# Binding of molecules to DNA and other semiflexible polymers

## I Introduction

Aqueous solutions containing polymers and small associating molecules such as folded proteins and amphiphiles (surfactants) are commonly found in biological systems and industrial applications. As a result, extensive efforts have been devoted in the past few decades to the study of polymer–surfactant interactions . In addition, there has been growing interest in the interactions between DNA macromolecules and surfactants, lipids and short polyamines . These interactions are relevant to various biochemical applications such as DNA extraction and purification  and genetic delivery systems . Association of folded proteins (e.g., RecA) with DNA plays a key role in genetic regulatory mechanisms. Structural details of this association have been studied in recent experiments .

Recently, we have presented a general theory for the self-assembly in aqueous solutions of polymers and smaller associating molecules . Two different scenarios emerge, depending on the flexibility of the polymer. If the polymer is flexible enough, it actively participates in the self-assembly, resulting in mixed aggregates jointly formed by the two species. The polymer conformation changes considerably upon self-assembly but remains extended on a global scale, as the chain undergoes only partial collapse . On the other hand, if the polymer is stiff, partial collapse is inhibited.

The criterion determining the ‘flexible’ vs. ‘stiff’ scenarios concerns the polymer statistics on a mesoscopic length scale characterizing correlations in the solution (usually a few nanometers). It was found  that the flexible (stiff) scenario holds if the exponent $`\nu `$, relating the number of monomers $`N`$ to the spatial size $`R`$ they occupy, $`RN^\nu `$, is smaller (larger) than $`2/d`$ on that length scale ($`d`$ being the dimensionality). This distinction is analogous to the one made in the critical behavior of certain disordered systems  — if the critical exponent $`\nu `$ of a system satisfies $`\nu <2/d`$, the critical behavior would be smeared by impurities (in analogy to the partial collapse), whereas if $`\nu >2/d`$, the critical point remains intact. Indeed, neutral flexible polymers in three dimensions, having $`\nu 3/5<2/3`$, are found by scattering experiments to associate with surfactants in the form of a ‘chain of wrapped aggregates’ . On the other hand, stiff DNA molecules, having $`\nu =1`$ on the relevant length scale, are found to either remain unperturbed by surfactant binding , or undergo a discontinuous coil-to-globule transition , provided the chain is much longer than the persistence length.

In previous publications  we concentrated on the flexible case and the corresponding partial collapse, where the polymer degrees of freedom play an important role. In the opposite extreme limit of stiff, rod-like molecules, the conformational degrees of freedom of the polymer can be neglected and the chain may be regarded as a linear ‘binding substrate’. Models for stiff polymers, inspired by the Zimm-Bragg theory , treat the bound molecules as a one-dimensional lattice-gas (or Ising) system with nearest-neighbor interactions . They have been widely used to fit experimental binding isotherms for polyelectrolytes and oppositely charged surfactants . Recently, more detailed electrostatic models have been proposed for the interaction between rod-like polyelectrolytes and oppositely charged surfactants . In addition, a theoretical work focusing on the specific binding of proteins to DNA has been recently presented , treating a pair of bound proteins as geometrically constraining inclusions on the DNA chain.

In the current work we address the intermediate case of semiflexible polymers. The polymer we consider is stiff in the sense defined above, i.e., its persistence length, $`l_\mathrm{p}`$, exceeds several nanometers and, hence, the polymer is characterized by $`\nu =1>2/3`$ on that length scale. The total chain length, however, is considered to be much larger than $`l_\mathrm{p}`$, and the entire polymer cannot be regarded, therefore, as a single rigid rod. This case corresponds, in particular, to experiments on long DNA molecules , whose persistence length is typically very large (of order 50 nm), but much smaller than the total chain length (which is usually larger than a micron) . We argue that such an intermediate system may, in certain cases, be governed by different physics. Although the polymer is too stiff to change conformation and actively participate in the self-assembly, its degrees of freedom induce attractive correlations between bound molecules. Those fluctuation-induced correlations are weak but have a long spatial range (of order $`l_\mathrm{p}`$) and, hence, may strongly affect the binding thermodynamics.

The model is presented in Sec. II. Bound molecules are assumed to modify the local features of polymer conformation, e.g., change its local stiffness. In the limit of weak coupling, our model reduces to the Kac-Baker model , which is solvable exactly. This limit is discussed in Sec. III. Although turning out to be of limited interest in practice, the weak-coupling limit provides insight into the mechanism of association, and helps us justify further approximations. Section IV presents a mean-field calculation for an arbitrary strength of coupling. This analysis leads to our main conclusions, and in Sec. V it is extended to polymers under external tension. The results are summarized in Sec. VI, where we also discuss several relevant experiments involving DNA and point at future directions.

## II The Model

Small molecules bound to stiff polymers are commonly modeled as a one-dimensional lattice gas (or Ising system) . Each monomer serves as a binding site, which can either accommodate a small molecule or be empty, and the surrounding dilute solution is considered merely as a bulk reservoir of small molecules. In the current work we stay at the level of a one-dimensional model, assuming that the polymer is still quite (yet not infinitely) stiff, i.e., the persistence length is much larger than the monomer size. In addition, a dilute polymer limit is assumed, where inter-chain effects can be neglected. We focus on the effect of introducing the polymer degrees of freedom and, hence, seek a simple meaningful coupling between the polymer and the bound ‘lattice gas’.

A polymer configuration is defined by a set of vectors, $`\{𝐮_n\}_{n=1\mathrm{}N}`$, specifying the lengths and orientations of the $`N`$ monomers. In addition, each monomer serves as a binding site which can be either empty ($`\phi _n=0`$) or occupied by a small molecule ($`\phi _n=1`$). A configuration of the entire system is defined, therefore, by specifying $`\{𝐮_n,\phi _n\}_{n=1\mathrm{}N}`$.

Since the polymer is assumed to be locally stiff, a natural choice would be to couple $`\phi _n`$ with the square of the local chain curvature, $`\phi _n(𝐮_{n+1}𝐮_n)^2`$, thus modifying the local chain stiffness. However, in the usual Kratky-Porod worm-like-chain model of semiflexible polymers , chain segments are taken as rigid rods of fixed length ($`|𝐮_n|=\text{const}`$), and each squared-curvature term contains only one degree of freedom (e.g., the angle $`\theta _n`$ between $`𝐮_n`$ and $`𝐮_{n+1}`$). Consequently, this coupling, $`\phi _n\mathrm{cos}\theta _n`$, would leave $`\{\phi _n\}`$ uncorrelated, leading merely to a trivial shift in the chemical potential of bound molecules . One option to proceed is to consider higher-order extensions of the worm-like-chain Hamiltonian, involving three consecutive monomers. This will introduce correlations between bound molecules at different sites.

We take, however, a simpler route and modify the worm-like-chain model by allowing the monomer length to fluctuate. This modification was originally presented by Harris and Hearst , using a single global constraint for the average chain length. The modified model was shown to successfully reproduce the results of the Kratky-Porod model as far as thermodynamic averages (e.g., correlation functions, radius of gyration) were concerned. It was less successful, however, in recovering more detailed statistics of the worm-like chain (e.g., distribution function, form factor), particularly in the limit of large stiffness. The Harris-Hearst model was later refined by Lagowski et al.  and Ha and Thirumalai , replacing the single global constraint by a set of local constraints for the average segment lengths. This further modification was shown to be equivalent to a stationary-phase approximation for the chain partition function, yielding reliable results for average quantities, as well as more detailed statistics . We note that a similar approach was used in a recent model of semiflexible polymer collapse . It should be borne in mind that, despite its success in the past, the constraint relaxation remains essentially an uncontrolled approximation. In the current work we restrict ourselves to thermodynamic averages, such as monomer-monomer correlations and free energies, for which the modified model with a single global contraint can be trusted.

Thus, the rigid constraints of the original Kratky-Porod model, $`u_n^2=1`$, are relaxed into thermodynamic-average ones, $`u_n^2=1`$, where the mean-square monomer size is taken hereafter as the unit length. Using the modified model for the chain, each $`\phi _n(𝐮_{n+1}𝐮_n)^2`$ term involves two consecutive monomers (and not merely the angle between them), leading to a meaningful coupling between binding and polymer conformation.

The partition function of the combined system of polymer and bound molecules is written, therefore, as

$`Z`$ $`=`$ $`\underset{\{\phi _n=0,1\}}{\text{Tr}}{\displaystyle \underset{n=1}{\overset{N}{}}\mathrm{d}𝐮_n\mathrm{exp}()}`$ (1)   
$``$ $`=`$ $`{\displaystyle \frac{3}{4}}l_\mathrm{p}{\displaystyle \underset{n=1}{\overset{N1}{}}}(1+ϵ\phi _n)(𝐮_{n+1}𝐮_n)^2+{\displaystyle \underset{n=1}{\overset{N}{}}}\lambda _nu_n^2\mu {\displaystyle \underset{n=1}{\overset{N}{}}}\phi _n.`$ (2)   
In Eq. (2) $`l_\mathrm{p}`$ is the persistence length of the bare chain, characterizing its intrinsic stiffness. It is assumed to be much larger than the monomer size, $`l_\mathrm{p}1`$. The coupling is introduced through the stiffness term, assuming that a bound molecule modifies the local stiffness by a fraction $`ϵ>1`$, which may be either negative or positive but cannot change the positive sign of the overall stiffness term . The second term contains a set of multipliers, $`\lambda _n`$, to be chosen so that the constraints $`u_n^2=1`$ are satisfied. However, replacement of the entire set $`\{\lambda _n\}`$ by a single multiplier $`\lambda `$ can be shown to yield a non-extensive correction , which becomes negligible in the limit $`N\mathrm{}`$. Hence, we use hereafter a single multiplier, $`\lambda `$. Finally, the system is assumed to be in contact with a reservoir of solute molecules. The last term in Eq. (2) accounts for this contact along with any other factors which couple linearly to the degree of binding. Typically, $`\mu `$ contains the chemical potential of the solute reservoir and the direct energy of solute molecule–monomer binding. (All energies in this work are expressed in units of the thermal energy, $`k_\mathrm{B}T`$.) Note that we have not included in Eq. (2) any direct short-range (e.g., nearest-neighbor) interactions between bound molecules. Thus, all interactions in the model arise from the coupling to the polymer degrees of freedom. Short-range interactions between bound molecules do exist in physical systems. Yet, in the limit of $`l_\mathrm{p}1`$ and $`|ϵ|1`$, which is of interest to the current work, such direct interactions have a minor effect on binding, as is demonstrated in the following sections. Hence, we omit them for the sake of brevity.

As a reference, let us start with the previously studied partition function of the bare polymer ,

$$Z_\mathrm{p}=\underset{n}{}\mathrm{d}𝐮_n\mathrm{exp}[\frac{3}{4}l_\mathrm{p}\underset{n}{}(𝐮_{n+1}𝐮_n)^2\lambda \underset{n}{}u_n^2].$$
(3)   
It is a Gaussian integral which can be calculated either by transforming it to Fourier space and integrating, or by analogy to the path integral of a three-dimensional quantum oscillator . The result in the limit $`N\mathrm{}`$ and for $`l_\mathrm{p}1`$ is

$$Z_\mathrm{p}^{1/N}=\left(\frac{4}{3\pi l_\mathrm{p}}\right)^{3/2}\mathrm{exp}\left(3\sqrt{3\lambda /l_\mathrm{p}}\right).$$
(4)   
The multiplier $`\lambda `$ can now be determined according to

$$\frac{1}{N}\frac{\mathrm{log}Z_\mathrm{p}}{\lambda }=u_n^2_\mathrm{p}=1\lambda =\frac{3}{4l_\mathrm{p}},$$
(5)   
where $`\mathrm{}_\mathrm{p}`$ denotes a thermal average over the bare chain statistics (i.e., using $`Z_\mathrm{p}`$). The corresponding free energy per monomer (in the ensemble of constrained $`𝐮_n`$) is

$$f_\mathrm{p}=\frac{1}{N}\mathrm{log}Z_\mathrm{p}\lambda =\frac{3}{2}\mathrm{log}l_\mathrm{p}+\frac{3}{4l_\mathrm{p}}+\text{const}.$$
(6)   
Various correlations in the bare chain can be calculated. The pair correlation between segment vectors along the chain sequence is

$$𝐮_m𝐮_n_\mathrm{p}=\mathrm{e}^{|mn|/l_\mathrm{p}},$$
(7)   
which explains why the parameter $`l_\mathrm{p}`$ has been defined as the persistence length. Two higher-order pair correlations are calculated as well:

$`g_1`$ $``$ $`(𝐮_{n+1}𝐮_n)^2_\mathrm{p}={\displaystyle \frac{2}{l_\mathrm{p}}}+𝒪(l_\mathrm{p}^2)`$ (8)   
$`g_2(m,n)`$ $``$ $`(𝐮_{m+1}𝐮_m)^2(𝐮_{n+1}𝐮_n)^2_\mathrm{p}g_1^2={\displaystyle \frac{8}{3l_\mathrm{p}^3}}\mathrm{e}^{2|mn|/l_\mathrm{p}}+𝒪(l_\mathrm{p}^4),`$ (9)   
and will be of use in the next section, where we re-examine the coupled system.

## III Weak Coupling

Let us return to the full partition function (2), which can be equivalently written as

$$Z=Z_\mathrm{p}\underset{\{\phi _n\}}{\text{Tr}}\mathrm{exp}(\mu \underset{n}{}\phi _n)\mathrm{exp}[\frac{3l_\mathrm{p}ϵ}{4}\underset{n}{}\phi _n(𝐮_{n+1}𝐮_n)^2]_\mathrm{p}.$$
(10)   
First we consider the weak-coupling limit, $`|ϵ|1`$, where the partition function (10) can be treated by a cumulant expansion. In this limit the model becomes analogous to the exactly solvable Kac-Baker model , and we show that identical results are derived from a simple mean-field calculation. We then use this observation to justify a mean-field calculation for an arbitrary value of $`ϵ`$.

A cumulant expansion of Eq. (10) to 2nd order in $`ϵ`$ leads to

$$ZZ_\mathrm{p}\underset{\{\phi _n\}}{\text{Tr}}\mathrm{exp}\left[\left(\mu \frac{3l_\mathrm{p}ϵ}{4}g_1\right)\underset{n}{}\phi _n+\frac{1}{2}\left(\frac{3l_\mathrm{p}ϵ}{4}\right)^2\underset{m,n}{}g_2(m,n)\phi _m\phi _n\right],$$
(11)   
where the correlations $`g_1`$ and $`g_2`$ were defined in Eq. (9). Substituting expressions (9), the partition function is decoupled into a polymer contribution and an effective contribution from the bound solute molecules,

$`Z`$ $``$ $`Z_\mathrm{p}Z_\mathrm{s}=Z_\mathrm{p}\underset{\{\phi _n\}}{\text{Tr}}\mathrm{exp}(_\mathrm{s})`$ (12)   
$`_\mathrm{s}`$ $`=`$ $`{\displaystyle \frac{1}{2}}{\displaystyle \underset{mn}{}}V_{mn}\phi _m\phi _n\widehat{\mu }{\displaystyle \underset{n}{}}\phi _n,`$ (13)   
where

$`V_{mn}`$ $``$ $`{\displaystyle \frac{3ϵ^2}{2l_\mathrm{p}}}\mathrm{e}^{2|mn|/l_\mathrm{p}}`$ (14)   
$`\widehat{\mu }`$ $``$ $`\mu {\displaystyle \frac{3ϵ}{2}}+{\displaystyle \frac{3ϵ^2}{4l_\mathrm{p}}}.`$ (15)   
The introduction of the polymer degrees of freedom and their coupling to the binding ones have led to two effects, as compared to previous lattice-gas theories. First, there is a shift in the chemical potential, $`\mu \widehat{\mu }`$. This is equivalent to an effective change in the affinity between the small molecules and the chain. As expected, if binding strengthens the local stiffness of the chain ($`ϵ>0`$), the affinity is reduced (i.e., the isotherm is shifted to higher chemical potentials), whereas if it weakens the stiffness ($`ϵ<0`$), the shift is to lower $`\mu `$. The second, more interesting effect is that bound molecules experience an attractive potential, $`V_{mn}`$, along the chain. The amplitude of this effective interaction is small ($`ϵ^2/l_\mathrm{p}`$), but its range is large — of order $`l_\mathrm{p}`$. When $`l_\mathrm{p}`$ is increased there are two opposing consequences — the interaction amplitude diminishes, while the interaction range is extended. The overall effect on the thermodynamics of binding, therefore, has to be checked in detail.

### A Analogy with the Kac-Baker Model

The effective Hamiltonian of the bound solute, $`_\mathrm{s}`$, is a lattice-gas version of the Kac-Baker model , which is exactly solvable. Moreover, the procedure relevant to our semiflexible polymer, i.e., increasing $`l_\mathrm{p}`$ while keeping $`1l_\mathrm{p}N`$, is precisely the one studied in detail by Kac and Baker. Their results, as applied to our binding problem, can be summarized as follows. For any finite $`l_\mathrm{p}`$, the bound molecules are always in a disordered state along the polymer chain, as in any one-dimensional system with finite-range interactions. Consequently, the binding isotherm, i.e., the binding degree $`\phi \phi _n`$ as function of $`\mu `$ (see, e.g., Fig. 2a), is a continuous curve. However, in the limit $`l_\mathrm{p}\mathrm{}`$, taken after the infinite-chain limit $`N\mathrm{}`$, there is a critical value of coupling above which the binding exhibits a discontinuous (1st-order) transition. According to Baker’s rigorous calculation , the critical value of the potential amplitude multiplied by $`l_\mathrm{p}`$ (equal, in our case, to $`3ϵ_\mathrm{c}^2/2`$) is 4, i.e.,

$$ϵ_\mathrm{c}^\pm =\pm \sqrt{8/3}\pm 1.63.$$
(16)   
Note that the symmetry with respect to the sign of $`ϵ`$ is merely an artificial consequence of our 2nd-order expansion, Eq. (11). In general, the results should not be the same if the stiffness is weakened ($`ϵ<0`$) or strengthened ($`ϵ>0`$), as is demonstrated in Sec. IV.

The negative critical value in Eq. (16), $`ϵ_\mathrm{c}^{}1.63`$, lies outside the range of validity of the original polymer binding model, $`ϵ>1`$ \[cf. Eq. (2)\]. The positive value, $`ϵ_\mathrm{c}^+1.63`$, does not satisfy the assumption of weak coupling, $`|ϵ|1`$, which have led to the analogy with the Kac-Baker model in the first place. Thus, the sharp binding isotherms obtained from the Kac-Baker model for $`|ϵ|>ϵ_\mathrm{c}`$ do not apply, strictly speaking, for our polymer binding problem. The weak-coupling calculation does demonstrate, however, how fluctuations in polymer conformation induce long-range attraction between bound molecules. This basic feature is expected to remain when one considers stronger coupling, $`|ϵ|>1`$, and the resulting many-body terms omitted in Eq. (11). This is further discussed in the following sections.

Finally, the polymers we consider have a large but finite $`l_\mathrm{p}`$. For example, the persistence length of a DNA macromolecule is typically of order 50–100 nm, whereas the length of a single base pair is $`0.34`$ nm. Hence, $`l_\mathrm{p}`$ is of order $`10^2`$ (in units of monomer length) . It is worth checking to what extent the sharpness of binding in the Kac-Baker model for $`|ϵ|>ϵ_\mathrm{c}`$ is affected by finite $`l_\mathrm{p}`$. For this purpose, let us define a cooperativity parameter for the binding, measuring the maximum slope of the binding isotherm,

$$C\frac{\phi }{\mu }|_{\mathrm{max}}\frac{1}{4}.$$
(17)   
This parameter is equivalent to the zero magnetic field susceptibility in the analogous spin system, and is commonly measured from the slope of binding isotherms obtained in potentiometric experiments . It has been defined in Eq. (17) so as to yield zero for vanishing interaction ($`ϵ=0`$) and diverge at a critical point. (In the current weak-coupling limit, the maximum slope is obtained for $`\phi =1/2`$.) Given $`l_\mathrm{p}`$ and $`ϵ`$, the cooperativity is numerically calculated using Kac’s exact solution , as is explained in the Appendix. Figure 1 presents the results for $`l_\mathrm{p}=10`$ and 50. For $`l_\mathrm{p}=50`$ the binding becomes highly cooperative for $`|ϵ|>ϵ_\mathrm{c}`$. For even larger values of $`l_\mathrm{p}10^2`$ (relevant, e.g., to DNA) the binding will be hardly distinguishable from that of an infinite $`l_\mathrm{p}`$.

### B Mean-Field Calculation

In fact, the results of the Kac-Baker model in the limit $`N\mathrm{},l_\mathrm{p}\mathrm{}`$, while keeping $`l_\mathrm{p}<N`$, can be also obtained from a simple mean-field calculation . The heuristic argument for this agreement is the following: as $`l_\mathrm{p}`$ is increased, the range of interaction is extended and each bound molecule interacts with an increasing number of neighbors. As a result, the averaging assumption underlying the mean-field approximation is justified, and becomes exact when the range of interaction is taken to infinity. The correspondence between infinite-range models and mean field was rigorously proved by Lebowitz and Penrose for a more general class of potentials .

Indeed, employing a mean-field approximation for the potential (15) in the limit of very large $`l_\mathrm{p}`$,

$`{\displaystyle \underset{mn}{}}V_{mn}\phi _m\phi _n{\displaystyle \frac{3ϵ^2}{2l_\mathrm{p}}}\left({\displaystyle \underset{mn}{}}\mathrm{e}^{2|mn|/l_\mathrm{p}}\right)\phi ^2{\displaystyle \frac{3ϵ^2}{2}}N\phi ^2,`$

where $`\phi `$ is an average, uniform binding degree, we are led to the following mean-field free energy per monomer:

$$f=f_\mathrm{p}+f_\mathrm{s}f_\mathrm{p}+\phi \mathrm{log}\phi +(1\phi )\mathrm{log}(1\phi )\frac{3ϵ^2}{4}\phi ^2\widehat{\mu }\phi ,\text{for }l_\mathrm{p}\mathrm{}.$$
(18)   
It is easily verified that the critical point of this free energy is $`ϵ_\mathrm{c}^2=8/3`$, in agreement with the rigorous result, Eq. (16). The cooperativity parameter can be calculated as well from Eq. (18), yielding

$$C=\frac{ϵ^2}{4(ϵ_\mathrm{c}^2ϵ^2)},\text{for }l_\mathrm{p}\mathrm{}.$$
(19)   
This expression shows the usual critical behavior obtained from mean-field theories, $`C|ϵϵ_\mathrm{c}|^\gamma `$ with $`\gamma =1`$. The dependence of $`C`$ on $`ϵ`$ according to Eq. (19) is shown by the solid line in Fig. 1. The curves obtained from Kac’s solution approach it, as expected, when $`l_\mathrm{p}`$ is increased. Recall that expressions (18) and (19) correspond to the original problem of bound molecules only in the limit of small $`ϵ`$.

## IV Strong Coupling

The interesting part of our theory requires $`|ϵ|1`$ and thus limits the interest in the analogy to the Kac-Baker model. Nevertheless, based on the heuristic argument given above, it is reasonable to assume that, in the limit $`l_\mathrm{p}1`$, the mean-field approximation is good for larger values of $`|ϵ|`$ as well . The preceding section, discussing the Kac-Baker model in the weak-coupling limit, may be regarded, therefore, as a justification for using the mean-field approximation for one-dimensional models with large $`l_\mathrm{p}`$ and $`|ϵ|1`$. Applying a mean-field approximation to the binding degrees of freedom $`\phi _n`$ in our starting point, Eq. (2), the tracing over $`u_n`$ can be done exactly. The resulting free energy is composed of the polymer free energy, $`f_\mathrm{p}`$, evaluated with an effective persistence length, $`l_\mathrm{p}l_\mathrm{p}(1+ϵ\phi )`$, and the entropy of mixing for $`\phi `$,

$$f=f_\mathrm{p}|_{l_\mathrm{p}l_\mathrm{p}(1+ϵ\phi )}+\phi \mathrm{log}\phi +(1\phi )\mathrm{log}(1\phi )\mu \phi .$$
(20)   
Using Eq. (6), we obtain

$$f=\phi \mathrm{log}\phi +(1\phi )\mathrm{log}(1\phi )+\frac{3}{2}\mathrm{log}[l_\mathrm{p}(1+ϵ\phi )]+\frac{3}{4l_\mathrm{p}(1+ϵ\phi )}\mu \phi .$$
(21)   
For $`ϵ1`$ and $`l_\mathrm{p}1`$ this expression reduces, as expected, to our previous result for the weak-coupling limit, Eq. (18).

In the limit $`l_\mathrm{p}1`$ the critical points of the free energy (21) are

$$ϵ_\mathrm{c}^{}=\frac{2}{3}\left(2\sqrt{10}\right)0.775,ϵ_\mathrm{c}^+=\frac{2}{3}\left(2+\sqrt{10}\right)3.44,$$
(22)   
both of which lie within our general range of validity, $`ϵ>1`$. (Note the loss of symmetry with respect to the sign of $`ϵ`$, which was a consequence of the weak-coupling approximation in Sec. III.) The corresponding critical chemical potentials are

$$\mu _\mathrm{c}^\pm =\frac{3ϵ_\mathrm{c}^\pm (ϵ_\mathrm{c}^\pm +2)}{4(ϵ_\mathrm{c}^\pm +1)}\mathrm{log}(ϵ_\mathrm{c}^\pm +1)\pm 1.67.$$
(23)   
The binding isotherm, $`\phi =\phi (\mu )`$, as derived from Eq. (21), satisfies

$$\mu =\mathrm{log}\frac{\phi }{1\phi }+\frac{3ϵ}{2(1+ϵ\phi )},l_\mathrm{p}1.$$
(24)   
Figure 2a shows three binding isotherms for three different values of $`ϵ`$ below and above the critical point. The corresponding binding cooperativity is

$$C=\frac{8(1+ϵ)^2}{3(2+ϵ)^2(ϵϵ_\mathrm{c}^{})(ϵ_\mathrm{c}^+ϵ)}\frac{1}{4},l_\mathrm{p}1.$$
(25)   
As in Eq. (19), this expression exhibits the usual mean-field critical behavior, $`C|ϵϵ_\mathrm{c}|^\gamma `$ with $`\gamma =1`$. The dependence of $`C`$ on $`ϵ`$ is plotted in Fig. 2b.

Finally, the binding phase diagram arising from Eq. (21) in the limit $`l_\mathrm{p}1`$ is depicted in Fig. 3. At the lower limit of model validity, $`ϵ1`$, the spinodal approaches a finite value, $`\mu _{\mathrm{sp}}=\mathrm{log}(2/3)5/22.91`$, whereas the binodal diverges. Indeed, for $`ϵ1`$ the free energy (21) tends to $`\mathrm{}`$ for $`\phi =1`$, regardless of the value of $`\mu `$, and the binodal is thus obtained at $`\mu \mathrm{}`$. In this respect, the limit $`ϵ=1`$ for the bound molecules is similar to the limit of zero temperature — the induced interaction is so strong that the molecules condense for any value of the chemical potential. Note that in this special limit, $`ϵ1,\phi 1`$, the effective stiffness, $`l_\mathrm{p}(1+ϵ\phi )`$, becomes vanishingly small. This limit cannot be accurately treated within the continuum form of the semiflexible polymer Hamiltonian .

Equations (22)–(25) and the phase diagrams in Fig. 3 summarize the results obtained so far. They indicate that in cases of semiflexible polymers, where binding of small molecules significantly affects local chain features, the binding should be a very sharp process. For finite $`l_\mathrm{p}`$ the slope of the binding isotherm is finite, i.e., the binding is always continuous, yet for $`l_\mathrm{p}10^2`$ like in DNA, the behavior will be practically indistinguishable from a discontinuous phase transition.

It should be borne in mind that the sharp binding, obtained despite the one-dimensionality of the model, relies on the long range of the induced interaction. A direct short-range interaction between bound molecules could not produce a similar effect. Hence, such a short-range interaction (e.g., a nearest-neighbor interaction), which was omitted in Eq. (2) for the sake of brevity, does not have an important effect on the binding in the domain of interest, i.e., $`l_\mathrm{p}1`$ and $`|ϵ|1`$.

## V Chains under Tension

In addition, we consider binding to semiflexible chains which are subject to external tension. This scenario is relevant to recent single-molecule manipulation experiments . Since the tension suppresses chain fluctuations, it is expected to have a significant effect on the fluctuation-induced mechanism presented in the preceding sections.

In order to incorporate the external tension into our model, a term is to be added to the chain Hamiltonian \[cf. Eq. (2)\] ,

$`Z`$ $`=`$ $`\underset{\{\phi _n=0,1\}}{\text{Tr}}{\displaystyle \underset{n=1}{\overset{N}{}}\mathrm{d}𝐮_n\mathrm{exp}(_\mathrm{t})}`$ (26)   
$`_\mathrm{t}`$ $`=`$ $`𝐭{\displaystyle \underset{n=1}{\overset{N}{}}}𝐮_n,`$ (27)   
where $``$ has been defined in Eq. (2), and $`𝐭`$ is the exerted tension (in units of $`k_\mathrm{B}T`$ divided by monomer length).

As in Sec. II, we begin with the previously studied problem of a bare semiflexible chain, yet it is now a chain under tension . The additional tension term has not changed the Gaussian form of the polymer part of $`Z`$. It can be calculated, therefore, in a similar way to that of Sec. II, yielding

$$Z_{\mathrm{pt}}^{1/N}=Z_\mathrm{p}^{1/N}\mathrm{exp}(t^2/4\lambda ),$$
(28)   
where $`Z_\mathrm{p}`$ is the tensionless polymer partition function given in Eq. (4). The equation for the multiplier $`\lambda `$ is, in this case,

$$\frac{1}{2}\left(\frac{3}{l_\mathrm{p}\lambda }\right)^{1/2}+\frac{t^2}{4\lambda }=1,$$
(29)   
which reduces to Eq. (5) for $`t=0`$. The resulting polymer free energy is

$$f_{\mathrm{pt}}=\frac{3}{2}\mathrm{log}l_\mathrm{p}+\left(\frac{3\lambda }{l_\mathrm{p}}\right)^{1/2}\frac{t^2}{4\lambda }\lambda ,$$
(30)   
where $`\lambda =\lambda (l_\mathrm{p},t)`$ is the solution to Eq. (29).

For $`l_\mathrm{p}t1`$, the solution for $`\lambda `$ is

$`\lambda {\displaystyle \frac{3}{4l_\mathrm{p}}}\left[1+{\displaystyle \frac{8}{9}}(l_\mathrm{p}t)^2+𝒪(l_\mathrm{p}t)^4\right],`$

and the free energy becomes

$$f_{\mathrm{pt}}f_\mathrm{p}\frac{l_\mathrm{p}}{3}t^2+𝒪(l_\mathrm{p}^3t^4),t1/l_\mathrm{p},$$
(31)   
where $`f_\mathrm{p}`$ is the tensionless free energy given in Eq. (6). This is the elastic regime, where the energy is quadratic (i.e., the relative chain extension is linear) in tension . Since we assume a large persistence length, this regime corresponds to very weak tension, $`t1/l_\mathrm{p}1`$. In the opposite limit, $`l_\mathrm{p}t1`$, the solution to Eq. (29) becomes

$`\lambda {\displaystyle \frac{t}{2}}\left[1+{\displaystyle \frac{1}{2}}\left({\displaystyle \frac{3}{2l_\mathrm{p}t}}\right)^{1/2}+𝒪(l_\mathrm{p}t)^1\right],`$

and the corresponding free energy is

$$f_{\mathrm{pt}}\frac{3}{2}\mathrm{log}l_\mathrm{p}t+\left(\frac{3t}{2l_\mathrm{p}}\right)^{1/2}+𝒪(l_\mathrm{p}^1t^0),t1/l_\mathrm{p}.$$
(32)   
In this regime the chain extension changes like the inverse square root of tension .

Let us turn now to the effect of tension on the system of polymer and bound molecules, Eq. (27). As in Sec. IV, we employ the mean-field approximation, valid for $`l_\mathrm{p}\mathrm{}`$. The resulting free energy is the same as Eq. (21), but with $`f_{\mathrm{pt}}`$ instead of $`f_\mathrm{p}`$,

$$f=f_{\mathrm{pt}}|_{l_\mathrm{p}l_\mathrm{p}(1+ϵ\phi )}+\phi \mathrm{log}\phi +(1\phi )\mathrm{log}(1\phi )\mu \phi .$$
(33)   
Due to the additional degree of freedom, namely tension, the binding phase diagrams of Fig. 3 become three-dimensional. In particular, the critical points $`ϵ_\mathrm{c}^\pm `$ become critical lines, $`ϵ_\mathrm{c}^\pm (t)`$. (Note that $`𝐭`$ is an external field coupled to $`\{𝐮_n\}`$ rather than $`\{\phi _n\}`$, and, hence, it does not destroy the critical behavior.) The ‘condensation’ of bound molecules in our model results from attraction induced by polymer fluctuations. By suppressing fluctuations, the tension should weaken the attraction and shift the critical coupling to higher values, i.e., increase the positive critical point, $`ϵ_\mathrm{c}^+`$, and decrease the negative one, $`ϵ_\mathrm{c}^{}`$. Using Eqs. (29), (30) and (33), the critical lines, $`ϵ_\mathrm{c}^\pm (t)`$, can be calculated. The results are shown in Fig. 4.

Before getting into the detailed effect of tension, we address the question whether the critical behavior can survive any strength of tension. In this respect there is an essential difference between stiffness-strengthening binding ($`ϵ>0`$) and stiffness-weakening one ($`ϵ<0`$). In the former case, since the value of $`ϵ`$ is unbound, there exists $`ϵ_\mathrm{c}^+(t)`$ for any value of $`t`$, such that the binding is a sharp transition for $`ϵ>ϵ_\mathrm{c}^+(t)`$. In other words, the critical line $`ϵ_\mathrm{c}^+(t)`$ exists for any $`0t<\mathrm{}`$. Indeed, substituting $`ϵ\mathrm{}`$ in Eq. (33) while using Eq. (32), we find that the free energy always describes a sharp transition, regardless of the value of $`t`$. On the other hand, in the latter case of stiffness-weakening binding, there is a lower bound for $`ϵ`$, $`ϵ>1`$, where the validity of the entire approach breaks (see previous section). Substituting $`ϵ=1`$ in Eqs. (33) and (32), we find that a critical point exists only for $`t<t^{}`$, where

$$\frac{t^{}}{l_\mathrm{p}}=\frac{4}{9}\left(337\sqrt{21}\right)0.410.$$
(34)   
Thus, the critical line $`ϵ_\mathrm{c}^{}(t)`$ terminates at the point $`(t^{},ϵ_\mathrm{c}^{}=1)`$, beyond which a sharp binding transition cannot be attained. This situation is similar to a case where the critical temperature $`T_\mathrm{c}`$ coincides with $`T=0`$ (e.g., in a one-dimensional Ising model), and the system is disordered at all temperatures $`T>0`$.

Several regimes are found as function of tension. For very weak tension, $`t<1/l_\mathrm{p}`$, the leading-order term which couples binding and tension is found from Eqs. (31) and (33) to scale like $`l_\mathrm{p}t^2ϵ\phi `$, i.e., it is only linear in $`\phi `$. Hence, to leading order in $`l_\mathrm{p}t`$ there is no effect on the critical point. Although the tension influences chain fluctuations (e.g., causing the chain to extend linearly with $`t`$), it is too weak to affect the fluctuation-induced interactions between bound molecules. The next-order term scales like $`l_\mathrm{p}^3t^4(1+ϵ\phi )^3`$, leading to a very small shift of $`l_\mathrm{p}^3t^4`$ in the critical point (see also Fig. 4).

For $`t>1/l_\mathrm{p}`$, the leading-order term in the free energy, according to Eqs. (32) and (33), is $`(t/l_\mathrm{p})^{1/2}(1+ϵ\phi )^{1/2}`$. Here two regimes should be distinguished. For intermediate tension, $`1/l_\mathrm{p}<t<l_\mathrm{p}`$, the critical line scales like $`(t/l_\mathrm{p})^{1/2}`$, reflecting a more significant, yet still weak effect of tension. Although the chain conformation is significantly stretched by tension in this regime, the induced interaction between bound molecules is not strongly affected. However, for $`t>l_\mathrm{p}`$, the tension term in the free energy \[$`(t/l_\mathrm{p})^{1/2}(1+ϵ\phi )^{1/2}`$\] becomes dominant, leading to a linear dependence of the critical point on tension, $`ϵ_\mathrm{c}^+t/l_\mathrm{p}`$.

The above analysis for the dependence of the critical coupling on tension is summarized in the following expression:

$$|ϵ_\mathrm{c}^\pm (t)ϵ_\mathrm{c}^\pm (0)|\{\begin{array}{cc}l_\mathrm{p}^3t^4\hfill & t<1/l_\mathrm{p}\hfill \\ & \\ (l_\mathrm{p}/t)^{1/2}\hfill & 1/l_\mathrm{p}<t<l_\mathrm{p}\hfill \\ & \\ l_\mathrm{p}/t\hfill & t>l_\mathrm{p},\text{relevant only to }ϵ_\mathrm{c}^+.\hfill \end{array}$$
(35)   
The various regimes are also clearly seen in Fig. 4. Note that for the large values of $`l_\mathrm{p}`$ considered in this theory the intermediate tension region, $`1/l_\mathrm{p}<t<l_\mathrm{p}`$, is very wide.

## VI Discussion and Conclusions

We have considered binding of small molecules to isolated semiflexible polymer chains, where the persistence length $`l_\mathrm{p}`$ is much larger than the monomer size but still smaller than the total chain length $`N`$. We have demonstrated that in such systems polymer fluctuations induce attraction between bound molecules. The long range of this interaction (of the same order as the persistence length) can lead to strong effects on the binding process. In particular, if bound molecules significantly affect local features of the chain, e.g., weaken or strengthen the stiffness by a factor of about 5 ($`ϵ<ϵ_\mathrm{c}^{}`$ or $`ϵ>ϵ_\mathrm{c}^+`$), then the binding is predicted to be extremely cooperative, occurring as a transition for a sharply defined solute concentration. This is an unusual, yet practical example for a one-dimensional system exhibiting a sharp transition due to long-range interactions. The results of the model should apply, in particular, to the association of DNA with smaller molecules such as surfactants and compact proteins.

Subjecting the polymer to external tension has been studied as well. By suppressing the fluctuation-induced interaction, the applied tension may strongly affect the binding. The effect is significant for sufficiently strong tension of order $`tl_\mathrm{p}`$. \[For DNA this implies $`t10^2k_\mathrm{B}T/(10\text{Å})10^2`$ pN.\] In cases where binding weakens the chain stiffness, such a high tension should make the sharp binding transition disappear altogether (i.e., regardless of the strength of coupling or temperature). In cases where binding strengthens the chain stiffness, a tension of $`tl_\mathrm{p}`$ significantly shifts $`ϵ_\mathrm{c}^+`$ to higher values. It is worth mentioning that tension-induced pairwise interaction between specifically bound proteins on a DNA chain was studied in a previous work .

The interaction of DNA with oppositely charged cationic surfactants has been thoroughly studied by potentiometric techniques  and fluorescence microscopy . Isotherms measured by potentiometry reveal a very cooperative, albeit continuous binding. Fluorescence microscopy convincingly demonstrated, however, that the binding to a single DNA molecule has a discrete nature resembling a 1st-order phase transition. It is usually accompanied by a coil-to-globule collapse of the DNA chain (which lies outside the scope of the current theory). The smoothness of potentiometric isotherms was shown to arise from averaging over an ensemble of DNA molecules, coexisting in bound and unbound states . Similar results were obtained for the association of DNA with spermidine . The microscopic origin of the observed cooperativity (or even discontinuous transition) has not been clarified. It is usually fitted to a phenomenological parameter describing strong interaction between nearest-neighboring bound molecules . On the other hand, it is reasonable to expect that oppositely charged surfactants bound to DNA chains significantly modify the chain stiffness (probably weakening it). Thus, our model demonstrates that the strong cooperativity observed in experiments can be well accounted for by weak, yet long-range interactions induced by polymer fluctuations.

Recently, the kinetics of non-specific binding of RecA proteins to DNA has been studied by single-molecule manipulation . RecA is a bacterial protein involved in DNA recombination and known to cause significant changes in the local structure of the double strand upon binding . It was found to increase the DNA stiffness by a large factor, estimated around 10 in one study  and above 4 in another . This corresponds to a large, positive $`ϵ`$ in our model. A very cooperative nucleation-and-growth kinetics was observed, as expected from the current model. Moreover, in certain situations it was possible to achieve a smaller increase of stiffness by binding of RecA. This led, correspondingly, to a less cooperative process . Yet probably the most compelling evidence is that the binding cooperativity was shown to be sensitive to external tension of order 10–100 pN. It was consequently deduced that DNA conformational fluctuations play a key role in RecA binding , in accord with the model.

The current work is restricted to one-dimensional interactions along the chain sequence, assuming that the polymer is locally stiff and obeys the worm-like-chain description. Apart from changing local properties of the polymer, an important feature not treated by the model is that bound molecules may also modify volume interactions between the monomers, thus affecting the three-dimensional conformation of the polymer. For example, binding of oppositely charged surfactants to a DNA molecule locally neutralizes the DNA charge. This should lead, indeed, to a modified stiffness, but also to a reduced 2nd virial coefficient, which may drive a coil-to-globule collapse . The collapse can be also driven by fluctuations in the concentration of ions adjacent to the chain, as has been demonstrated by recent theoretical studies .

In order to check the theory presented in this work more experiments are required, focusing, in particular, on the effect of persistence length and tension on binding. The fluorescence microscopy techniques, which have been successfully used for DNA–surfactant association, may be applied to chains under tension or flow, thus examining the role of fluctuations. It would be interesting to study a system consisting of a semiflexible polymer and bound molecules in computer simulations, and thereby check the applicability of our mean-field approximation. An important extension of the model, as mentioned above, would be to introduce volume interactions and obtain binding-induced collapse as observed in experiments.

###### Acknowledgements.

We greatly benefited from discussions and correspondence with R. Bar-Ziv, M. Feingold, A. Libchaber, R. Netz, A. Parsegian, R. Podgornik, M. Schwartz and V. Sergeyev. Partial support from the Israel Science Foundation founded by the Israel Academy of Sciences and Humanities — Centers of Excellence Program, and the Israel–US Binational Science Foundation (BSF) under grant No. 98-00429, is gratefully acknowledged. HD would like to thank the Clore Foundation for financial support.    

## Numerical Details

The aim of the numerical scheme is to calculate the results of the Kac-Baker model for finite $`l_\mathrm{p}`$, which are presented in Fig. 1. Using Kac’s solution , the partition function of bound solute molecules, Eqs. (13)-(15), is expressed in the limit $`N\mathrm{}`$ as

$$Z_\mathrm{s}=\text{const}\times e_0^N,$$
(36)   
where $`e_0`$ is the largest eigenvalue of the following ‘transfer kernel’:

$$K(x,y)=[(1+\mathrm{e}^{\mu 3ϵ/2+\sqrt{J}x})(1+\mathrm{e}^{\mu 3ϵ/2+\sqrt{J}y})]^{1/2}\mathrm{exp}\left[\frac{y^2x^2}{4}\frac{(y\mathrm{e}^{2/l_\mathrm{p}}x)^2}{2(1\mathrm{e}^{4/l_\mathrm{p}})}\right],$$
(37)   
where $`J3ϵ^2/2l_\mathrm{p}`$, and $`x,y(\mathrm{},\mathrm{})`$ are real variables.

We define a vector, $`\{x_i\}=\{(2iM)d\}_{i=0\mathrm{}M}`$, where $`M`$ is an even integer and $`d`$ a real number, and use it to discretize the kernel $`K(x,y)`$ into a transfer matrix,

$$K_{ij}K(x_i,x_j).$$
(38)   
In addition, we define the diagonal matrix

$$A_{ij}x_i\delta _{ij}.$$
(39)   
Given $`l_\mathrm{p}`$, $`ϵ`$ and $`\mu `$, the transfer matrix $`K_{ij}`$ is diagonalized and its largest eigenvalue, $`e_0`$, is found.

The binding degree, $`\phi `$, can be calculated in two ways. The first is by calculating the variation of $`\mathrm{log}e_0`$ with respect to $`\mu `$,

$$\phi =\mathrm{log}e_0/\mu .$$
(40)   
The second way is by using the equation

$$\phi =\stackrel{~}{A}_{00}/(B\sqrt{J}),$$
(41)   
where $`B\mathrm{coth}(1/l_\mathrm{p})`$, and $`\stackrel{~}{A}`$ is the matrix $`A`$ transformed to the basis where $`K`$ is diagonal .

The cooperativity parameter, $`C`$, as defined in Eq. (17), is found by calculating the variation of $`\phi `$ with respect to $`\mu `$ around the point $`\phi =1/2`$. The value $`\mu =\mu _{1/2}`$ which gives $`\phi =1/2`$ is analytically found by transforming the lattice-gas partition function, Eqs. (13)-(15), into an Ising one ($`\phi _ns_n=2\phi _n1`$), and requiring that the ‘magnetic field’ coefficient should vanish. The result is

$$\mu _{1/2}=3ϵ/2JB/2.$$
(42)   
For each calculation (i.e., for each set of $`l_\mathrm{p}`$, $`ϵ`$ and $`\mu `$) the discretization parameters, $`M`$ and $`d`$, were tuned until the result became insensitive to further refinement to six significant figures. In addition, the two methods for calculating $`\phi `$ were used and verified to yield identical results to six figures. All algebraic manipulations were performed using Mathematica.