Issue April 2009

category image Volume 26
No. 5 (p 525-662)
April 2009
ISSN 0739-110

Dependence of Deformability of Geometries and Characteristics of Intramolecular Hydrogen Bonds in Canonical 2?-Deoxyribonucleotides on DNA Conformations (p. 653-661)

The molecular structure and deformability (with respect to average geometry) of methyl ethers of canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (mTMP), 2-deoxycytidine-5'-phosphate (mCMP), 2-deoxyadenosine-5'-phosphate (mAMP) and 2'-deoxyguanosine-5'-phosphate (mGMP) in different types of DNA have been calculated using B3LYP/cc-pvdz method. Comparison of energy at equilibrium conformations of nucleotides and conformations with torsion angles of backbone fixed to average values for different types of DNA reveals that incorporation of nucleotides to A-DNA macromolecules requires the minimum amount of deformation energy. Therefore, this type of DNA should be the least strained from viewpoint of intramolecular deformations of monomers. Modeling of environmental effects within the PCM approach reveals that the immersion of nucleotides in polar medium results in significant decrease of energy differences between anti conformers of all DNTs and syn conformers of mGMP. This also leads to reduction by almost a half nucleotides? deformation energy facilitating formation of DNA macromolecule. Change of DNTs conformation causes switch between different types of intramolecular H bonds. Every type of DNA possesses unique set of intramolecular hydrogen bonds in nucleotides.

Gennady V. Palamarchuk1,2
Oleg V. Shishkin1,2,3,*
Leonid Gorb2,3,4
Jerzy Leszczynski2,3

1SSI ?Institute for Single Crystals?
National Academy of Science of Ukraine
60 Lenina Ave.
Kharkiv 61001, Ukraine
2Ukrainian-American Laboratory of Computational Chemistry
Kharkiv, Ukraine
and Jackson, Mississippi
3Computational Center for Molecular Structure and Interactions
Jackson State University
4Department of Molecular Biophysics
Institute of Molecular Biology and Genetics
National Academy of Science of Ukraine
150 Zabolotnogo str.
Kyiv 03143, Ukraine

*Email: shishkin@xray.isc.kharkov.com

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