Open Access
Molecular Therapy - Nucleic Acids, volume 25, pages 316-327
The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
Morozov Dmitry
1
,
Mironov Vladimir
2
,
Shchugoreva Irina A.
4
,
Artyushenko Polina V.
4
,
Zamay Galina S.
5
,
Kolovskaya Olga S.
5
,
Zamay Tatiana N.
6
,
Krat Alexey V.
6
,
Molodenskiy Dmitry
7
,
Zabluda Vladimir N
8
,
Veprintsev Dmitry B.
6
,
Sokolov Alexey E.
3
,
Zukov Ruslan A.
6
,
Berezovski Maxim V.
9, 10, 11
,
Tomilin Felix N.
4
,
Fedorov D. V.
12
,
Alexeev Yuri
13
,
4
7
European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany.
|
9
10 Marie Curie Ottawa ON K1N 6N5 Canada
|
10
University of Ottawa
11
Department of Chemistry and Biomolecular Sciences
12
Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
|
13
Computational Science Division, Argonne National Laboratory, Lemont, IL, USA.
|
Publication type: Journal Article
Publication date: 2021-09-01
Journal:
Molecular Therapy - Nucleic Acids
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 8.8
ISSN: 21622531
Drug Discovery
Molecular Medicine
Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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1 publication, 7.14%
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1 publication, 7.14%
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Citations by publishers
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3 publications, 21.43%
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2 publications, 14.29%
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1 publication, 7.14%
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Springer Nature
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1 publication, 7.14%
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Wiley
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1 publication, 7.14%
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1
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Morozov D. et al. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer // Molecular Therapy - Nucleic Acids. 2021. Vol. 25. pp. 316-327.
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Morozov D., Mironov V., Moryachkov R. V., Shchugoreva I. A., Artyushenko P. V., Zamay G. S., Kolovskaya O. S., Zamay T. N., Krat A. V., Molodenskiy D., Zabluda V. N., Veprintsev D. B., Sokolov A. E., Zukov R. A., Berezovski M. V., Tomilin F. N., Fedorov D. V., Alexeev Y., Kichkailo A. S. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer // Molecular Therapy - Nucleic Acids. 2021. Vol. 25. pp. 316-327.
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TY - JOUR
DO - 10.1016/j.omtn.2021.07.015
UR - https://doi.org/10.1016%2Fj.omtn.2021.07.015
TI - The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
T2 - Molecular Therapy - Nucleic Acids
AU - Morozov, Dmitry
AU - Mironov, Vladimir
AU - Moryachkov, Roman V
AU - Shchugoreva, Irina A.
AU - Artyushenko, Polina V.
AU - Zamay, Galina S.
AU - Kolovskaya, Olga S.
AU - Zamay, Tatiana N.
AU - Krat, Alexey V.
AU - Molodenskiy, Dmitry
AU - Zabluda, Vladimir N
AU - Veprintsev, Dmitry B.
AU - Sokolov, Alexey E.
AU - Zukov, Ruslan A.
AU - Berezovski, Maxim V.
AU - Tomilin, Felix N.
AU - Fedorov, D. V.
AU - Alexeev, Yuri
AU - Kichkailo, Anna S.
PY - 2021
DA - 2021/09/01 00:00:00
PB - Elsevier
SP - 316-327
VL - 25
SN - 2162-2531
ER -
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@article{2021_Morozov,
author = {Dmitry Morozov and Vladimir Mironov and Roman V Moryachkov and Irina A. Shchugoreva and Polina V. Artyushenko and Galina S. Zamay and Olga S. Kolovskaya and Tatiana N. Zamay and Alexey V. Krat and Dmitry Molodenskiy and Vladimir N Zabluda and Dmitry B. Veprintsev and Alexey E. Sokolov and Ruslan A. Zukov and Maxim V. Berezovski and Felix N. Tomilin and D. V. Fedorov and Yuri Alexeev and Anna S. Kichkailo},
title = {The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer},
journal = {Molecular Therapy - Nucleic Acids},
year = {2021},
volume = {25},
publisher = {Elsevier},
month = {sep},
url = {https://doi.org/10.1016%2Fj.omtn.2021.07.015},
pages = {316--327},
doi = {10.1016/j.omtn.2021.07.015}
}