Open Access
Biophysica, volume 1, issue 2, pages 179-193
Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer
Publication type: Journal Article
Publication date: 2021-05-14
General Medicine
Abstract
Nucleic acid aptamers are artificial recognizing molecules that are capable of specific binding to a wide variety of targets. Aptamers are commonly selected from a huge library of oligonucleotides and improved by introducing several mutations or modular constructions. Although aptamers hold great promise as therapeutic and diagnostic tools, no simple approach to improve their affinity has been suggested yet. Our recent analysis of aptamer–protein complexes revealed that aptamer affinity correlates with the size of an amino acid sidechain in the protein interface that was explained by efficient dissipation of the energy released during complex formation. G-quadruplex-based thrombin aptamers are not involved in the described dependence. Moreover, aptamers to the same thrombin site have 100-fold differences in affinity. Here we focused on a detailed analysis of the nucleic acid interface of thrombin–aptamer complexes. High affinity of the aptamers was shown to correlate with the solvent accessibility of the apolar part of recognizing loops. To prove the concept experimentally, these loops were modified to enhance contact with the solvent. Dissociation rates of the aptamer–thrombin complexes were drastically slowed due to these modifications. In full correspondence with the energy dissipation hypothesis, the modifications improved both the stability of the G-quadruplexes and affinity to thrombin. The most evident effect was shown for unstable Na+-coordinated G-quadruplexes. These data are of high interest for a directed improvement of aptamers introducing unnatural modifications into the ‘hot spot’ residues.
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Zhdanov G. A. et al. Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer // Biophysica. 2021. Vol. 1. No. 2. pp. 179-193.
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Zhdanov G. A., Arutyunyuan A., Kopylov A., Zavyalova E. Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer // Biophysica. 2021. Vol. 1. No. 2. pp. 179-193.
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TY - JOUR
DO - 10.3390/biophysica1020014
UR - https://doi.org/10.3390/biophysica1020014
TI - Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer
T2 - Biophysica
AU - Arutyunyuan, Alexander
AU - Zhdanov, Gleb A
AU - Kopylov, Alexey
AU - Zavyalova, Elena
PY - 2021
DA - 2021/05/14 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 179-193
IS - 2
VL - 1
SN - 2673-4125
ER -
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@article{2021_Zhdanov,
author = {Alexander Arutyunyuan and Gleb A Zhdanov and Alexey Kopylov and Elena Zavyalova},
title = {Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer},
journal = {Biophysica},
year = {2021},
volume = {1},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {may},
url = {https://doi.org/10.3390/biophysica1020014},
number = {2},
pages = {179--193},
doi = {10.3390/biophysica1020014}
}
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Zhdanov, Gleb A., et al. “Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer.” Biophysica, vol. 1, no. 2, May. 2021, pp. 179-193. https://doi.org/10.3390/biophysica1020014.