1db6

From Proteopedia

---

Revision as of 00:47, 25 November 2007

proteopedia linkproteopedia link

spinqualitylabelsall models 1db6 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

Overview

The structure of a DNA aptamer, which was selected for specific binding to, arginine, was determined using NMR spectroscopy. The sequence forms a, hairpin loop, with residues important for binding occurring in the loop, region. Binding of argininamide induces formation of one Watson-Crick and, two non-Watson-Crick base pairs, which facilitate generation of a binding, pocket. The specificity for arginine seems to arise from contacts between, the guanidino end of the arginine and phosphates, with atoms positioned by, the shape of the pocket. Complex binding kinetics are observed suggesting, that there is a slow interconversion of two forms of the DNA, which have, different binding affinities. These data provide information on the, process of adaptive recognition of a ligand by an aptamer.

About this Structure

1DB6 is a Protein complex structure of sequences from [1] with AAR as ligand. Full crystallographic information is available from OCA.

Reference

Structure determination and binding kinetics of a DNA aptamer-argininamide complex., Robertson SA, Harada K, Frankel AD, Wemmer DE, Biochemistry. 2000 Feb 8;39(5):946-54. PMID:10653638

Page seeded by OCA on Sun Nov 25 02:54:53 2007