1k8n

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NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24

Overview

A variety of monothio- and dithiosubstituted duplex aptamers targeting, NF-kappaB have been synthesized and designed. The specificity and affinity, of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was, determined by gel shift experiments. The NMR solution structures for, several unmodified and dithioate backbone modified 14-base paired duplex, aptamers have been determined by a hybrid, complete matrix, (MORASS)/restrained molecular dynamics method. Structural perturbations of, the dithioate substitutions support our hypothesis that the dithioate, binds cations less tightly than phosphoryl groups. This increases the, electrostatic repulsion across the B-form narrow minor groove and enlarges, the minor groove, similar to that found in A-form duplexes. Structural, analysis of modeled aptamer complexes with NF-kappaB homo- and, heterodimers suggests that the dithioate backbone substitution can, increase the aptamer's relative affinity to basic groups in proteins such, as NF-kappaB by helping to "strip" the cations from the aptamer backbone.

About this Structure

1K8N is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB., Volk DE, Yang X, Fennewald SM, King DJ, Bassett SE, Venkitachalam S, Herzog N, Luxon BA, Gorenstein DG, Bioorg Chem. 2002 Dec;30(6):396-419. PMID:12642125

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