements for the Degree of Doctor of Philosophy
Hong Yu
May 2007
Chair: Richard A. Yost
Maj or Department: Chemistry
A resorcinol-formaldehyde (RF) polymer and matrix-embedded RF polymers were
developed to be used as substrates for improved matrix-assisted laser desorption/ionization mass
spectrometry (MALDI-MS) analysis and for selective analysis of biological samples.
Matrix molecules can be embedded within this polymer, which renders excellent spectra
without the interference imposed by the matrix molecules for low molecular weight analytes. By
embedding the matrix molecules in this polymer more uniform spectra are obtained, solving the
prevalent problem associated with the traditional MALDI sample preparation methods.
The phenol groups on the polymer made it possible to attach aptamers selective to
reactive green 19 and cocaine onto it directly, and gave high specific affinity toward the reactive
green 19 and cocaine, respectively. The phenol groups on the polymer also made it possible to
attach carboxylic acid groups which could then be reacted with amine-modified aptamers. This
indirect aptamer-modified RF polymer has higher reaction efficiency than the direct aptamer-
modified RF polymer, yield more aptamers at higher density on the polymer for affinity capture
of analyte. This high specificity provided by the aptamers could make it a valuable tool to
specifically retain the biomarkers of diseases and could be used for screen test for diseases.
In the history of analytical chemistry, new technologies of analysis and instruments have
been developed to better determine the compositions and structures of substances in order to
identify them in the pursuit of understanding the world around us. The analytical methods that
have been used include some very rudimentary but still widely used techniques such as titration,
density, melting point, boiling point, flame test, and combustion, which are methods still taught
to new chemistry students. As the tasks for chemical identification became more complicated
and difficult, many new technologies were developed to peek into the microscopic world of
chemistry. These technologies include atomic absorption, ultraviolet/visible (UV-vis)
absorption, IR, fluorescence, flame, atomic emission, Raman, X-ray, X-ray crystallography,
NMR, electrochemistry, gravimetric analysis, calorimetry, and thermogravimetric analysis
(TGA), etc. Each of these more sophisticated technologies, based on a specific theory, utilizes
specific chemical and/or physical properties of the substance, and requires a specific instrument
to obtain specific information of the analyzed substance.'
A mass spectrometer is an instrument which was first invented at the beginning of the
twentieth century, but took off in its application in the past thirty or forty years as a tool to
identify various analytes. From gaseous molecules to volatile small organic molecules, then to
involatile large organic molecules, and eventually to proteins, DNA, cells, and bacteria, the range
of the analytes than can be analyzed has expanded since then. The high sensitivity, speed,
specificity, and reproducibility of mass spectrometry (MS) have made it an irreplaceable tool for
its application in protein analysis--including discovery, identification (i.e., peptide mapping and
sequencing), and structural characterization.2
Introduction to Mass Spectrometry: 3-D and 2-D Quadrupole lon Trap Mass Spectrometry
Introduction to Mass Spectrometry
The first mass spectrometer, built in 1907 by J.J. Thomson, was used to detect positive
rays based on the mass-to-charge ratio (m/z) of the particles; this was the basis of modern mass
spectrometry.3 The modern mass spectrometer is used to obtain the information on molecular
mass according to the mass-to-charge ratio and even structures of molecules according to
fragmentation patterns.4 The ionization device coupled to the mass analyzer has evolved because
of the demand of an expanded variety of analytes. Electron ionization (EI) was the first used,
followed by chemical ionization (CI), fast atom bombardment (FAB), electrospray ionization
(ESI), and matrix-assisted laser desorption/ionization (MALDI).
Analyte molecules are ionized by addition or loss of an electron or a proton or other ion.
The mass spectrum consists of the molecular-type ions (M [M+H] [M-H]-, ect.) and often
fragment ions, the pattern of which may be unique for each molecule. The mass spectrometer
was first used to identify elements and their isotopes.' Soon after, petroleum chemists used the
mass spectrometer to identify organic molecules.6 Now, the applications of the mass
spectrometry have broadened to include biochemistry, explosives, fullerenes, toxics, and
environmental pollutants.3
A mass spectrometer is named according to the mass analyzer which is its determining
component. During the process of the development of the mass spectrometer, many different
types of mass analyzers have been invented, which include magnetic-sector, quadrupole mass-
Eilter, 3-D quadrupole ion trap, 2-D quadrupole ion trap, and time-of-flight.3 Each of the mass
analyzers has its forte and suitability for analysis of certain types of analytes and is chosen
according to the task and budget.
Introduction to 3-D Quadrupole lon Trap Mass Spectrometry
The quadrupole ion trap was invented by German physicist Wolfgang Paul and co-workers
in the early 1950s.7 The quadrupole ion trap can be used to confine ions in a small volume using
just high-frequency electric fields without a material container.8 This invention later earned Paul
the 1989 Nobel Prize in Physics.9 Figure 1-1 illustrates a traditional 3-D quadrupole ion trap.
This 3-D quadrupole ion trap has two hyperbolic end-cap electrodes with entrance and exit holes
in the center of both end-caps. The hyperbolic ring electrode in-between the end-caps has a
radius ro.10 The distance between the two end-caps is 2zo, where ideally, Zo=ro/92. Ions entering
the trap are trapped at the center of the ion trap by a quadrupolar field which is created by a radio
frequency (RF) waveform applied to the ring electrode when the two end-caps are grounded.
Equations 1-1 and 1-2 are derived from the Mathieu equation for a "stretched" ion trap,
where e is the charge, U is the DC potential, typically kept at zero; V is the amplitude of the RF,
and 0Z is the angular frequency of the applied RF. Solutions to these two equations define
whether an ion with particular m/z will be stable inside the quadrupolar field according to their
position in the Mathieu stability diagram (Figure 1-2).10
az=-1 6eU/m(r02+2z02) ~22 1
qz=-8eV/m(r02+2z02) 22 (1-2)
The quadrupole ion trap confines ions in the small volume between the ring electrode and
two endcap electrodes by appropriate oscillating (RF) electric fields. In modern ion trap, an AC
waveform, termed the resonance ejection waveform, is applied across the endcaps. The
frequency is typically set to be slightly less than half of the RF frequency, G2. Since the
oscillating frequency, co, the ion motion in the z direction is given by DZBz/2 (see Figure 2 for Bz
values), this will correspond to a ej ect V value less than 0.908. When the amplitude of the
applied RF is linearly ramped up, a mass spectrum is obtained via the mass-selective instability
scan. In this instability scan, ions are ej ected from the trap with increasing na : with respect to
time when they come into resonance with the resonance ej section waveform. Higher na: ions are
still trapped; the limitation of mass range is due to an inability to reach the needed RF voltage
levels required to ej ect higher m/z ions out of the trap. In normal operation, for the instrument
used for this research, the maximum na: detectable is 650. Lowering the AC resonance ej section
frequency applied across the endcaps will allow ions to come into resonance earlier in the RF
ramp, extending the mass range by lowering the qz according to the equation 1-3.11
(nz z) new = (nz z) old q eject new/ q eject old) (1-3)
A quadrupole ion trap can be connected with external ion sources such as matrix-assisted
laser desorption/ionization (MALDI) and electrospray ionization (ESI). The range of ionization
sources that can be used, in addition to its MSn capability, makes the quadrupole ion trap a very
useful tool for compound identification.
Introduction to 2-D Quadrupole lon Trap Mass Spectrometry
The 2-D ion trap, the linear variant of the 3-D ion trap are based on the four-rod 2-D
quadrupole mass filter, omitting the quadrupolar-trapping field along one of the three spatial
The 2-D ion trap shown in Figure 1-3 12 is composed of three sections in which ions are
mass selectively ej ected radially through two slits in the two opposite rods in the center section.
Ions are trapped in the z direction by more positive DC voltages applied to the two end sections
for axial trapping of positive ions (Figure 1-4).12 The ions are trapped radially by the RF applied
in two phases to opposite rod pairs, as shown in Figure 1-4.12 A supplementary AC voltage is
applied across the x-rod pair in two phases for isolation, collision-induced dissociation (CID),
and resonant ej section of ions (Figure 1-4)12
Ions confined within a linear trap can be mass-selectively ej ected in a direction
perpendicular to the central axis of the trap (radial ej section) or can be ej ected along its axis (axial
ej section Having the detectors at both radial exit slits doubles the number of detected ions in
radial ejection design. The axially-ejected ions can be introduced into a second mass analyzer
such as a Fourier-transform ion cyclotron resonance (FT-ICR) analyzer to form a hybrid
Relative to the well-established 3-D ion-trapping instruments with similar mass range, the
2-D linear trap with radial ej section has significantly higher trapping efficiency and increased ion
capacity that improves the detection sensitivity at least 5 to 10-fold. This linear trap can conduct
all the typical scan modes intrinsic to 3-D traps with comparable mass resolution but at higher
overall scan rates.8
Development of Ionization Methods for MS Analysis: from LD to 1MALDI and from
MALDI to SELDI
The ionization method used is determined by the type of the analyte and determines the
characteristics of the mass spectrum obtained. The most common ionization methods include EI,
CI, ESI, and MALDI.
Electron ionization was the first ionization method developed, and was used in the
instrument invented by JJ Thompson. Electrons with an energy of about 70 eV collide with the
vaporized analyte in vacuum (10- -10-4 torr)3 to ionize the analyte molecules (Figure 1-5).13 The
spectra obtained with El are characterized by significant fragmentation of the molecular ions
([M] ). Later, when a softer ionization method was required for more fragile compounds
chemical ionization (CI) was developed. With CI, electrons collide with a reagent gas present in
large excess compare to the analyte to produce reagent ions which will later pass their charge to
the analytes by collision without transferring an excess of energy (Figure 1-6).14 The spectra
obtained with CI are characterized by less fragmentation of the analyte and more abundant
molecular-type ions ([M+H] ) than with EI. For these two ionization methods, the analytes have
to be vaporized before they can be ionized, which is a problem for less volatile compounds.
Typically, the higher the molecular weight, the less volatile the molecules. With El and CI, it is
difficult to ionize most of the large organic molecules and is nearly impossible to ionize
With increasing demand for analyzing large nonvolatile molecules, ionization methods that
can ionize large, nonvolatile molecules were developed such as fast atom bombardment (FAB).
With FAB, a beam of atoms bombard the analyte, which is dissolved in a low volatile liquid
matrix, to produce the analyte ions (Figure 1-7).15 Since the analyte molecules are not vaporized
before they are ionized, FAB can be used to ionize polar, ionic, thermally labile, and relatively
high molecular weight compounds that are not suitable for normal EI/CI analysis. Depending
upon whether the cation or the anion is of interest, positive-ion or negative-ion FAB/MS
analyses can be performed. FAB can ionize molecules up to 2000-3000 Da.3
Laser desorption (LD) ionization was also developed to tackle the problem associated with
less volatile large compounds. Introduced in the early 1960s, LD irradiated low-mass organic
molecules with a high-intensity laser pulse to form ions that could be successfully mass
analyzed. With LD, nonvolatile large molecules with the ability to absorb the energy from the
laser beam can be ionized. Although LD expanded the range of the analyte that can be ionized,
there were some limitations that came along with LD. The wavelength of the laser used in LD
has to match the wavelength of the analyte molecule' s absorbance for the laser energy to be
utilized for ionization. This may be difficult when a variety of analytes need to be analyzed. LD
was also considered as an ionization method which is too energetic for labile analytes since laser
energy is imparted directly into the molecules, which my cause a large amount of thermal
degradation and fragmentation.
First developed in 1980s, ESI was developed to ionize large and thermally labile
molecules. By forcing a solution of the analyte through a small capillary held at high voltage,
the solution sprays into tiny droplets with charges on each droplet. After the solvent is
evaporated, ions from nonvolatile compounds with one or more charges are generated, as shown
in Figure 1-8.16 The existence of multiple charges on high mass ions lowers the mass-to-charge
ratio, which expands the mass range of the molecules can analyzed.3 As a soft ionization
method, ESI makes it is possible to investigate even intact noncovalent complexes. The
invention is so important and revolutionary that the inventor, John B. Fenn of the Virginia
Commonwealth University, shared with Koichi Tanaka of the Shimadzu Corp. half of the 2002
Nobel Prize in Chemistry for his invention of ESI.1
Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization method that rivals
ESI for mass spectrometric analyses of biological macromolecules and the noncovalent
complexes between peptides and metal ions,17, 18, 19' 20' 21, 22,23 Single-stranded DNA, 21, 24, amino
acids,25 drugs,26 and other peptides.27,28,2930 In 1985, Michael Karas and Franz Hillenkamp
published the laser desorption results of the mixture of aromatic amino acid which absorbs laser
energy with aliphatic amino acid which does not absorb laser energy.31 In 1987, Karas and
Hillenkamp successfully used a matrix in LD to ionize and analyze high molecular weight
molecules.32 Matrices are organic molecules with aromatic groups that can absorb laser energy
in UV. The most commonly used matrices are 2,5-dihydroxybenzoic acid (DHB), trans-3,5-
dimethoxy-4-hydroxycinnamic acid or sinapic acid (SA), nicotinic acid (NA), trans-3-methoxy-
4-hydroxycinnamic acid or ferulic acid (FA), 3-hydroxypicolinic acid (3HPA), 4-hydroxy-a-
cyanocinnamic acid (4HCCA), and (in the infrared) succinic acid and glycerol (Figure 1-9).
With MALDI, a low concentration of the analyte is mixed with a large excess of organic matrix
to completely isolate analyte molecules from each other to homogenous 'solid solution'. The
laser beam is focused onto the surface of the matrix-analyte solid solution. The matrix molecules
absorb the laser energy at the incident laser wavelength and then pass that energy on to analyte
molecules, producing a pulse of ions with each laser pulse. The clusters ejected from the surface
consist of analyte molecules surrounded by matrix and salt ions. The matrix molecules
evaporate away from the clusters to leave the free analyte in the gas-phase. The photo-excited
matrix molecules are stabilized through proton transfer to the analyte. Cation attachment to the
analyte is also encouraged during this process. It is in this way that the characteristic [M+X]
(X= H, Na, K etc.) analyte ions are formed. These ionization reactions take place in the
desorbed matrix-analyte cloud just above the surface. The ions are then extracted into the mass
spectrometer for analysis. MALDI allows a larger variety of analytes to be ionized by the same
laser than LD.33 Figure 1-1014 iS an illustration of ionization process of MALDI. The
application of MALDI to biological macromolecules demonstrated by Koichi Tanaka 34 led him
to receive a quarter of the 2002 Nobel Prize for chemistry."
The matrix-to-analyte ratio ranges from 100 to 50,000.3 MALDI overcame the problem
associated with the LD, but inevitably suffers from the interference from matrix molecules with
analytes of low molecular weight. The excessive amount of matrix molecules poses interference
to the interpretation of the mass spectra of low molecular weight analytes. Some effort has been
put into developing matrix-free laser desorption/ionization methods to eliminate the interference
from matrix. Desorption/ionization on porous silicon (DIOS) is one of the methods developed
which utilizes the large surface area of an UV absorbing semiconductor treated electrochemically
to produce spectra without the interference of matrix clusters.35, 36, 37,38 DIOS certainly has its
success, but suffers from the relatively less than ideal sample-to-sample reproducibility, stability
of targets, molecular weight limitation, low analyte signal intensity and is sensitive to how the
samples are deposited on them-cracks can form with an inappropriate sample deposition method.
Since MALDI opened the gate for the MS analysis of macromolecules, biological samples
have been subj ect to the MS analysis for disease biomarker discovery and clinical diagnostics.
Disease biomarkers are the characteristic amount or the existence of a certain substance or
substances.39 Biological samples taken directly from humans or animals such as blood, serum,
plasma, urine, and cellular secretion products also contain extremely large numbers of
components which are not of interest and can interfere with the MS analysis.40 These unwanted
components include biological molecules and organic and inorganic salts which can make the
MS analysis extremely difficult. Liquid chromatography (LC), high-pressure liquid
chromatography (HPLC), membrane dialysis, centrifugation, immunoprecipitation, gel
electrophoresis and other separation techniques have been used to separate and extract the target
analyte from the biological sample prior to the MS analysis. Theses separation techniques are
usually tedious and time-consuming and suffer loss of the analyte during the process, especially
for the low abundant components.40
Surface-enhanced laser desorption/ionization (SELDI) was introduced by Hutchens and
Yip in 1993 in order to achieve better sample preparation.41 SELDI is based on MALDI but with
the surface of the substrate modified to have a specific affinity toward certain types of molecules
to achieve an on-probe, one-step clean-up procedure before the sample is analyzed. There are
several companies which provide SELDI chips, such as Ciphergen Biosystems (Palo Alto, CA).
Affinity capturing for enrichment and clean-up of analyte is borrowed from affinity
chromatography. Among them, immobilized metal affinity capture (IMAC), antibody and
protein affinity capture, lectin affinity capture, inherent hydrophobic interaction bio-capture, and
bio-molecular interaction capture are attractive ones, and have been used to retain biomolecules
such as proteins and peptides.42 Figure 1-11 shows the biochemical and chemical modified
affinity surfaces available from Ciphergen.42 The chemical modification of the substrate surface
is well established. It retains a class of molecules which is useful for certain applications.
Biochemically modified surfaces have specificity toward one specific molecule. Antibodies,
DNA, enzymes, and receptors have been used in biochemical surface modification.
Aptamers are pieces of synthetic DNA or RNA oligonucleotides which recently been
applied to SELDI affinity capturing.73 Aptamers are screened from a randomly generated
population of DNA/RNA sequences for their ability to bind with desired molecular targets such
as peptides with high specificity, and can be designed and synthesized easily with a DNA
synthesizer. Aptamers have not yet been widely used for SELDI and are not available
Introduction to Aptamers
Aptamers have been employed in applications such as chromatography, capillary
electrophoresis, biosensors, and signaling because of its ability of affinity capture small
molecules, peptides, and proteins.43 Aptamers has also been used for mass spectrometry sample
preparation in surface enhanced laser desorption/ionization (SELDI).
Definition and Synthesis of Aptamers
Aptamers are pieces of synthetic DNA or RNA with 3-D structures which provide the
targets binding capability. The name "aptamer" is derived from the Latin word "aptus" which
means "to fit". Aptamers can be selected "to fit" small molecules, biopolymers, surfaces or even
whole cells.43 Because of the high specific affinity, aptamers can be used as recognition
elements in heterogeneous assays to replace antibodies.44, 45 The selective binding affinity
toward the target is due to specific interactions such as hydrogen bonding or association with the
phosphate groups of the aptamer.46 The sequence-specific tertiary structure of the aptamer helps
these interactions, which provides a rigid platform for the arrangement of functionalities of the
aptamer. The 3-D structures have been discovered to include the stem-loop/bulge (Figures 1-12
and 1-14),47, 48 the helix, the hairpin (Figure 1-13),47 the pseudoknot (Figure 1-14),49 and the G-
quartet structure (Figure 1-15).5o Under certain condition such as the buffer with certain pH,
certain components, and concentration; aptamer can form 3-D configuration which retains a
specific protein or molecule which can fit in this 3-D configuration. Because of its affinity
capture capability, aptamers have been used in chromatography for separation and purification of
mixtures.48, 51
An aptamer for a particular target is discovered and produced by the method called
systematic evolution of ligands by exponential enrichment (SELEX), which utilizes in vitro
selection and amplification procedures to isolate aptamers for any small molecule or protein
target.52, 53 This automatic method was developed independently by Joyce, Szostak, and Gold.52,
54, 55 First, a library of oligonucleotide molecules with the size of 101 ~ 101 is generated
chemically in a standard oligonucleotide synthesizer." The greater the number of randomized
nucleotide positions, the more complex a library is and the more likely the success of finding the
molecules that interact with a target.44 Each member in a library has a unique sequence which is
designed to contain a contiguous randomized region flanked by two fixed sequence regions.
Technological advances already have made it possible to eliminate the requirement for the fixed
regions in random sequence libraries used for the SELEX process, thereby producing short
aptamer sequences. A mixture of phosphoramidites containing all four building blocks: A, G, C,
and T is delivered to the synthesizer to synthesize each nucleotide position in the contiguous
random region. The ratios of the four phosphoramidites in the mixture are adjusted based on the
coupling efficiencies of individual monomers to obtain an unbiased library with equal
representation of all four nucleotides. Because aptamers are identified from DNA as well as
from RNA libraries, chemically synthesized DNA libraries are enzymatically converted to RNA
The screening process is the next step, in which a random sequence oligonucleotide (RNA
or DNA) library is incubated with a target of interest in a buffer of choice at a given temperature
(see Figure 1-16).5 A very small fraction of individual sequences tend to interact with the
target, and these sequences are separated from the rest of the library by any one of the physical
separation techniques. Typically, nitrocellulose filter partitioning is used with protein targets
that are retained on the nitrocellulose. Small molecular targets are generally immobilized on a
solid support to generate an affinity matrix in which case, sequences that do not interact with the
target on the solid support can be removed easily by a simple washing step. The mixture of
aptamer candidates recovered from the target represents a mixture of sequences containing both
high- and low-affinity binding molecules to the target.44 The sequences bound to the target are
isolated and amplified to obtain an enriched library to be used for the selection/amplifi cati on
The DNA aptamer candidate mixture is amplified directly by the polymerase chain
reaction (PCR), while RNA sequences are amplified by PCR after being converted from DNA by
reverse transcription (RT).55 The single-stranded DNA (ssDNA) population obtained by strand
separation of PCR products is incubated with a fresh sample of the target for the next round of
selection. The RNA population is obtained by in vitro transcription. Several iterations of the
selection process are carried out under increasingly stringent conditions to enrich the high-
affinity sequences and eliminate the low-affinity binder. The enrichment efficiency of high-
affinity binders is controlled by the stringency of selection at each round. Analysis of enriching
populations against the target is carried out to determine the progress of the enrichment of high-
affinity binders.44 The number of cycles required for aptamer identification is usually dependent
on the degree of stringency imposed at each round as well as on the nature of the target. For most
targets, affinity enrichment is reached within 8-15 cycles. In general, one cycle of SELEX takes
two days. The enriched library is cloned and sequenced to obtain the sequence information of
each member until the chosen sequences dominate the population.'" A typical SELEX
experiment may take approximately 2-3 months including cloning and sequencing.'
Aptamers that come out of a SELEX experiment are full-length sequences which are
generally 70-80 nucleotides long, and can be truncated to eliminate nucleotide stretches that are
not important for direct interaction with a target or for folding into the structure that facilitates
target binding. The truncation of aptamers to the minimal target-binding domain has been
successfully carried out to obtain functional aptamers less than 40 nucleotides long.58 59, 60' 61, 62,
63 Once the sequence is identified, an aptamer is produced by chemical synthesis.
Aptamers have remarkable specificity and can discriminate targets on the basis of subtle
structural differences such as the presence or absence of a methyl group64, 65 Or a hydroxyl
group66' 67 and the D- vs. L-enantiomer of the target.66, 68 Because of the selective demand in the
SELEX process that eliminates sequences that bind closely related analogs of the target,
sometimes the degree of specificity of aptamers is better than that of antibodies.64 Practically,
elimination of the sequences that bind closely related analogs of the target is achieved by the
process called "counter-SELEX" that effectively discards ligands that have an ability to bind the
target as well as closely related structural analogs of the target.64 During counter-SELEX
selection, the population of aptamers bound to the target is subj ected to affinity elution with
structural analogs and the sequences eluted are discarded.
The counter-SELEX strategy is a valuable tool in identifying aptamers aimed at a specific
target in a complex mixture, even without prior knowledge of the target. For example; in the
search for aptamers that bind to an "epitope" only present on the surface of cancer cells but not in
healthy cells, the cells from healthy tissue are used to remove sequences that bind to the
background that does not contain the epitope of interest before the library is challenged with
cancer cells.
The Advantages of Using Aptamers vs. Antibody and the Applications in Bioanalysis
Both antibodies and aptamers are utilized in bioanalysis based on their molecular
recognition capability. Antibodies are the most popular class of molecules providing molecular
recognition." They have been used in SELDI because of its high specificity and selective
affinity towards a specific target.
Antibodies started to get attention since thel950s and became very popular in the 1970s.5
Although antibodies have the advantages of having a very high selective affinity, they also have
several limitations.
First, antibody generation involves untidy cell cultures and lab animals since antibodies
must be selected and produced in a living organism. Antibodies of non-human origin have
implications in diagnostic applications;69 thus, the use of antibodies in therapeutic applications is
limited since the generation of hybridomas is restricted to rats and mice. Heterophilic antibodies
(human antibodies that recognize antibodies of non-human origin) that exist in humans might
lead to false-positive results because a capture antibody can be linked with a detector antibody of
non-human origin in the absence of the specific analyte.70
Second, stocks of antibody-producing cells need to be stored at multiple sites to prevent
the complete loss of the cell lines because of the possibility of accidental losses or the death of
cell lines. Typically, high yields of monoclonal antibodies are obtained by growing the
hybridomas in the peritoneal cavities of animals and purifying the antibody from ascites
(abdominal dropsy) fluid. Some hybridomas are difficult to grow in vivo, thus restricting this
route of antibody production.44
Third, molecules that are not well tolerated by animals, such as toxins have difficulty being
employed to produce antibodies in living organisms.44 Furthermore, it is difficult to raise
antibodies against inherently less immunogenic molecules.44
Fourth, the identification and production of monoclonal antibodies are laborious and could
become very expensive for searches of rare antibodies that require screening of a large number
of co omies.44
Fifth, the consistent performance of the same antibody from batch to batch is poor; thus,
immunoassays need to be optimized with each new batch of antibodies.44
Sixth, since the antibodies are produced in vivo and subj ect to in vivo variations, it is not
practical to identify antibodies that could recognize targets under conditions other than
physiological conditions.4
The ability of aptamers to bind to various targets makes aptamers applicable as biosensors,
imaging probes, MALDI targets, and drugs.51 First, the properties of aptamers can be changed
on demand44 because aptamers are identified through an in vitro process that does not depend on
in vivo conditions. Furthermore, selection conditions can be designed to obtain aptamers with
properties desirable for in vitro diagnostics.44
Second, as opposed to antibodies, toxins as well as molecules that do not elicit a good
immune response can be used to generate high-affinity aptamers because animals and cells are
not involved in aptamer identification.44
Third, aptamers are stable during long-term storage and can be transported at ambient
temperature. Aptamers can undergo reversible denaturation process and easily recover from
exposure to undesirable conditions within minutes. The in vitro selection process for aptamers
can be carried out under conditions akin to those used in the assay for which the aptamer is being
developed. The aptamer will maintain its structure and function in the final assay and not fall
apart as antibodies do."
Fourth, aptamers with any sequences that can recognize any class of target molecules with
high affinity and specificity can be discovered with SELEX process. Once the sequence of a
particular DNA aptamer is known, it is easy and inexpensive to synthesis the aptamer in a DNA
synthesizer with high accuracy and reproducibility. They are then purified under denaturing
conditions to achieve very a high degree of purity with little or no batch-to-batch variation in
aptamer production.44, 51
Fifth, additional chemistries can be added on without a loss in function because aptamers
are chemically synthesized, which gives aptamers superiority over antibodies. When chemical
groups are attached to the ends of the aptamers, their life span in the bloodstream increases, they
can be targeted to particular locations, or they can be immobilized onto a surface. Immobilizing
aptamers without potential loss of function makes it superior to antibodies." Reporter molecules
such as fluorescein and biotin can be attached to aptamers at exact locations designed by the
user. Functional groups that allow subsequent derivatization of aptamers with other molecules
can also be attached during the chemical synthesis of aptamers.44
Sixth, aptamers can also be used for the development of sandwich assays for small
molecules or modified into a molecular-beacon format (a DNA strand with a fluorescent tag and
a quencher) for reagentless assays, which is beyond the capability of antibodies."
Seventh, aptamers have smaller molecular weight, which offer advantages such as ease to
penetrate tissue, shortened residence time in blood, and a smaller footprint when being attached
to a surface to get a higher binding density."
Because of the advantages the aptamers posses over antibodies, the aptamers can be used
to replace antibodies to retain molecules, although the recognition ability of aptamers is not as
high as antibodies."
A lot of effort has been put into research to explore the usability of aptamers in analytical
chemistry. SomaLogic (Boulder, CO) is developing aptamer proteomic chips as diagnostic tools
that screen for biomarkers in serum. Ellington's group from Department of Molecular Biology,
Massachusetts General Hospital, Boston, has demonstrated that aptamers can be immobilized on
beads, introduced onto a sensor array, and used for the detection and quantitation of proteins."
Kennedy's group from University of Florida showed that DNA aptamers immobilized on a
chromatographic support can selectively bind and separate adenosine monophosepahte (AMP),
cyclic-AMP, adenosine diphosphate, adenosine triphospahte, NAD+, and adenosine from
mixtures as complex as tissue extracts.72 McGown from Duke University successfully used a
thrombin-binding DNA aptamer for affinity capture for MALDI-MS.73 In her work, she attached
aptamer pieces onto a treated fused-silica glass surface and then used the aptamer-attached glass
to capture the thrombin from a protein mixture. The result showed that the thrombin-binding
aptamer has high affinity toward the thrombin.
Overview of Dissertation
The importance of developing a new MALDI substrate and the suitability of the RF
polymer for MALDI-MS analysis was emphasized at the beginning of the dissertation.
A new RF polymer and matrix-derived RF polymers have been developed and
characterized as discussed in Chapter 2 for elimination of the background noises fro matrix
molecules used in MALDI-MS analysis and for more even distribution of signal intensity of
analyte across the sample spot.
Surface modification of the RF polymer with carboxylate groups and then with amine-
modified aptamers have been performed and characterized as discussed in Chapter 3 for
attachment of functional groups and then attachment of functionally-modified aptamers onto the
RF polymer.
With the affinity capture capability of this SELDI-MS substrate, it is possible to perform
an on-probe one-step clean-up for the specific small molecules such as reactive green 19 and
cocaine before the MS analysis of a biological sample. The polymer and modification
procedures are capable of being applied later on disease biomarkers. This is crucial for large-
scale cancer screening to be accessible for the vast maj ority of the population at lower cost and
higher accuracy.
It RING
Figure 1-1. Scheme of parts of the 3-D quadrupole ion trap. [Adopted from March, R.E. An
introduction to quadrupole ion trap mass spectrometry Journal of Mass Spectrometry
1997, 32, 351]
Entrance Ring Exit
Endcap Electrode Endcap
.Stability diagram in (a, q, ) space for the region of simultaneous stability in both the
r- and z-directions near the origin for the three-dimensional quadrupole ion trap ; the
iso-B, and iso-BZ lines are shown in the diagram. The q-axis intersects the jL=1
boundary at q,=0.908, which corresponds to qmax in the mass-selective instability
mode. [Adopted from March, R.E. An introduction to quadrupole ion trap mass
spectrometry Journal of~a~ss Spectrometry 1997, 32, 351]
1.0 0
Pq o0.8,C 0.1 .~, q,=-0.908
--0.2 -
--0.4 -i
Figure 1-2
Figure 1-3. Basic design of the two-dimensional linear ion trap. [Adopted from Schwartz, J.C.;
Senko, M.W. A two-dimensional quadrupole ion trap mass spectrometer Journal of
the American Society of~a~ss Spectrometry 2002, 13, 659]
Radial Quadrupolar Tra3pping
Axial Trapping
Radial Dipola Excitation
Figure 1-4. Scheme for application of DC, RF trapping, and AC excitation voltages necessary
for operation of the 2-D ion trap. [Adopted from Schwartz, J.C.; Sento, M.W. A two-
dimensional quadrupole ion trap mass spectrometer Journal of the American Society
of~a~ss Spectrometry 2002, 13, 659]
FI~l~m ~it.it Ilri
F1n~i l~I~ TO I~~~t 1 31
Figure 1-5. Electron ionization schematic. [Adapted from
F' ?lniti~lit IIi~li~t
I ~JI rd ;r-]
FI i I1ii nl r iri oi~ -;
I1~ t
cnal ~ -er
Figure 1-6. Chemical ionization schematic. [Adapted from
twt ppltt~~~~tttt~~~~tttr~~~c
ush rlatts twl
e;r~p~e~ 8a
Figure 1-7. Illustration of FAB. [Adapted from http://www.chm.bris. ac.uk/ms/theory/fab-
lon Formation By ESI
SAdapted frorn Kebarle and Tang, Aral Chern. 65, 2, 972A-985A (1993)
Figure 1-8. Electrospray ionization schematic. [Adapted from
http ://www.noble.org/plantbio/MS/iontech. esi.html]
Taylor Cone
Succimic Acid
Figure 1-9. Most commonly used MALDI matrices
MAL D I De rorption~llon lmilan
hrOpJ cal fbcuslrg lene
Figure 1-10. A schematic diagram of the mechanism of MALDI. [Adapted from
i lr
Figure 1-11. The chemical and biochemical surfaces available for SELDI from Ciphergen
provides. [Adopted from Tang, N.; Tornatore, P.; Weinberger, S.R. Current
developments in SELDI affinity technology Ma~ss Spectrometry Reviews 2004, 23,
BiiochemicalT Surfalces
Chemical Surfaces
muth1, Kd~l l
G mutA3, Kd= >> 200 nM
G-C m K,K= 10~t0.7 nM
SLII, K = 3 & 0.5 nM
A-u SLII(S13)
c-a Kd=> 0n
Kd=>>200nM U-G
C-GC Kd=>>200nM
Kd=410.3nM A-U
C-G Kd 210.4 nM
Figure 1-12. The bulge and stem structure of aptamers. [Adopted from Biroccio, A.; Hamm, J.;
Incitti, I.; Francesco, R.D.; Tomei, L. Selection of RNA aptamers that are specific and
high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase
Journal of Virology 2002, 76, 3688]
Juncilns; Internal loops Bullge HI rpln loop
Two-stern ~ ~ ~ ~ ~ ~ ~~9 The-tm Furse smeti yie
-~ ~ 551 AU, UA G 0 Uo G --AA C G U
AU ,orGAG A C U rU
Fiur 1-3 h ari tutr fatmr A ote rmBrciA;H m ,J;Icti .
Fraceco R.D. ToeL eeto fN paer htaeseii n ih
Virlog 2002, 76,, 3688] ~I
C-oneeQeu Pisalndama (o 18 isolum)
Loop 1
Stem 1
lil 18 111 la
11 1 15 1 12
XX'- x- X-~ .X`- X- 31
Coop 2
Figure 1-14. The pseduknot structure of aptamer. [Adopted from Tuerk, C.; MacDougal, S.;
Gold, L. RNA pseudoknots that inhibit hunman-immunodefficiency-virus type-1
reverse-transcriptase Proceedings of the National Academy of Sciences of the Chrited
States of America 1992, 89, 6988]
GG Ge-ic-A-
15 r-_~;c3
Fiur -1.Th -qate trcur f a pae.[dpe frro Wag K.. M~rdS
Figue 1-in hibt Gqatthrmi exhibitsr ane sptmrucua mAoptif fror DNAn Bichmity. 1993r, 32,
~.~W.I............lrr ~[I~CC
I~R.. ~6~Rldd~L
Random sePquce9
olgonrucleatkle I~bray
Tarlge~lkotdrt EI
ras ougolwidotide
Clone & Seqluence
Figure 1-16. Generalized scheme indicating the key steps in the SELEX process. [Adopted
from Klug, S.J.; Famulok, M. All you wanted to know about SELEX M~olecular
Biology Reports 1994, 20, 97]
Since the invention of MALDI-MS, it has been used to analyze macro-biomolecules such
as peptides mixtures,76 prOteins,76 Oligosaccharides,7 enzymatic protein digests,78 underivatized
DNA, and oligomers.79 Although MALDI-MS is a powerful analysis method, it has problems
associated with the sample preparation methods. Identifying and solving the problems can
improve the quality of MALDI-MS spectra.
Problems Associated with MALDI-MS Sample Preparation Methods
As a widely used ionization method for mass spectrometric analysis for macromolecules,
MALDI has shortcomings associated with the methodology of sample preparation. These
problems include background interference from matrix molecules when the molecular weight of
the analyte is less than 2-3 times the molecular weight of the matrix molecule74 and poor signal
uniformity of the signal intensity of analyte across the sample from the inhomogeneous
distribution of the matrix-analyte co-crystals. 93 These problems can either interfere with the
interpretation of MS spectra of low-mass analytes or require significant effort to locate the
"sweet spot" both of which routine analysis with MALDI-MS more difficult. Therefore, to
eliminate the interference from matrix molecules and at the same time to increase the uniformity
of the analyte signals intensities in MS spectrum, development of a polymeric substrate which
has the physical properties amenable to MALDI-MS analysis and has the chemical properties to
incorporate matrix molecules into its structure is highly desirable.
Background Interference from Matrix Molecules in MALDI-MS
MALDI ionization coupled with mass spectrometry made the analysis of nonvolatile
molecules possible. In MALDI, an excessive amount of matrix molecules, with the matrix-to-
analyte ratio typically in the range of 100 to 50,000, is mixed with analyte in order to ionize the
analyte particles. The excessive matrix molecules are not anchored to any support, and,
inevitably, the matrix molecules will be released and ionized upon ablation of the laser beam,
and appear in the mass spectrum together with the analyte. Signals produced by the matrix
molecules present in the mass spectrum along with the signals from analyte pose interference in
analysis of low molecular weight analyte.
Much effort has been devoted into Einding the mechanism of MALDI which can lead to the
development of matrix suppression methods. Competition model, in which competition between
matrix and analyte for free protons based on the proton affinity,so, sl is one of them. According
to this model, matrix suppression takes place when adjusting the matrix-to-analyte ratio for every
protonated matrix molecule to interact with at least one analyte with higher proton affinity than
the matrix molecule during desorption. In another proposed mechanism, analyte molecules are
ionized by non-ionic matrix precursor species which are vibrationally and electronically excited
matrix molecules.82 Knochenmuss and Dubois proposed a model combining the previous two
models. In this model excited, but not ionized, matrix molecules are the common precursor for
all subsequent ion products and the simultaneous neighboring presence of two such excitations is
required for ionization of each analyte molecule.83 This model explained matrix suppression
phenomena observed in a medium matrix-to-analyte ratio with relatively low analyte signal
intensity and less matrix suppression in a high matrix-to-analyte ratio. According to this
mechanism, suppression of the matrix signals has to be compromised to get high enough analyte
signal intensity, or vice versa, when only the matrix-to-analyte ratio is involved.
Modiaications other than adjusting the matrix-to-analyte ratio in MALDI sample
preparation have been made in order to reduce the matrix interference in mass spectrometric
analyses. These modifications include adding iodine to the matrix to suppress the signals from
the matrix-related ions and increase the signals from analyte ions,84 USing alkali
dihydroxybenzoic acid salts as cationizing agents to suppress the DHB related ions, mixing
graphite powder with glycerol to reduce the interference,86, 90 and using nitrocellulose as a
substrate together with matrix to eliminate the matrix signals.8 In each case the modification
can reduce the signal intensities from matrix molecules but cannot completely eliminate them.
In all those methods, the matrix molecules are not covalently attached to any support but merely
interact with the support by dipole-dipole interaction and van der Waals force; which are at the
magnitude of one-thousandth and one-ten thousandth of the strength of the covalent bond,
respectively. Therefore, are easy to be ablated and ionized when the energy of the laser beam
shot on the target is much higher than the energy required to break these interactions.
In an effort to fundamentally solve the matrix related problem, Lin and Chen incorporated
matrix molecules into the gel formed from the tetraethoxysilane (TEOS) precursor via sol-gel
method." Total elimination of the matrix molecule signals was observed when small proteins,
peptides, amino acids, and small organic were analyzed. In the experiment, the matrix (DHB)
was mixed with the monomer precursor to form the sol-gel solution and was claimed to become
part of the polymer structure after the solution is polymerized. The mechanism of the
polymerization reaction was proposed as shown in Figure 2-1. The hydroxyl groups on the
matrix molecules can form covalent bonds with the hydroxyl groups in the silicic acid and thus
covalently incorporated into the TEOS polymer as shown in Figure 2-2.
Since the energy required to break the covalent bond between the matrix molecule and the
polymer is greater than the laser energy used in MALDI, trapping the matrix molecules
covalently into the polymeric structure make it possible to totally eliminate the matrix ions'
background interference in a MS spectrum. One problem associated with the TEOS gel, which
was not mentioned in the paper, is that cracks formed when an aqueous solution was applied
onto it since the structure of the gel is not strong and can be easily broken. Developing a
different matrix-embedded polymer which has better physical properties than the TEOS polymer
is valuable for the polymeric substrate to be useful for MALDI-MS analysis with analytes in
aqueous solution.
The Uneven Distribution of Analyte Molecules with the Traditional MALDI-MS Sample
Preparation Methods
There have been many investigations on the effect of MALDI sample preparation methods
on the quality of mass spectrometric analyses. MALDI-MS analyses results have strong
dependence on the sample preparation method. Every single choice such as the solvent, matrix,
and pH in sample preparation procedure can affect the outcome of the MALDI measurements.89,
90, 91, 92, 93, 94, 95, 96 The different combination of matrices, concentration of matrix, and solvent
produce different distribution of matrix molecules across the sample as shown in Figure 2-3.97
The problem which concerns the mass spectrometry analysts the most is the poor spot-to-spot
and sample-to-sample reproducibility caused by inhomogeneous distribution of the matrix-
analyte co-crystal.93
The methods used for the application of the analyte sample includes the rudimentary
"dried-droplet" method which is to deposit matrix and sample mixture on the target with the
matrix-to-analyte ratio as 103 to 105 and let it dry.98 This method is also called the "air dried"
method.99 The formation of small co-crystals which contain matrix molecules and analyte
molecules in the dried-droplet method is crucial for the ionization of the analyte molecules. The
crystals formed in the sample prepared from dried-droplet method are not evenly distributed
throughout the sample plate. The analyte-matrix co-crystals are found mostly at the edge of the
droplet when DHB is used as matrix1oo, 101 as shown in Figure 2-4102 according to the partitioning
process when solvent slowly evaporates. When the solvent slowly evaporates the analyte
molecules are excluded from the matrix crystal.99 An analyst would, therefore, to find "sweet
spot" by scanning the sample surface.
A "thin-layer" sample preparation method has been developed based on the dried-droplet
method1oo using a volatile solvent to create homogeneous matrix microcrystals because quick
evaporation of the solvent can minimize the partition process which occurs under the slow
evaporation process. A drop of matrix solution in volatile solvent was deposited onto a target
plate and was allowed to spread and dry quickly to form a thin layer of homogeneous matrix
microcrystals. Then a drop of analyte solution was deposited on the top of the matrix layer.92
The spectra obtained from the thin-layer method produce more uniformed distribution of the
analyte-matrix crystals than from the dry droplet method, therefore more uniformed analyte
signal intensity across the sample (Figure 2-4).
"Sandwich" sample preparation method is a combination of the thin layer and the dried-
droplet method.98 It is called sandwich because sample solution is applied on one layer of matrix
crystals, then another matrix solution is added on the sample spot. This method has better
mapping results than the dried-droplet method.
To utilize the quick evaporation of the solvent further, electrospray sample preparation
method was used to further improve homogeneity of the components distribution in MALDI-ToF
MS than the use of volatile solvents and/or rapid evaporation under vacuum or heating and the
small and evenly distributed droplets can.99 This method produced much better spot-to-spot and
sample-to-sample reproducibility in the mass spectra than dried-droplet method.
Since the selection of the matrix is very importance in some cases, experiments using more
than one matrix for the sample preparation have been also conducted.94 These improvements are
made on a case-by-case basis. Limiting the size of the droplet is another technique that has been
tested to improve the MALDI-MS analysis quality.103
Over all, there is not a universal sample preparation method that produces high quality
mass spectra for variety of analytes. Mass spectra quality can be improved by modifications
made to the sample preparation methods. Elimination of the poor spot-to-spot reproducibility of
the analyte molecules (the uneven distribution of analyte across the sample) is impossible with
the efforts have been done, because this problem is related to the process of the crystallization.
In the matrix-embedded polymeric MALDI-MS substrate, the matrix molecules are evenly
distributed throughout the polymer structure on the molecular level and cannot be changed
during the sample preparation process and no analyte-matrix co-crystals are formed, thus, the
matrix-embedded polymer has the capability of solving this problem.
Introduction to the RF Polymer
According to the discussion above, a matrix-embedded polymeric substrate is the solution
to the background noise from matrix molecules in mass spectra and the poor spot-to-spot and
sample-to-sample reproducibility of MALDI mass spectra. Matrix-derived TEOS polymer was
used by Lin and Chen75 and was synthesized and tested in our lab. The matrix-derived TEOS
polymer was able to significantly lower the matrix signals when using MALDI-MS. Although
the TEOS gel has the advantage of lowering the chemical noise from matrix molecules, the
structure of the gel is fragile and is easy to break apart, cracks when aqueous solutions were
deposited on it. This shortcoming made it a less than ideal substrate for MALDI-MS since
aqueous solutions are usually used and made it impossible for easy manipulation and further
chemical modification. Resorcinol-formaldehyde (RF) polymer was finally chosen because of
its tough physical structure and abundant phenol groups on it which render the capability of
being chemically modified. Resorcinol-formaldehyde resins have been used as adhesion
promoters to increase adhesion of rubber to fabric or metal.
RF sol-gels were first synthesized by Pekala and co-workers according to a hydrolysis-
condensation reaction mechanism (Figure 2-5).104 Figure 2-6 shows the base catalyzed
polymerization reaction of RF polymer. The "R" in the RF polymer is referred to "resorcinol",
the "F" in the RF polymer is referred to "formaldehyde". A patent was filed by Pekala on the
synthesis of RF polymer.104 Resorcinol-formaldehyde resins have been used as adhesion
promoters to increase adhesion of rubber to fabric or metal.
A lot of research has been conducted since then on the effect of different reaction
conditions on the final structures of the polymers which affect the physical, chemical, and
electrochemical properties ofRF aerogels and xerogels.los Many patents have been filed and
approved for RF polymers with different reaction conditions. Those reaction conditions include
the ratio between the resorcinol and formaldehyde, the solvent and catalyst, the initial pH of the
reaction, the ratio between the catalyst and the resorcinol, the temperature of the reaction, and
initial ratio between the reactants and the solvent.106 With these variables there are tremendous
possibilities of combinations of the conditions which make it a very versatile reaction that can be
tailored for the desired properties.
The RF polymers are categorized according to the solvent used. The gels with water
solvent are called hydrogels or aquagels; the gels with organic solvents are called lyogels.107 The
initial reactants and the solvent ratios of the reaction affect the final density of the gel's size.10s
Using higher concentrations of solvent can result in "dilute effect" which results in increased
particle size.10s Using the higher concentrations of the reactants can result in higher density of
the formation of the RF crosslinked clusters.
The most commonly used stoichiometric resorcinol / formaldehyde (R/F) molar ratio is 1:2
104 Using more formaldehyde than twice the amount of the resorcinol as the starting material
would cause a "dilute effect"-the effect caused by higher solvent concentration.'os
The most commonly used catalyst is sodium carbonate. The molar resorcinol -to-cataly st
(R/C) ratio is usually between 50 and 300, or can be as high as 1500. The lower the R/C ratio,
the smaller the polymer particles and the higher density of the gels. In some cases acids such as
HCIO4107 Or HNO3109 were used as catalyst, respectively, with reduced gelation time.110 Using
an acid catalyst combined with low concentration of reactants can result in small, smooth, fractal
aggregates of gel particles.10
The pH should be controlled between 5.4 and 7.6 "1 since high pH can hinder the
polymerization-condensation reactionl12 and reactants precipitate at low pH113. Diluted acid
such as HNO3, HCIO4 and bases such as NH40H can be used to adjust the initial pH of the
reaction solution.
Systematic Investigation in Preparation of the RF and Matrix-Derived RF Polymers
To address the problems facing analysts working on MALDI-MS, RF polymers were
synthesized to be suitable as substrate for MADLI-MS. The RF polymers developed were wet
gels without any further drying processes. These polymers are made via the quick and easy sol-
gel method which makes it easy to be customized with any desired composition, on any surface,
and any shape and size. The solutions can be stored in freezer for about 6 months. The polymer
has a very strong structure due to the 1,3 bonding position on the aromatic rings in the polymer.
The polymer did not crack upon the deposition of aqueous solution and can only be broken by a
severe impact.
Usually the resorcinol formaldehyde ratio is 1: 2, both acid and base were used as a
catalyst with different molar ratio of resorcinol/catalyst (R/C). Water, acetone, methanol,
ethanol, n-propanol, and iso-propanol can all be used as the solvent. The catalyst used, ratio of
R/C, the solvent, and concentration of the starting materials determine the final structure and
properties of the gel. Eventually, acid (HC1) was chosen as the catalyst to provide H+ ions which
are necessary for MALDI; acetone was chosen as solvent for quick polymerization; different
matrices were used to investigate the ionization capability. The matrix molecules used for
MALDI with similar structure as the RF polymer can be embedded into the polymer via covalent
The ratio of the resorcinol and formaldehyde is chosen as 1:2 since the ratio of the
resorcinol and formaldehyde in the structure is 1:2. Water, alcohol, and acetone have all been
used in the literature and suitable as the solvent of the RF polymerization reaction. Different
solvents have been tested and eventually acetone was chosen as the solvent throughout the rest of
the synthesis. With acetone as solvent, the temperature of the curing stage can be lowered
significantly (from 80 oC to 40 OC) with reasonable gelation time.104 The initial concentration of
the reactants was chosen as (R+F)/solvent 30% w/w. The sodium carbonate was first chosen as
the catalyst because it is the most commonly used in the previous literature. The higher the ratio,
the smaller the polymer particles and the higher density of the gel. The R/C ratio can be as high
as 200:1 was chosen as the R/C ratio. Since an acidic polymer can provide H+ which is
necessary in MALDI to ionize analyte, acids were tested. HCIO4 WAS used as first acid catalyst
because it was used in the literature. Later, HCI was used throughout the rest of the synthesizing
because it is a commonly used acid in lab, although there is no evidence in the literature about
using HCI as catalyst in RF polymer synthesis.
The initial synthesis of the RF polymer was tested with the following procedure: 4.00 g
Resorcinol (0.036 mol), 5.00 mL formaldehyde (0.072 mol), 12.00 mL acetone, and 0.0078 g
Na2CO3 (0.036 mmol) were added to the flask which was sealed and immersed in a 450C water
bath. The formaldehyde-to-resorcinol ratio is 2:1 and the resorcinol-to-Catalyst ratio is 1000:1.
Every half hour several drops of solution were taken out of the flask and deposited on a glass
slide. The solutions taken out at one hour and after one hour all successfully polymerized. Thus,
the reaction time was then determined as one hour. The solution is stored in a vial in the freezer
with -200C. The solution can be used for six months after synthesis. This RF polymer was
given the serial number as RF-1.
There were thirty nine experiments that have been conducted in an effort to systematically
investigate the properties of the RF polymerization process. The tests were conducted using a
combination of different solvents such as acetone, ethanol, and water; different
resorcinol/catalyst ratios; different catalysts; different matrices with varying concentration; and
addition of different doping agents. Every RF solution was named with "RF" followed by the
serial number assigned from one to thirty nine.
Thirteen RF polymers have been synthesized with Na2CO3 aS a catalyst and acetone as
solvent as shown in Table 2-1. These polymers have a different resorcinol-to-catalyst ratio, with
the addition of different matrices with varying concentration and the addition of doping agents in
order to bring functional groups into the polymer.
The resorcinol-to-catalyst was changed to 500 and 100 which are assigned the serial
numbers RF-2 and RF-39, respectively. These two polymers, together with the RF-1 polymer,
all polymerized. After the successful synthesis of the RF-1 and RF-2 polymers, RF-3 polymer
was synthesized with 1000 ppm of DHB which also polymerized as expected. The RF-20
polymer was able to polymerize when the concentration of the DHB was raised to 40,000 ppm
with the high catalyst concentration (resorcinol-to-catalyst ratio as 100).
After DHB was successfully incorporated into the RF polymers, CHCA was tested for
incorporation into the RF polymers with different concentrate on, different resorcinol -to-cataly st
ratio, and different concentration of 4-(imidazole-1 -yl)phenole with or without being cued with
HCI which were assigned the serial numbers from RF-27 to RF-35. RF-29, RF-30, and RF-31
polymerized, while others did not. The R/C can be as high as 1000 for the sol to polymerize as
long as there is no imidazole added even when there is matrix added. When there is imidazole
added, the R/C can not be higher than 50. The concentration of the matrix can be as high as
10,000 ppm when CHCA was used.
Ethanol was tested as a solvent for RF-4 with 1000 resorcinol-to-catalyst ration and 1000
ppm DHB, and RF-5 with 500 resorcinol-to-catalyst ration and 1000 ppm DHB. Both of the sol
crystallized instead of polymerized (Table 2-2).
Nine polymers (RF-6 to RF-12, RF 15, and RF 19) were tested in the water as solvent
with varying concentration of Na2CO3 aS catalyst, varying concentration of DHB, and addition of
Fe2 13-H20 in order to add metal chelating capability as shown in Table 2-3. All of these
polymers polymerized with varying reaction time.
HCIO4 WAS the first acid catalyst used in the synthesis ofRF-12 polymer with water as
solvent. The necessity to test an acid catalyst is based on the need of the protons in order to
ionize analyte molecules in MALDI. HCIO4 is documented as an acid catalyst for the synthesis
of RF polymer, thus was chosen.104 Since storing HCIO4 requiring extra caution, HCI was test as
catalyst in the synthesis of RF polymer. Although there is no evidence in the literature about
using HCI as a catalyst for RF synthesis, the experiment was a success.
There are thirteen polymers (RF-14, RF-16 to RF-18, RF-21 to RF 26, and RF-36 to RF
38) that were synthesized with HCI as catalyst for its proton; with acetone as solvent for the fast
evaporation during the gel process; and with different matrices and varying concentration, with
addition of imidazole, EDTA, and vinylimidazole; as shown in Table 2-4. Only seven of tem
polymerized (RF-14, RF-16, RF-21 to RF23, RF-25, and RF-3 8).
Among the thirty nine tests twenty four of them were able to polymerize. Nineteen of the
polymerized solutions contain matrix. For each matrix-containing polymer, mass spectrometry
was conducted with the sol-gel solution deposited on a stainless steel probe. After the solution
was polymerized, the polymer was taped onto the stainless steel with double-sided tap, and then
100 ppm spiperone in methanol was deposited on the polymer. After the spiperone solution
dried the sample was analyzed in a custom built MALDI ion trap mass spectrometer.
Among the twenty four matrix-embedded RF polymers, only the CHCA-embedded RF
polymers produced MS signals with 100 ppm spiperone. As the concentration of the CHCA
increases, the intensity of the analyte signal increases under the same analysis condition. There
is an up limit of the concentration of the matrix in the solution for the matrix-embedded
resorcinol formaldehyde solution to polymerize which is 20,000 ppm. When 40,000 ppm of the
matrix is added, the polymer (RF-24) forms a lot of cracks which is not suitable as a MALDI-MS
substrate. RF-16, which contained 20,000 ppm CHCA, produced satisfactory MS analysis result
and is used throughout the rest of the MS analysis.
The solution is colorless while polymer polymerized from the solution is dark red. The
color change indicates the formation of bonds on the conjugated structure which is the aromatic
rings in this reaction. The mechanism of the resorcinol formaldehyde polymerization shown in
Figure 2-5 is proposed by Lin and Ritter "l which has an addition and a condensation step. Base
was used as the catalyst in the addition step. In the second step the acid was used as catalyst to
cure the solution. In the experiment reported here only base, only acid, and base first then acid
as catalyst(s). In all cases there are successful examples, with the base catalyzed solution took
longer time than the acid catalyst solution to polymerize. Figure 2-6 is the mechanism I
proposed for the base-only catalyzed resorcinol formaldehyde polymerization reaction.
Analysis of the Spiperone on the CHCA Derived RF Polymer for Lower Background
Interference from Matrix Molecules
This comparative analysis was performed with a microprobe quadrupole ion trap mass
spectrometer (QITMS) which was built in the Yost laboratory by Christopher Reddick in 1997.11
The UV laser (Laser Science Inc. model VSL-337ND) used for all MALDI MS analysis has 20
Hz pulsed nitrogen laser with a wavelength of 337. 1 nm and a 3 ns pulse width."l The maximum
energy output of the laser is >250 CIJ/ pulse with a peak power of 85 kW."1 Since the laser is
near-diffraction limited, the beam can be focused to a diameter within a few times the laser' s
wavelength; for the studies reported here, the laser spot size ranged from a diameter of 25 to 50
Clm. The laser is focused into the mass spectrometer chamber by a single fused silica lens
(Melles-Griot) with a focal length of 25.4 cm as illustrated in Figure 2-7.11 The laser is
externally triggered after a 1 ms delay by a Wavetek model function generator so the ion source
gate has fully opened before ionization."l The position of the sample plate can be adjusted
manually along x and y axes." Photosensitive paper is used to determine the position of the
laser beam with respect to the sample plate to align the incident laser light." The software used
to control the mass scan and data acquisition has been developed in our research group which is
used to control auxiliary modulation frequency and amplitude to extend mass range.ll As shown
in Figure 2-8, ions are produced during the MALDI process, and then bend 900 into the ion trap
by using a DC quadrupole deflector. This is to reduce the possibility of neutral collisions
occurring within the ion trap caused by neutral molecules. After being ej ected by the QIT from
the exit end, ions are detected using a conversion dynode and electron multiplier which is behind
the exit end electrode of the QIT.11 The data taken by this instrument was converted to excel file
to generate the spectrum.
The analyte used here, spiperone, is an antidepressant. Figure 2-9 shows the fragmentation
path ways of spiperone. Different matrices such as DHB, sinapinic acid, caffeic acid, and CHCA
have been embedded into the RF polymer and the matrices-embedded polymers have been tested
for the ability to ionize spiperone. MS analysis showed that the RF polymer with CHCA was the
only combination that generated a spiperone MS signal (Table 2-1 to 2-4). This phenomenon
can be explained by the result from the UV-vis spectra of the various matrix-embedded RF
polymers (Figure 2-10). The discontinuity of spectrum at 350 nm is caused by the changing of
light source from UV to visible. The CHCA had the highest absorption at 337 nm at the same
concentration compare with other matrices; the absorbance of the other matrices may render
them less effective MALDI matrices. Figure 2-11 shows the UV absorbance of CHCA in
acetone (purple), the pure RF polymer (blue), and the RF polymer embedded with CHCA
(orange) which were analyzed on Varian Cary-100 Conc UV-visible spectrometer from Varian
(Palo Alto, CA). The CHCA-embedded RF polymer showed UV absorption at 337 nm which is
not the case in the pure RF polymer. Since the solution of CHCA in acetone shows high
absorbance around 337 nm range, it is obvious that the CHCA-embedded RF polymer obtained
its high UV absorbance at 337 nm from embedding CHCA into it.
A polymerized RF 16 (20,000 ppm CHCA embedded RF polymer) pellet was attached
onto the stainless steel MALDI microprobe with double-sided tape. A 0.2 CLL volume of 100
ppm spiperone was deposited onto each polymer directly with pipette. After five minutes the
sample is ready for MALDI-MS analysis.
A 0.2 CIL volume of 2mM CHCA was also deposited onto the stainless steel microprobe
with pipette; it was dry after 5 min past, then 0.2 CIL of 100 ppm spiperone was deposited onto
the matrix spot with pipette.
The results are shown in Figure 2-12 a and b, each showing the average of six spectra. The
spectrum of 100 ppm spiperone with 20,000 ppm CHCA on the stainless steel showed [M+H]+
(m/z 396) peak together with fragments from CHCA (m z 123.2 and m/z 172.5) which pose
interference to the interpretation of the spectrum while the spectrum of 100 ppm spiperone on
2% CHCA-embedded RF polymer showed high [M+H]' (m/z 396) peak and no noticeable
fragment from CHCA. By embedding matrix molecules into RF polymer, the matrix molecules
form covalent bonds with the polymer and are fixed into the polymer. Figure 2-13 is the
illustration of one of the several possible bindings. Since the covalent bond between the polymer
structure and the matrix molecules are much stronger than the hydrogen bond or the van der
Waals force and thus requires much more energy to break the bond, the polymer keeps the
matrix from being ablated while the matrix still has the ability to absorb laser energy to transfer
to spiperone molecules and provide H+ for ionization. Moreover, while using the same laser
power for both analyses, the spectrum of spiperone on CHCA-embedded RF polymer showed
lower intensities of daughter ions of spiperone (m/z 291.5, 238; m/z 165.5, 885) than the
spectrum of spiperone with CHCA on stainless steel (m/z 291.5, 700; m/z 165.5, 3760).
Comparing these two spectra, the spectrum obtained with spiperone on the CHCA-embedded RF
polymer showed improved quality.
Analysis of the Spiperone on the CHCA-Derived RF Polymer vs. Analysis of the Spiperone
on the Stainless Steel Using CHCA as Matrix for More Uniform Analyte Signal Intensity
Across the Sample
The LTQ linear ion trap with vMALDITM ion source from ThermoFinnigan (Figure 2-14)
which is capable of imaging was used in this experiment. The laser power is 250 CLJ/ pulse. The
laser beam was set up to move in 120 Cpm steps across the sample spot (3mm in diameter) and the
data are collected automatically by the XcaliburTM data system to generate the image of the
signal intensity of the analyte throughout the analyzed area.
The dried-droplet method was chosen for the comparison experiment because this method
is still widely used for MALDI-MS analysis despite the fact that the matrix-analyte co-crystals
are unevenly distributed across the sample which causes uneven distribution of signal intensity
of analyte across the sample spot. It would be exciting to see the improvement the CHCA-
embedded RF polymer can make by simply using dry droplet method, and make the using dried-
droplet method by mass spectrometry analyst with less effort needed for search of "sweet spots".
For comparison of the dry droplet on stainless steel analysis vs. spiperone solution on
CHCA embedded RF polymer analysis; 0.2 CLL of 0.5 M CHCA in MeOH was applied on the
stainless steel; after the matrix solution was dried, 0.2 pIL of 100 ppm spiperone solution in
MeOH was applied on the dried matrix spot and on the CHCA embedded RF polymer,
respectively. The microscopic image of the sample spot prepared with dried-droplet method
before MS analysis is shown in Figure 2-15. After the sample plate was inserted into the
instrument, the image of the sample plate was taken by the CCD camera and a circle was drawn
by hand. The instrument started to run MALDI analysis throughout the circled area with each
analysis spot 120 Cpm apart both in x direct and y direction. The position parameters (x- and y-
axis) were recorded as attachment of each spectrum for each analysis spot by the vMALDI
software to be used to generate the image of the sample spots with the information of mass
spectra after the analysis. Both image of the distribution of intensity of TIC (total ion counts)
and image of the distribution of intensity of the ions within certain range can be generated. RSD,
relative standard deviation which is calculated by dividing the standard deviation by the average
value, was calculated for m/z 304 (for cocaine) by surfer 8 based on all the spectra taken
throughout the circled area and reported in "grid report". Typical results from the sample
prepared with dry droplet method on the stainless steel sample plate are shown in Figure 2-16
with relative standard deviation (RSD) as 228%.
Figure 2-17 is the microscopic image of the CHCA-embedded RF polymer pellet after the
deposition of 0.2 CLL of 100 ppm spiperone. Same mass spectrometry analysis as for the dried-
droplet of spiperone on stainless steel was run for dried-droplet of spiperone on CHCA-
embedded RF polymer. Both image of the distribution of intensity of TIC (total ion counts) and
image of the distribution of intensity of the ions within certain range can be generated. RSD was
calculated for m/z 304 (for cocaine) by surfer 8 based on all the spectra taken throughout the
circled area and reported in "grid report". Typical results from the sample prepared with dry
droplet method on the CHCA-embedded RF polymer are shown in Figure 2-18 with relative
standard deviation (RSD) as 103%.
Compared to the results obtained from the dry droplet method on the stainless steel (Figure
2-16), the results from the dried-droplet on the CHCA-embedded RF polymer (Figure 2-17)
produced more even distribution of the analyte across the sample with the RSD of the sample
prepared on the CHCA-embedded RF polymer is about the half of that with the sample prepared
with the dried-droplet method on stainless steel; thus, analyte signals can be detected easily
without searching for the "sweet spot". The more even distribution of the analyte signal resulted
from the incorporation of matrix molecules into the rigid polymeric structure of RF polymer,
since the matrix molecules are evenly distributed throughout the whole polymeric structure on
the molecular level. The morphology of the analyte crystals only depends on the distribution of
the analyte across the sample and no concern of distribution of matrix molecules is necessary.
With the 1, 4 polymerization position on the aromatic ring, RF polymers can withstand the
harsh condition of chemical modification and washing with aqueous solution which is the
condition for most biological sample. With the aromatic groups in the RF polymers and reaction
sites on the aromatic rings it is possible to incorporate aromatic groups containing matrix
molecules in the polymeric network with covalent bonds. By trapping the matrix molecules in
the polymeric network with covalent bonds it still provides the assistant to ionization but can
reduce the amount of matrix molecules been ablated by laser which can interfere with the MS
signals from analyte with low molecular weight because it needs more energy to break a covalent
bond than to break a intermolecular noncovalent bond.75 By incorporating the matrix molecules
into the polymeric network structure, it can help solve the problem of unevenly distributed signal
throughout the sample plate which is always a problem in MALDI-MS analysis. Many different
sample preparation methods were developed to minimize the problem. The new resorcinol-
formaldehyde (RF) polymers developed have physical and chemical properties suitable for
embedding matrix molecules in the substrate for lowering the background noise from matrix
molecules. With the nature of the matrix-embedded polymer the matrix molecules distributed in
the polymer evenly at the molecular level, thus provide the possibility to produce uniform signal
intensity of analyte across the sample. This property also provides the possibility for
quantization of the analyte in MALDI which is an important issue related to MALDI sample
(a) Mydes~esis
Br~relrrn inn .2H cm A
HO-~ 5 f+t I-l K-i--G~-5RGH
DHl CFUH ONr I- emp
Figure 2-1. The mechanism of the TEOS sol-gel reaction. [Adopted from Lin, Y.; Chen, Y.
Laser desorption/ionization time-of-flight mass spectrometry on sol-gel-derived 2,5-
dihydroxybenzoic acid film Analytical Chemistry 2002, 74, 5793]
Figure 2-2. Illustration of incorporation of DHB molecules in the TEOS gel. [Adopted from
Lin, Y.; Chen, Y. Laser desorption/ionization time-of-flight mass spectrometry on
sol-gel-derived 2,5-dihydroxybenzoic acid film Analytical Chemistry 2002, 74, 5793]
t .
Figure 2-3. Microscope pictures showing the sample surfaces of manually prepared samples
with the dried-droplet (DD) or the seed layer (SL) method using (a) a-cyano-
hydroxycinnamic acid (CHCA) DD, (b) CHCA SL, (c) sinapinic acid (SA) DD, (d)
SA SL, (e) ferulic acid (FA) DD, (f) FA SL. [Adopted from Onnerfjord, P,.;
Ekstrom, S,.; Bergquist, J.; Nilsson, J.; Laurell, T,.; Marko-Varga, G. Homogeneous
sample preparation for automated high throughput analysis with matrix-assisted laser
desorption/ionization time-of-flight mass spectrometry Rapid' Communications in
M~ass Spectrometry 1999, 13, 315]
Figure 2-4. MALDI ion images showing intensities for selected peptides using (A) the thin-film,
a-CHC sample and (B) the dried-droplet, DHB sample. Approximately 250 fmol of
al.3, 250 fmol of AP, and 1 pmol of ELH were prepared with each matrix. The black-
to-red color map corresponds to the arbitrary intensity values specified for each
peptide, while the grid lines correspond to 50 Cpm increments within each image.
[Adopted from Garden, R.W.; Sweedler, J.V. Heterogeneity within MALDI samples
as revealed by mass spectrometric imaging Analytical Chemistry 2000, 72, 30]
1. Addition Reaction
2. Condensation Reaction
2 1
Figure 2-5. Mechanism of the polymerization of RF polymer proposed by Lin and Ritter.
[Adopted from AL-Muhtaseb, S.A.; Ritter, J.A. Preparation and properties of
resorcinol-formaldehyde organic and carbon gels Advanced Materials 2003, 15, 101]
Figure 2-6. Base-catalyzed RF polymerization.
Laser Microprobe
lon Trap Mass Spectrom eter
Figure 2-7. Cross-section of the ion trap mass spectrometer. [Adopted from Reddick, C.D. The
detection of pharmaceutical drug compounds from intact biological tissue by matrix-
assisted laser desorption ionization method (MALDI) quadrupole ion trap mass
spectrometry 1997 PhD dissertation. University of Florida, Gainesville, Florida.]
Laser Beam in Ions out
Figure 2-8. Illustration of the path of laser and ions in mass spectrometer. [Adopted from
Reddick, C.D. The detection of pharmaceutical drug compounds from intact
biological tissue by matrix-assisted laser desorption ionization method (MALDI)
quadrupole ion trap mass spectrometry 1997 PhD dissertation. University of Florida,
Gainesville, Florida.]
[Spiperone + H]' m/z 396.49
m/z 165.19
m z 291.35
m/z 232.31 m/z 260.36
Figure 2-9. Fragment path ways of spiperone.
4.5 -1 I~,nlu,uuu ppm cl-los In re- gel
10,000 ppm Sinapinic acid in RF gel
a 3.0
E2.5 -1nl 10,000 ppm caffeic acid
<(2.0 -r/ 10,000 ppm DHB in RF gel
1.0 RF gel
250 300 350 400 450 500
Wavelength (nm)
Figure 2-10. UV absorbances of the various matrix-embedded RF polymers.
CHCA in acetone solution
r RF polymer
3 / 10,000 ppm CHCA in RF polymer
250 300 350 400 450 500
Wavelength (nm)
Figure 2-11i. UV absorbances of the RF polymer (blue), CHCA-embedded RF polymer (orange),
and CHCA solution (pink). The spike at 320 and 350 is caused by the instrument
used for analysis.
[spiperone + H1
[spiperone + H]+ C13H17N30
155 [spiperone + H]+ C7H,
350 400
450 500 550 600 650
[spiperone + Hi
[spiperone + H]+ C13H17N30
I spiperone + Hi' C7H7
50 150 250 350 450 550 650
Figure 2-12. Mass spectrum of the 100 ppm spiperone on A) 20,000 ppm CHCA embedded RF
polymer, and B) stainless steel with CHCA as matrix.
Figure 2-13. CHCA embedded in the RF polymer structure.
Figure 2-14. LTQ with vMALDI ion source from ThermoFinnigan.
Figure 2-15. The microscopic image of the sample well after the dry droplet sample preparation
before MS analysis (3 mm in diameter).
Y (micron) 2000,
r 5.000e+006\
X (micron)
Figure 2-16. The distribution of the spiperone intensity (m z 396) across the sample using dry
droplet method on stainless steel. A) 2-D image. B) 3-D image.
Figure 2-17. The microscopic image of the RF-16 polymer pellet after the deposition of 0.3 CLL
of 100 ppm spiperone before MS analysis.
400 1500 1600 1700 1800 1900 2000
01 1
Y (micron) 2000
soo0 ,
Figure 2-18. The distribution of the spiperone intensity (m z 396) across the sample using dry
droplet method on RF-16 polymer pellet. A) 2-D image. B) 3-D image.
Table 2-1. RF polymers with acetone as solvent and Na2CO3 aS catalyst: 4.00 g Resorcinol +
5.00 mL formaldehyde in 12.00 mL acetone with Na2CO3 as catalyst
0.0078 g
Na2CO3 (/
0.0156 g
Na2CO3 (/
0.078 g Na2CO3
0.0156 g
Na2CO3 (/
0.039 g Na2CO3
0.0156 g
Na2CO3 (R/C
0.0156 g
Na2CO3 (R/C
0.0156 g
Na2CO3 (R/C
0.156 g Na2CO3
0.156 g Na2CO3
0.078 g Na2CO3
0.078 g Na2CO3
0.034 g Na2CO3
0.034 g Na2CO3
0.0168 g DHB (1000 ppm)
0.672 DHB (40,000 ppm)
0.4146 g CHCA (20,000 ppm) + 0.3492 g 4-
(imidazole-1 -yl)phenole (20,000 ppm)
0.4146 g CHCA (20,000 ppm) + 0.3492 g 4-
(imidazole-1 -yl)phenole (20,000 ppm) 2 h later add 1.6
mL 0.1 M HCI to cue
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1 -yl)phenole (16,000 ppm) ), 2 h later add
1.6 mL 0.1 M HCI to cue
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1 -yl)phenole (16,000 ppm)
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1 -yl)phenole (16,000 ppm), 2 h later add
1.6 mL 0.1 M HCI to cue
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1 -yl)phenole (16,000 ppm)
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1 -yl)phenole (16,000 ppm), 2 h later add
1.6 mL 0.1 M HCI to cue
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1 -yl)phenole (16,000 ppm)
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1 -yl)phenole (16,000 ppm), 2 h later add
1.6 mL 0.1 M HCI to cue
Table 2-2. RF polymers with ethanol as solvent and Na2CO3 aS catalyst: 4.00 g Resorcinol + 5.00
mL formaldehyde in 12.00 mL ethanol
0.0078 g Na2CO3
0.0156 g Na2CO3
0.0168 g DHB (1000 ppm)
0.0168 g DHB (1000 ppm)
Crystalline no
Crystalline no
Table 2-3. RF polymers with water as solvent and Na2CO3, Or HC1, or HCIO4 aS catalyst: 4.00 g
Resorcinol + 5.00 mL formaldehyde in 12.00 mL H20
Catalyst Matrix Polymerized Signal
0.0156 g Na2CO3
RF-19 (R/C 50) no too quick no
0.0156 g Na2CO3
RF-6 (R/C 500) 0.0168 g DHB (1000 ppm) yes (5 hrs) no
0.0156 g Na2CO3 0.0168 g DHB (1000 ppm) + 0.266 g of
RF-7 (R/C 500) FeCl3-6H20 (1000 ppm) too quick (15 mins) no
0.0156 g Na2CO3 0.0168 g DHB (1000 ppm) + 0.0266 g
RF-8 (R/C 500) FeCl3-6H20 (100 ppm) yes (2 hrs) no
0.0156 g Na2CO3 0.0336 g DHB (2000 ppm) + 0.0266 g
RF-9 (R/C 500) FeCl3.6H20 (100 ppm) yes (3 hrs) no
0.0156 g Na2CO3
RF-10 (R/C 500) 0.0336 g DHB (2000 ppm) yes (2 hrs) no
0.0156 g Na2CO3
RF-11 (R/C 500) 0.168 g DHB (10,000 ppm) yes (2 hrs) no
0.1737 mL1 M
RF-12 HCIO4 (R/C 200) 0.168 g DHB (10,000 ppm) yes (1 hr) no
1.6 mL 0.1 M HCI
RF-15 (R/C 200) 0.336 g DHB (20,000 ppm) yes (< 0.5 hr) no
Table 2-4. RF polymers with acetone as solvent and HCI as catalyst: 4.00 g Resorcinol + 5.00
mL formaldehyde in 12.00 mL acetone with HCI as catalyst
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
1.6 mL of 0.1 M
3.2 mL of 0.1 M
0.16 mL of 1 M
0.49 mL 1-vinylimidazole (100,000 ppm)
0.1593 g EDTA (10,000 ppm)
0.3492 g 4-(imidazole-1-yl)phenole (20,000 ppm)
yes (< 0.5 hr) sol
became milky in
0.336 g DHB (20,000 ppm)
0.4146 g CHCA (20,000 ppm)
0.8292 g CHCA (40,000 ppm)
0.2073 g CHCA (10,000 ppm)
0.488 g SA (20,000 ppm)
0.390 g caffeic acid (20,000 ppm)
0.312 g 3-amino-qumiline (20,000 ppm)
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1-yl)phenole (16,000 ppm)
0.2073 g CHCA (10,000 ppm) + 0.2746 g 4-
(imidazole-1-yl)phenole (16,000 ppm)
yes (1 hr)
Because of the complexity of biological samples obtained from individuals for disease
screening tests and the chemicals used during the sample handling process, one or more cleaning
or separation steps is usually employed to remove most of the unwanted species and pre-
concentrate the biomarkers before MALDI-MS analyses.114 Those separation and enrichment
methods are usually tedious, time-consuming, and require large amounts of sample.
Many investigations have been performed to reduce the interference from the
uninformative components in MALDI analyses without a cleaning step. Several polymers were
used to achieve on-probe reduction of contaminations. High-density polyethylene membrane,
high-density polypropylene, octyl (Cs) and octadecyl (Cls) extraction disk from 3M (St. Paul,
MN) were used successfully to remove salt, detergent, and glycerol contaminants from peptide
and protein sample solutions. Immobilization of proteins onto nylon-66 and positive charge-
modified nylon (Zetabind) membranes removed the water soluble contaminates before MS
analysis.116 Perfluorosulfonated ionomer film were used to analyze biological mixtures such as
chemical digests of proteins, proteins in milk and egg white, cell lysate, and oligonucleotide
without pre-purification with enhanced results.ll On-probe purification also achieved by using
digests nitrocellulose for MALDI-MS analysis of PCR (Polymerase chain reaction) products and
DNA fragment.' Polyethylene membrane was used for high-mass proteins (100,000 Da)
MALDI-MS analysis with enhanced spectral quality.119 Hydrophilic poly(acrylic acid) (PAA)
was used for its selective adsorption of partially digested myoglobin to remove contaminants by
rinsing with water.120 Metals such as patterned gold with poly(acrylic acid)121 as analysis
surfaces were tested to reduce the contaminations in the samples.
Surface modifications have been performed in several cases with polymeric materials in
order to covalently bind a certain class of analyte for purification from solution for enhanced
performance (SELDI). A surface of poly(4-vinylpyridine) which was extended with spacer arms
(-N-ethyl succinamyl-) and terminated with leaving groups (N-hydroxysulfosuccinimi de) for
covalent attachment of an 18-residue peptide (N terminus of human ci-casein) was used for on-
probe purification for pre-analysis purification.122 Poly-lysine-immobilized poly-2-hydroxyethyl
methacrylate membrane was used to selectively absorb DNA from aqueous solution.123
Affinity adsorption without the formation of covalent bonds allows relatively easy mass
spectrometric analysis. Surface modification, which adds specific affinity to the substrate
surface for affinity extraction, was developed. The extremely strong avidin glycoprotein-biotin
interaction (kd= 10 i) was utilized to retain the biotinylated analyte onto the avidin immobilized
agarose beadsl24, 125 Or polymer thin films.126 Lectins have been immobilized onto gold foils to
affinity capture bacteria from the contents in the sample solution.12 Several dextrans were
immobilized onto the fresh gold support as a self-assembled monolayer to retain binding
molecules which capture analytes of interest.12 DNA has been immobilized onto the
poly(ethylene terephthalate) microfiber to capture anti-DNA antibodies.129
Although surface modification with affinity agents is superior to simply using the
polymers as substrates for MALDI-MS analysis, each of the methods has its limitation. The
avidin modified substrate requires the analyte to be biotinylated; lectins can be used to capture
bacteria but lacks specificity; the dextran-modified gold surface can work the same way as
IMAC does and both lack specificity; DNA has higher specificity but with the drawback of
difficulty in obtaining and handling DNA, plus the large size of DNA causes less amount to be
attached onto the solid support. A universal one-step on-probe clean-up method which has a
high specificity towards biomarkers, high enough density of recognizing sites, with low cost and
yet easy to manipulate for biological sample analysis has been developed. This method is a
surface modification of a RF polymer with aptamers for affinity capture. Antibodies have the
highest specific affinity among the biological receptors used for modifications, though is one of
the most expensive. Aptamers have numerous advantages over antibodies, yet, have not been
wildly tested.
As shown in Figure 3-1, there are two phenol groups on each aromatic ring which make up
most of the RF polymer structure. These phenol groups provide plenty of reaction sites for direct
surface modification with aptamer and surface modification with aptamer via carboxylation, i.e.,
indirect surface modification. The phenol groups on the RF polymer have a pKa of 9.86 and the
hydroxyl groups on the silica particle surface have a pKa of 9.82; thus, the reactivity of the
phenol groups should be very close to the hydroxyl groups on the glass nanoparticles. The
surface modification of the RF polymer can follow the procedures used in the research lab of Dr.
Weihong Tan (University of Florida) for the surface modification of silica particles.
Aptamers Used for RF Polymer Surface Modification
Aptamers have been used as molecular beacons in Weihong Tan's lab ( University of
Florida) for in vitro fluorescent detection. Molecular beacons detect the existence of an analyte
according to the changing fluorescent signal intensity when the beacon changes the conformation
as the result of the affinity capture of the analyte. Fluorescent signal detection for analyte with
molecular beacon works very well if the analyte of detection in known to exist in the tested
solution, otherwise, there can be a false positive result and a definite identification is impossible.
Tandem mass spectrometry analysis (MSn) has the capability for definite identification of a
substance based on its fragmentation pattern. Coupling the high specific recognition capability
of molecular beacon with the informing power of mass spectrometry would be the answer for the
limitations of molecular beacons. Thrombin-binding aptamers were covalently attached to the
surface of a glass slide and were used successfully for affinity capture of thrombin in MALDI
targets by McGown at Duke University.73 The RF polymer developed in our lab has enough
reaction sites, with similar reactivity as silica slides, to be used as solid support for aptamer
attachment and with the flexibility in the size and shape the sol-gel polymerization method
There is a long list of aptamers has been generated by SELEX process; moreover, an
aptamer can be produced with affinity towards any specific target molecule by the SELEX
process. The choice of the aptamer to be attached onto the RF polymer is based on the concern
that the successful attachment of the aptamers onto the RF polymer should be verified before the
affinity capture of a specific molecule is proved by mass spectrometric analysis. Verification of
the attachment of the aptamers on the RF with MS would include MS-related variables into the
verification process; thus, include more uncertainty in the detection. Since the task in this
proj ect is to develop a methodology for affinity capture of analyte of interest prior to MS
analysis, choosing an existing aptamer with high affinity of a specific molecule would save a lot
of effort in generating a new aptamer. An aptamer with high affinity towards a molecule that can
be detected by the naked eye and be measured by UV-vis was chosen.
The molecule chosen is reactive green 19 and belongs to a group of reactive dyes used in
textile industry.130, 131 This group of dyes has been used in dye-ligand affinity chromatography
for the purification of proteins because of the high selectivity and the reversibility of the affinity
binding between the dye and the protein.132 These synthetic dyes interact with the active sites of
many proteins by mimicking the structure of the substrates, cofactors, or binding agents for these
proteins. The aromatic triazine dye structure resembles the nucleotide structure of nicotinamide
adenine dinucleotide and the dye interacts with the dinucleotide fold in these proteins. These
reactive dyes can bind proteins by electostatic and hydrophobic interactions and by more specific
"pseudoaffinity" interactions with ligand-binding sites.131 The degree of purification achieved
with dye-ligand chromatography is generally better than that obtained with less specific
techniques such as ion-exchange or gel filtration chromatography. The reactive dyes are
relatively inert and unaffected by enzymes in crude cellular extracts.131 Figure 3-2133 Shows the
structure of the reactive green 19 molecule. This dye molecule has absorbance peak at around
630 nm wavelength and can be detected by the naked eye and UV-vis spectrometry.
The sequence of the aptamer with high specific affinity toward reactive green 19 is
ACCCG GCGTT CGGGG GGTAC CGGGTwhich was discovered by Ellinton and Szostak in
1992134, 135 and can be synthesized in a DNA synthesizer.132 In 20 mM Tris buffer at pH 7.6 with
0.5 M LiCl and 1 mM MgCl2, the aptamer folds into a stem-loop structure as shown in Figure 3-
3133 and can be used in a bioassay when labeled with fluorescein.136
After the reactive green 19-retaining aptamer was successfully attached onto the RF
polymer, a cocaine-retaining aptamer was chosen to be attached onto the RF polymer for the
cocaine capturing and MS analysis. Cocaine is an alkaloid found in leaves of the South
American shrub Erythroxylon coca. The active ingredient of the coca plant was first isolated in
the West by the German chemist Friedrich Gaedcke in 1855. Albert Niemann described an
improved purification process for his PhD which he named as "cocaine". Cocaine is a
powerfully addictive stimulant drug which was tried by approximately 33.7 million Americans
ages 12 and older, representing 13.8% of the population, at least once in their lifetimes according
to the 2005 National Survey on Drug Use and Health.137 Although detection of cocaine by GC-
MS is well established, it will be helpful if cocaine can be captured from biological sample such
as blood and urine and to be analyzed by MALDI-MS. Actually, after this aptamer affinity
capture procedure is established, any disease biomarker could be captured and analyzed by MS
the same way as reactive green 19 and cocaine.
Aptamer affinity capture of cocaine can be achieved by attaching a cocaine-retaining
aptamer onto the RF polymer. An aptamer with the affinity towards cocaine (Figure 3-4 b), one
of the two cocaine isomers, was constructed by Landry et al., as shown in Figure 3-545 which
forms a three-way junction in 20 mM Tris buffer with pH 7.4, 140 mM NaC1, and 2 mM MgCl2
to accommodate a cocaine molecule at the center of the aptamer tertiary structure. With
dissociation constant of 0.4 10 pLM between cocaine and the cocaine-retaining aptamer,45
cocaine-retaining aptamer was used as a fluorescent sensor for cocaine45 and colorimetric probe
for the detection of cocaine.133
Direct Surface Modification of the RF Polymer with Aptamer
The reactive green 19-retaining aptamer and cocaine-retaining aptamer were directly
attached onto the RF polymer in the nucleic acid synthesizer (Applied Biosystems 3400 DNA
Synthesizer, Figure 3-6). The Applied Biosystems 3400 DNA Synthesizer from Applied
Biosystems (Foster City, CA) is a fully programmable instrument that provides four-column
simultaneous synthesis, and features automatic base dilution and analysis of coupling efficiency.
The RF polymer pellets were first polymerized by depositing RF solution onto the top of a
stainless steel microprobe and allowing several hours for the solution to polymerize. These
pellets were then hammered to small pieces to fit in the columns of the DNA synthesizer. These
RF polymer pieces were loaded into the reaction column as solid support for aptamer attachment.
The sequence of the aptamer was set up using the software and the synthesis of the aptamers was
controlled by the computer. In each step, the solution is pumped through the column which is
attached to the reagent delivery lines and the nucleic acid synthesizer. Each base is added via
computer control of the reagent delivery. After the synthesis was finished the RF polymer pieces
were taken out to be immersed in NH30H / CH3 H2 ratio as one at room temperature for three
hours for de-protection of the aptamers.
Surface Modification of the RF Polymer with Aptamers via Surface Modification of the RF
Polymer with Carboxylic Groups
Research has been conducted in the research group of Dr. Weihong Tan group on
carboxylation of silica nanoparticles and reaction of the carboxylic acid groups with amine
modified aptamers for indirect surface modification. According to the procedure, the RF
polymer will be carried out by immersion in freshly prepared 1% (v/v) solution of distilled (3-
(trimethoxy silyl)propyl)di ethyl enetri amine (DETA) and 1 mM aceti c aci d for 30O min at room
temperature. The DETA modified RF polymer will be rinsed with deionized water to thoroughly
remove excess DETA. The amine-functionalized polymer was then treated with succinic
anhydride in dry tetrahydrofuran (THF) in presence of an argon atmosphere for 6 h. Figure 3-7
shows the scheme of the surface modification.
After the RF polymer was carboxylated amine-modified cocaine aptamers were attached
onto the RF polymer via the formation of an amide bond following the procedure used by
Weihong Tan's lab.136
Characterization of the Carboxylic Group-Modified RF Polymer
The verification of the carboxylation was performed by labeling the RF polymer with 1-
pyrenyldiazomethane (PDAM) (Figure 3-8), a new fluorescent labeling reagent from Molecular
Probes (Eugene, OR) with an amine group on it.139 The covalent attachment of the PDAM to the
carboxylated RF polymer was performed according to the procedure described by Gaber et al.139
The carboxylated RF polymer pieces (sample) and non-carboxylated RF polymer pieces
(control) were placed in two separate vials and immersed in an aliquot of 10 mM PDAM solution
in ethanol. The two suspensions were mixed vigorously on a vortex mixer for two hours at room
temperature before the polymer pieces were thoroughly rinsed with ethanol. The polymer pieces
were transferred to two separate vials and were rinsed three times with ethanol.
The excitation wavelength of PDAM is 3 51 nm and the fluorescent emission wavelength is
392 nm. Fluorescence emission intensity spectra of the sample and control in ethanol were
obtained by readings from Tecan Microplate Reader from Tecan (Mannedorf/Zurich,
Switzerland) to verify the success of surface modification of the RF polymer (Figure 3-9). The
PDAM-bond polymer pieces has a much higher emission at 392 nm wavelength after excited at
351 nm than the control which proved the existence of carboxylic acid groups on the RF
The determination of the amount of the carboxylic groups on the RF polymer was
evaluated from the uptake of a basic dye molecule, toluidine blue O (Figure 3-10),140 by the
carboxylated RF polymer. Toluidine blue O complexes to equivalent moles of carboxylate
groups which is the base for calculating the amount of the carboxylic acid groups according to
the amount of the toluidine blue O absorbed by the carboxylated RF polymer.140 The
carboxylated RF polymer pieces were immersed in 500 Cpm toluidine blue O of pH 10 at 30 OC
for five hours before the RF polymer pieces were rinsed thoroughly with 5.0 x 10-4 N NaOH
aqueous solution. The polymer pieces were rinsed three times after they were transferred to
another vial. The dye molecules were desorbed from the RF polymer by immersing the RF
polymer pieces in 50% acetic acid solution.
All the UV spectra in this proj ect were recorded on Varian Cary-100 Conc UV-visible
spectrometer (Palo Alto, CA). Toluidine blue O has UV absorbance at 285 and 623 nm. The
UV absorbance of the toluidine blue O desorbed from the carboxylated and noncarboxylated RF
polymer served as a second proof of the existence of the carboxylic acid groups on the RF
polymer (Figure 3-11).
The UV absorbance of the toluidine blue O solutions with different concentrations (Figure
3-12) was used to construct a calibration curve at 285 nm (Figure 3-13). Bases on the linear
regression fit shown, the concentration of the toluidine blue O desorbed from twelve round
pieces (3.5 mm diameter) of carboxylated RF polymer and non-carboxylated RF polymer in 9
mL of the 50% acetic acid solution was 7.8x10-6 M and 4.8x 10-6 M, respectively. The
difference of the concentration of toluidine blue O desorbed between the carboxylated RF and
non-carboxylated RF polymer pieces was 3.0x10-6 M mol by subtracting the concentration of
toluidine blue O desorbed from the noncarboxylated RF polymer from the concentration of the
toluidine blue O desorbed from the carboxylated RF polymer. The difference of the amount of
toluidine blue O in 9 mL of solutions between the carboxylated RF and non-carboxylated RF
polymer pieces was calculated by timing the difference of the concentration of toluidine blue O
between the carboxylated RF and non-carboxylated RF polymer pieces with 9 mL to get 2.7x10~
SM. The density of the carboxylic groups on the polymer was calculated by dividing 2.7x10-s
mol by the total surface area of the twelve polymer pieces with two sides (23 1 mm2) to get
1.2x10-10 mol/mm2. The number of carboxylic groups available to be ablated by a 100
micrometer radius laser pulse is thus 3.7x 10-12 mel, which is more than adequate to yield a
strong MALDI signal.
Affinity Capture of RG 19 with RG 19-Retaining Aptamer-Modified RF Polymer and
Characterization of the Modified RF Polymer
The affinity capture of the RG 19 by the RG 19-retaining aptamer was demonstrated by
desorption of this dye as detected by UV-vis spectrometry. The aptamer-modified RF polymer
pieces and non-modified RF polymer pieces were immersed in the 20 mM Tris-Cl buffer with
RG 19 in two separate plastic vials for four hours. The polymer pieces were rinsed thoroughly
with the Tris buffer before they were transferred to two different vials in order to avoid the non-
specific capture of the RG 19 on the plastic vial wall. The polymers were rinsed three times
again before deionized (DI) water was added to the vial to desorb the RG 19. The DI water in
the vial containing the aptamer-attached RF polymer turned blue instantly, while the DI water in
the vial contained the non-modified RF polymer did not change color. UV spectrum was taken
for the desorption solution from both vials (Figure 3-14).
In order to determine the amount of aptamer on the polymer surface, the concentration of
RG 19 desorbed into solution was measured by its UV absorbance. A calibration curve was
constructed (Figure 3-15) according to the UV absorbance at 634 nm of the reactive green 19
solutions different concentration. The equation of the calibration curve as y=0.00061x + 0.0019.
According to the calibration curve the amount of the RG 19 was calculated to be 0.20 mM from
the 0.123 UV absorbance of the sample. The amount of the RG 19 in the 5 mL solution was
7.8x10-7 mol. Two round pieces of the RF polymer have a total surface area of 38.5 mm2. The
density of the reactive green 19 absorbed on the aptamer-attached polymer was calculated as
2.03x10-s mol/mm2. The number of reactive green 19 can be ablated by laser (the radius of the
laser shot is estimated to be 100 Cpm) is 6.0x10-10 mol /spot, which is plenty for MALDI-MS
analy si s.
Affinity Capture of Cocaine with Direct and Indirect Cocaine-Retaining Aptamer-
Modified RF Polymer
The affinity capture of cocaine from a cocaine solution by the direct aptamer modified RF
polymer was first detected using a visual detection method, conducted according to the
procedure described by Landry et al.53 Diethylthiatricarbocyanine iodide, a cyanine dye, can be
captured by the cocaine-retaining aptamer. The addition of the cocaine solution into the
diethylthiatricarbocyanine iodide-aptamer complex containing would release the dye molecule to
capture the cocaine molecule (Figure 3-16)53 which serves as an easy visual detection of the
existence of the cocaine-retaining aptamers on the RF polymer. The pieces of the cocaine
retaining-aptamer modified RF polymer and pieces of non-modified RF polymer were put into
two separate vials with 500 CIL of 20 mM Tris buffer. A 50 CLL of 7 CLM of
diethylthiatricarbocyanine iodide in methanol was added into the vial followed by vigorous
mixing on the Vortex for several seconds. After five minutes, both suspensions were thoroughly
rinsed with buffer solution and transferred to two vials. The polymer pieces were rinsed with
buffer three times before 5 CIL of cocaine solution (1 mg/mL acetonitrile) was added into both
vials with 500 CLL Tris buffer. The solution in the vial with non-modified RF polymer pieces did
not change color, while the solution in the vial with the cocaine retaining-aptamer modified RF
polymer changed from colorless to blue. The color of the solution faded several hours later due
to the hydrolysis of the dye molecules in the slightly basic buffer."
MALDI-MS spectra of the cocaine-retaining-aptamer modified RF polymer and
unmodified RF polymer were taken on the LTQ with vMALDI source. Three pieces of cocaine
retaining-aptamer modified RF polymer and three pieces of non-modified RF polymer were
immersed in 500 CIL of 20 mM Tris buffer for the aptamers to form the affinity capturing
configuration. Then 5 CIL of cocaine solution (1 mg/mL acetonitrile, 3mM) was added into the
vials, waited for five minutes before they were thoroughly rinsed with 20 mM Tris buffer
solution. The polymer pieces were transferred to another two vials to be rinsed three times
before they were taken out and inspected under the microscope (Figure 3-17).
The polymers were taped onto the sample slide with double-sided tape and inserted into
the instrument. Sinapinic acid (SA), 2,5-dihydroxybenzoic acid (DHB), and a-cyano-4-
hydroxycinnamic acid (CHCA) were used as MALDI matrices on three of the modified polymer
respectively and on three non-modified respectively. The cocaine retaining-aptamer modified
RF polymer showed cocaine signal (the [M+H]+ ion at m/z 304) when SA was used as the
matrix, meanwhile there was no cocaine signal when DHB or CHCA was used as matrices,
which is consistent with the results McGown observed with SA for her aptamer-captured
thrombin sample.73 The polymer without the cocaine retaining aptamer (Figure 3-18a) showed
no cocaine ( m/z 304) compared to the cocaine retaining aptamer attached polymer (Figure 3-
18b). The 2-D and 3-D images of the intensity of the m/z at 304 ions of cocaine on the RF
polymer is shown in Figure 3-19.
An indirect cocaine retaining-aptamer modification of the RF polymer was also conducted
for the in Weihong Tan's lab after the polymer pellets were carboxylated in our lab. Three
pieces of cocaine retaining-aptamer modified RF polymer were immersed in 500 CLL of 20 mM
Tris buffer for the aptamers to form the affinity capturing configuration. Then 5 CLL of cocaine
solution (1 mg/mL acetonitrile, 3mM) was added into the vial, waited for five minutes before
they were thoroughly rinsed with 20 mM Tris buffer solution. The polymer pieces were
transferred to another vial to be rinsed three times before they were taken out and examed under
the microscope (Figure 3-20). The polymer pellets were taped onto the sample slide with double
sided tape and insert into the instrument. Sinapinic acid (SA) was used on the polymer as the
matrix. The cocaine retaining-aptamer modified RF polymer showed cocaine signal (m/z 304)
with SA as matrix (Figure 3-21). The 2-D and 3-D image of the intensity of the cocaine (m/z
304) on the RF polymer is shown in Figure 3-22. The amount of the cocaine detected on the
aptamer-indirect modified polymer by the MS is substantially higher than that on the direct
modified polymer (more spots with cocaine) due to the expected higher reaction efficiency of the
indirect modification.
With the phenol groups on the RF polymer, it is relatively straight-forward to follow the
established procedure to attach aptamer directly onto the RF polymer to surface modify it. The
up-take of reactive green 19 and cocaine proved the existence of the aptamers on the RF polymer
and the affinity capture capability of the aptamers.
With the phenol groups on the RF polymer, it is easy to follow the established procedure to
attach carboxylic acid groups onto the RF polymer, then react with amine modified aptamers to
surface modify the RF polymer with aptamers. The carboxylation of the RF polymer was proved
by the detection of the up taking of toluidine blue O and PDAM. The amount of the cocaine
detected on the aptamer indirect modified polymer by the MS is substantially higher than that on
the direct modified polymer due to the expected higher reaction efficiency of the indirect
With the procedure of attaching the aptamers onto the RF polymer established in the
research proj ect, other disease biomarker retaining-aptamers could be attached onto the RF
polymer following the same procedure, which can be used for pre-analysis clean-up for MALDI-
MS analysis for disease screening.
Figure 3-1. The structure of the RF polymer.