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Estimation of strength in different extra Watson–Crick hydrogen bonds in DNA double helices through quantum chemical studies
Author(s) -
Bandyopadhyay D.,
Bhattacharyya D.
Publication year - 2006
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20542
Subject(s) - molecular structure of nucleic acids: a structure for deoxyribose nucleic acid , chemistry , hydrogen bond , base pair , preprint , crystallography , ab initio , molecule , bent molecular geometry , computational chemistry , dna , thermodynamics , chemical physics , quantum mechanics , physics , organic chemistry , biochemistry
Abstract It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross‐strand bifurcated or Extra Watson–Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6‐31G(2d,2p) and B3LYP/6‐31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N—H···O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4–9 kcal/mol). The N—H···N and C—H···O type interactions, however, are not so stabilizing. Hence, consideration of EWC N—H···O H‐bonds can lead to a better understanding of DNA sequence directed structural features. © 2006 Wiley Periodicals, Inc. Biopolymers 83:313–325, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com