2O4Y

Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide

2O4Y の概要

• エントリーDOI: 10.2210/pdb2o4y/pdb
• 分子名称: DNA (5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*G)-3'), DNA (5'-D(*CP*GP*TP*TP*GP*TP*AP*C)-3') (2 entities in total)
• 機能のキーワード: dna universal base nitroindole intercalation dynamics, dna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 4923.28

構造登録者

Gallego, J.,Loakes, D. (登録日: 2006-12-05, 公開日: 2007-04-24, 最終更新日: 2023-12-27)

主引用文献

Gallego, J.,Loakes, D.
Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide.
Nucleic Acids Res., 35:2904-2912, 2007

PubMed Abstract: Universal bases hybridize with all other natural DNA or RNA bases, and have applications in PCR and sequencing. We have analysed by nuclear magnetic resonance spectroscopy the structure and dynamics of three DNA oligonucleotides containing the universal base analogues 5-nitroindole and 5-nitroindole-3-carboxamide. In all systems studied, both the 5-nitroindole nucleotide and the opposing nucleotide adopt a standard anti conformation and are fully stacked within the DNA duplex. The 5-nitroindole bases do not base pair with the nucleotide opposite them, but intercalate between this base and an adjacent Watson-Crick pair. In spite of their smooth accommodation within the DNA double-helix, the 5-nitroindole-containing duplexes exist as a dynamic mixture of two different stacking configurations exchanging fast on the chemical shift timescale. These configurations depend on the relative intercalating positions of the universal base and the opposing base, and their exchange implies nucleotide opening motions on the millisecond time range. The structure of these nitroindole-containing duplexes explains the mechanism by which these artificial moieties behave as universal bases.

PubMed: 17438041
DOI: 10.1093/nar/gkm074

実験手法

SOLUTION NMR