Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer

Nucleic acid aptamers are artificial recognizing molecules that capable of specific binding to a wide variety targets. Aptamers commonly selected from huge library oligonucleotides and improved by introducing several mutations or modular constructions. Although hold great promise as therapeutic diagnostic tools, no simple approach improve their affinity has been suggested yet. Our recent analysis aptamer–protein complexes revealed aptamer correlates with the size an amino sidechain in protein interface was explained efficient dissipation energy released during complex formation. G-quadruplex-based thrombin not involved described dependence. Moreover, same site have 100-fold differences affinity. Here we focused on detailed nucleic thrombin–aptamer complexes. High shown correlate solvent accessibility apolar part loops. To prove concept experimentally, these loops were modified enhance contact solvent. Dissociation rates aptamer–thrombin drastically slowed due modifications. In full correspondence hypothesis, modifications both stability G-quadruplexes thrombin. The most evident effect for unstable Na+-coordinated G-quadruplexes. These data high interest directed improvement unnatural into ‘hot spot’ residues.