Analytical and Bioanalytical Chemistry, volume 411, issue 25, pages 6723-6732
Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation
Tomilin Felix N.
1, 2
,
Moryachkov Roman
1, 3
,
Shchugoreva Irina
2, 3
,
Zabluda Vladimir N
1
,
Peters Georgy
4
,
Platunov Mikhail
1
,
Spiridonova Vera
5
,
Melnichuk Anastasia
5
,
Atrokhova Anastasia
5
,
Zamay Sergey S
1, 3
,
Ovchinnikov Sergey G.
1, 2
,
Zamay Galina S
3, 6
,
Sokolov Alexey
1, 2
,
Zamay Tatiana N.
3, 6
,
Berezovski Maxim V.
7
,
Kichkailo Anna S.
3, 6
7
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
|
Publication type: Journal Article
Publication date: 2019-08-08
Quartile SCImago
Q2
Quartile WOS
Q1
Impact factor: 4.3
ISSN: 16182642, 16182650
Biochemistry
Analytical Chemistry
Abstract
Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule’s electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids.
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- We do not take into account publications that without a DOI.
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- Statistics recalculated weekly.
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Tomilin F. N. et al. Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation // Analytical and Bioanalytical Chemistry. 2019. Vol. 411. No. 25. pp. 6723-6732.
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Tomilin F. N., Moryachkov R., Shchugoreva I., Zabluda V. N., Peters G., Platunov M., Spiridonova V., Melnichuk A., Atrokhova A., Zamay S. S., Ovchinnikov S. G., Zamay G. S., Sokolov A., Zamay T. N., Berezovski M. V., Kichkailo A. S. Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation // Analytical and Bioanalytical Chemistry. 2019. Vol. 411. No. 25. pp. 6723-6732.
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TY - JOUR
DO - 10.1007/s00216-019-02045-0
UR - https://doi.org/10.1007%2Fs00216-019-02045-0
TI - Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation
T2 - Analytical and Bioanalytical Chemistry
AU - Zabluda, Vladimir N
AU - Peters, Georgy
AU - Spiridonova, Vera
AU - Melnichuk, Anastasia
AU - Atrokhova, Anastasia
AU - Zamay, Galina S
AU - Moryachkov, Roman
AU - Shchugoreva, Irina
AU - Zamay, Sergey S
AU - Zamay, Tatiana N.
AU - Berezovski, Maxim V.
AU - Kichkailo, Anna S.
AU - Ovchinnikov, Sergey G.
AU - Tomilin, Felix N.
AU - Platunov, Mikhail
AU - Sokolov, Alexey
PY - 2019
DA - 2019/08/08 00:00:00
PB - Springer Nature
SP - 6723-6732
IS - 25
VL - 411
SN - 1618-2642
SN - 1618-2650
ER -
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@article{2019_Tomilin,
author = {Vladimir N Zabluda and Georgy Peters and Vera Spiridonova and Anastasia Melnichuk and Anastasia Atrokhova and Galina S Zamay and Roman Moryachkov and Irina Shchugoreva and Sergey S Zamay and Tatiana N. Zamay and Maxim V. Berezovski and Anna S. Kichkailo and Sergey G. Ovchinnikov and Felix N. Tomilin and Mikhail Platunov and Alexey Sokolov},
title = {Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation},
journal = {Analytical and Bioanalytical Chemistry},
year = {2019},
volume = {411},
publisher = {Springer Nature},
month = {aug},
url = {https://doi.org/10.1007%2Fs00216-019-02045-0},
number = {25},
pages = {6723--6732},
doi = {10.1007/s00216-019-02045-0}
}
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Tomilin, Felix N., et al. “Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation.” Analytical and Bioanalytical Chemistry, vol. 411, no. 25, Aug. 2019, pp. 6723-6732. https://doi.org/10.1007%2Fs00216-019-02045-0.