1SY8

Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics

1SY8 の概要

• エントリーDOI: 10.2210/pdb1sy8/pdb
• 関連するPDBエントリー: 1D54 1D58
• NMR情報: BMRB: 6186
• 分子名称: 5'-D(P*TP*GP*AP*TP*CP*A)-3' (1 entity in total)
• 機能のキーワード: tpg/cpa basepair step, 2d-nmr of d-tgatca, restrained molecular dynamics, sequence related conformation, dna flexibility, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3616.46

構造登録者

Barthwal, R.,Awasthi, P.,Narang, M.,Sharma, U.,Srivastava, N. (登録日: 2004-04-01, 公開日: 2005-01-04, 最終更新日: 2024-05-01)

主引用文献

Barthwal, R.,Awasthi, P.,Narang, M.,Kaur, M.,Sharma, U.,Srivastava, N.,Barthwal, S.K.,Govil, G.
Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics
J.STRUCT.BIOL., 148:34-50, 2004

PubMed Abstract: The 5' d-TpG 3' element is a part of DNA sequences involved in regulation of gene expression and is also a site for intercalation of several anticancer drugs. Solution conformation of DNA duplex d-TGATCA containing this element has been investigated by two-dimensional NMR spectroscopy. Using a total of 12 torsional angles and 121 distance constraints, structural refinement has been carried out by restrained molecular dynamics (rMDs) in vacuum up to 100 ps. The structure is characterized by a large positive roll at TpG/CpA base pair step and large negative propeller twist for AT and TA base pairs. The backbone torsional angle, gamma(O5'-C5'-C4'-C3'), of T1 residue adopts a trans-conformation which is corroborated by short intra nucleotide T1H6-T1H5' (3.7A) distance in nuclear overhauser effect spectroscopy (NOESY) spectra while the backbone torsional angle, beta(P-O5'-C5'-C4'), exists in trans as well as gauche state for T1 and C5 residues. There is evidence of significant flexibility of the sugar-phosphate backbone with rapid inter-conversion between two different conformers at TpG/CpA base pair step. The base sequence dependent variations and local structural heterogeneity have important implications in specific recognition of DNA by ligands.

PubMed: 15363786
DOI: 10.1016/j.jsb.2004.05.005

実験手法

SOLUTION NMR