1DB6

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

1DB6 の概要

• エントリーDOI: 10.2210/pdb1db6/pdb
• 関連するPDBエントリー: 1OLD 2ARG
• 分子名称: DNA, ARGININEAMIDE (2 entities in total)
• 機能のキーワード: aptamer, arginine, argininamide, single-strand, hairpin, selex, dna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 6903.55

構造登録者

Robertson, S.A.,Harada, K.,Frankel, A.D.,Wemmer, D.E. (登録日: 1999-11-02, 公開日: 2000-02-03, 最終更新日: 2024-05-22)

主引用文献

Robertson, S.A.,Harada, K.,Frankel, A.D.,Wemmer, D.E.
Structure determination and binding kinetics of a DNA aptamer-argininamide complex.
Biochemistry, 39:946-954, 2000

PubMed Abstract: 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.

PubMed: 10653638
DOI: 10.1021/bi9915061

実験手法

SOLUTION NMR