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Programming Biomimetically Confined Aptamers with DNA Frameworks.

Active sites of proteins are generally encapsulated within three-dimensional peptide scaffolds that provide the molecular-scale confinement microenvironment. Nevertheless, the ability to tune thermodynamic stability in biomimetic molecular confinement relies on the macromolecular crowing effect lack of stoichiometry and reconfigurability. Here, we report a framework nucleic acids (FNA)-based strategy to increase thermodynamic stability of aptamers. We demonstrate that the molecular-scale confinement increases the thermodynamic stability of aptamer via facilitated folding kinetic, which is confirmed by the single-molecule FRET (smFRET). Unfavorable conformations of aptamers are restricted as revealed by the Monte-Carlo simulation. The binding affinity of the DNA framework-confined aptamer is improved by ~3-fold. With a similar strategy we improve the catalytic activity of hemin-binding aptamer. Our approach thus shows high potential for designing protein-mimicking DNA nanostructures with enhanced binding affinity and catalytic activity for biosensing and biomedical engineering.