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

Al’ona Furmanchuk, Oleg V. Shishkin, Olexandr Isayev, Leonid Gorb, Jerzy Leszczynski*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)9945-9954
Number of pages10
JournalPhysical Chemistry Chemical Physics
Volume12
Issue number33
DOIs
StatePublished - 2010

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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