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Groove width and depth of B-DNA structures depend on local variation in slide

Bhattacharyya, Dhananjay and Bansal, Manju (1992) Groove width and depth of B-DNA structures depend on local variation in slide. In: Journal of Biomolecular Structure & Dynamics, 10 (1). pp. 213-226.

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The groove widths of DNA helix, esp. minor groove width, are generally believed to be important for recognition of DNA by various types of ligands. It has been postulated earlier that large neg. propeller twist in the AT rich regions compresses the minor groove of duplex DNA. A systematic study has now been carried out by generating models with different values of local doublet and intra-base-pair parameters and calcg. their minor groove widths. It is found that several local doublet parameters affect the minor groove width but it depends most strongly on the local step parameters roll and slide when each parameter is considered individually. However, a detailed anal. of the various local parameters within the B-DNA family of crystal structures indicates that propeller twist and slide are most strongly correlated with the obsd. values of minor groove width. The groove depth is also strongly correlated with slide. Thus the local base sequence-dependent variations in slide can modify both the groove width and depth and consequently det. the ligand binding properties of DNA.

Item Type: Journal Article
Publication: Journal of Biomolecular Structure & Dynamics
Publisher: Adeninepress
Additional Information: Copyright of this article belongs to Adeninepress
Keywords: B-DNA;duplex DNA
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 25 Feb 2008
Last Modified: 27 Aug 2008 13:08
URI: http://eprints.iisc.ac.in/id/eprint/12803

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