1AO9

INTRAMOLECULAR DNA DUPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GAGAGA-X-TCTCCT), NMR, 12 STRUCTURES

1AO9 の概要

• エントリーDOI: 10.2210/pdb1ao9/pdb
• 関連するPDBエントリー: 1AT4
• 分子名称: DNA (5'-D(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*C)-3') (1 entity in total)
• 機能のキーワード: dna, intramolecular duplex, deoxyribonucleic acid
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 3966.81

構造登録者

Bartley, J.P. (登録日: 1997-07-22, 公開日: 1998-01-28, 最終更新日: 2024-05-22)

主引用文献

Bartley, J.P.,Brown, T.,Lane, A.N.
Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex.
Biochemistry, 36:14502-14511, 1997

PubMed Abstract: The solution properties of the parallel intramolecular DNA triplex d(GAGAGA-oct-TCTCTC-oct-CTCTCT) (oct = -O-(CH2)8-O-PO2-O-(CH2)8-O-PO2-) and the duplex d(GAGAGA-oct-TCTCTC) have been examined by UV melting and high-resolution nuclear magnetic resonance spectroscopy (NMR). All nucleotides were primarily in the S conformation (i.e. near C2'-endo) in both the duplex and the triplex. However, the sugars of the Hoogsteen pyrimidine strand had a lower fraction of the S state than the Watson-Crick strands. Glycosidic torsion angles derived from nuclear Overhauser effect (NOE) build-up curves were found in the range -103 degrees to -133 degrees, with a clear alternation in magnitude along the GAGAGA strand in the triplex, whereas the glycosidic torsion angles were more similar in the duplex. Internucleotide NOEs were also consistent with an overall B-like geometry, rather than the A family. However, particularly in the Hoogsteen strand, some sequential NOE intensities were intermediate between those of the B and A forms. Distance and torsion constraints derived from NMR experiments were used to generate structures and were refined by restrained molecular dynamics. Extensive chemical shift differences between residues in the triplex and duplex were found for the purine strand, and there were remarkable differences in the pattern of shift differences for the A and G residues that correlated with differences in glycosidic torsion angles. Although there are differences in structure between the free duplex and that in the triplex, they are in important respects similar, indicating that only small conformational adjustments are needed to make parallel triple helices.

PubMed: 9398169
DOI: 10.1021/bi970710q

実験手法

SOLUTION NMR