<p>Molecular dynamics study of complexes of a DNA aptamer with AMP and GMP</p>

Ramazanov R.R.; Sokolov P.A.

Issue 6, 2021 Vol. 13

All issues

2024 Vol. 16
- Issue 5
- Issue 4
- Issue 3
- Issue 2
- Issue 1 (special issue)
2023 Vol. 15
- Issue 6
- Issue 5
- Issue 4 (special issue)
- Issue 3
- Issue 2 (special issue)
- Issue 1
2022 Vol. 14
- Issue 6
- Issue 5
- Issue 4 (special issue)
- Issue 3
- Issue 2 (special issue)
- Issue 1
2021 Vol. 13
- Issue 6
- Issue 5
- Issue 4
- Issue 3
- Issue 2 (special issue)
- Issue 1
2020 Vol. 12
- Issue 6
- Issue 5
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2019 Vol. 11
- Issue 6
- Issue 5
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2018 Vol. 10
- Issue 6
- Issue 5 (special issue)
- Issue 4
- Issue 3 (special issue)
- Issue 2
- Issue 1
2017 Vol. 9
- Issue 6
- Issue 5
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2016 Vol. 8
- Issue 6
- Issue 5
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2015 Vol. 7
- Issue 6
- Issue 5
- Issue 4
- Issue 3 (special issue)
- Issue 2
- Issue 1
2014 Vol. 6
- Issue 6 (special issue)
- Issue 5
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2013 Vol. 5
- Issue 6 (special issue)
- Issue 5
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2012 Vol. 4
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2011 Vol. 3
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2010 Vol. 2
- Issue 4
- Issue 3
- Issue 2
- Issue 1
2009 Vol. 1
- Issue 4
- Issue 3
- Issue 2
- Issue 1

Molecular dynamics study of complexes of a DNA aptamer with AMP and GMP

Ramazanov R.R., Sokolov P.A.

pdf (4787K)

This study is devoted to a comparative study of the conformational stability of the DNA aptamer to adenosine derivatives in a free state and in a complex with AMP and HMP molecules by use of molecular dynamics. It was shown that, in the free state, the structure of the inner loop of the DNA aptamer hairpin, due to the special packing of guanines, closes the cavity of the binding site from external ligands, and the condition for the specific selection of adenosine derivatives in comparison with guanine arises. New stabilization factors of the AMP and aptamer complex have been revealed — hydrogen bonds between the O3’ of the ribose atom of the ligands with the oxygen of the nearest phosphate group. It was also shown that guanines, which form hydrogen bonds with AMP within the binding site, are additionally stabilized by hydrogen bonds with phosphate groups opposing along the chain. The proposed scheme is in qualitative agreement with the experimental data, according to which the aptamer in solution acquires a hairpin conformation with the formation of a binding site, while the formed site exhibits high specificity when interacting only with adenosine derivatives.

Keywords: мolecular dynamics, DNA aptamer, AMP, мolecular recognition

Citation in English: Ramazanov R.R., Sokolov P.A. Molecular dynamics study of complexes of a DNA aptamer with AMP and GMP // Computer Research and Modeling, 2021, vol. 13, no. 6, pp. 1191-1203

DOI: 10.20537/2076-7633-2021-13-6-1191-1203

URL: http://crm-en.ics.org.ru/journal/article/3151/

Computer Research and Modeling - 2021 - Issue 6

This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.

Indexed in Scopus

Full-text version of the journal is also available on the web site of the scientific electronic library eLIBRARY.RU

The journal is included in the Russian Science Citation Index

The journal is included in the RSCI

International Interdisciplinary Conference "Mathematics. Computing. Education"