1kbd

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SOLUTION STRUCTURE OF A 16 BASE-PAIR DNA RELATED TO THE HIV-1 KAPPA B SITE

Overview

1H and 31P NMR spectroscopy have been used together with molecular, modelling to determine the fine structure of a non-palindromic 16 bp DNA, containing the NF-kappa B binding site. Much emphasis has been placed upon, NMR optimization of both two-dimensional 31P NMR techniques to extract, structural information defining the phosphodiester backbone conformation, and selective homonuclear 2D COSY experiments to determine sugar, conformations. NMR data show evidence for a dynamic behaviour of steps, flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII, equilibrium at these steps is demonstrated and two models for each extreme, conformation are proposed in agreement with NMR data. In the refined BII, structures, the NF-kappa B binding site exhibits an intrinsic curvature, towards the major groove that is magnified by the four flanking steps in, the BII conformation. Furthermore, the base-pairs are translated into the, major groove. Thus, we present a novel mode of dynamic intrinsic curvature, compatible with the DNA curvature observed in the X-ray structure of the, p50-DNA complex.

About this Structure

1KBD is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex., Tisne C, Hantz E, Hartmann B, Delepierre M, J Mol Biol. 1998 May 29;279(1):127-42. PMID:9636705

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