Issue 33, 2010
From the journal:

Physical Chemistry Chemical Physics

New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics†

Al'ona Furmanchuk,a   Oleg V. Shishkin,b   Olexandr Isayev,c   Leonid Gorbad  and  Jerzy Leszczynski*a  

* Corresponding authors

a Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi 39217, USA
E-mail: jerzy@icnanotox.org

b STC “Institute for Single Crystals”, National Academy of Sciences of Ukraine, 60 Lenina Avenue, Kharkiv 61001, Ukraine

c Department of Chemistry, Case Western Reserve University, Cleveland, USA

d Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, 150 Zabolotnogo Street, Kyiv 03143, Ukraine

Abstract

The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car–Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface.

Graphical abstract: New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics

About
Cited by
Related
Download options Please wait...

Supplementary files

Article information

DOI
https://doi.org/10.1039/C002934C
Article type
Paper
Submitted
11 Feb 2010
Accepted
06 May 2010
First published
08 Jun 2010

Phys. Chem. Chem. Phys., 2010,12, 9945-9954

Permissions

Request permissions

New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics

A. Furmanchuk, O. V. Shishkin, O. Isayev, L. Gorb and J. Leszczynski, Phys. Chem. Chem. Phys., 2010, 12, 9945 DOI: 10.1039/C002934C

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements