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C-H..O Hydrogen Bonds in Minor Groove of A-tracts in DNA Double Helices

Ghosh, Anirban and Bansal, Manju (1999) C-H..O Hydrogen Bonds in Minor Groove of A-tracts in DNA Double Helices. In: Journal of Molecular Biology, 294 (5). pp. 1149-1158.

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Analysis of available B-DNA type oligomeric crystal structures as well as protein-bound DNA fragments (solved using data with resolution <2.6 \AA) indicates that in both data sets, a majority of the (3′-Ade) H2..O2(3′-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance. Since the electropositive C2-H2 group of adenine is in close proximity of the electronegative keto oxygen atoms of both pyrimidine bases in the antiparallel strand of the double-helical DNA structures, it suggests the possibility of intra-base-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within the A.T base-pairs could be a natural consequence of Watson-Crick pairing. However, the close cross-strand interactions between the bases at the 3′-ends of the AA.TT and GA.TC steps arise due to the local sequence-dependent geometry of these steps. While the base-pair propeller twist in these steps is comparable to the fibre model, some of the other local parameters such as base-pair opening angle and inter-base-pair slide show coordinated changes, leading to these shorter C2-H2..O2 distances. Hence, in addition to the well-known minor groove hydration, it appears that favourable C2-H2..O2 cross-strand interactions may play a role in imparting a characteristic geometry to AA.TT and GA.TC steps, as well as $A_n. T_n$ and $GA_n. T_nC$ tracts, which leads to a narrow minor groove in these regions.

Item Type: Journal Article
Publication: Journal of Molecular Biology
Publisher: Academic Press
Additional Information: Copyright of this article belongs to Academic Press.
Keywords: C-H..O hydrogen bonds;C-H..N hydrogen bonds;Cross-strand hydrogen bonds;DNA minor groove;A-tract structure
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 01 Oct 2007
Last Modified: 19 Sep 2010 04:39
URI: http://eprints.iisc.ac.in/id/eprint/11990

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