5KIH

Structural impact of single ribonucleotides in DNA

5KIH の概要

• エントリーDOI: 10.2210/pdb5kih/pdb
• 関連するPDBエントリー: 5KGV 5KI7 5KIB 5KIE 5KIF
• NMR情報: BMRB: 30117
• 分子名称: DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3') (2 entities in total)
• 機能のキーワード: dna, rna, ribonucleotides
• 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: 5487.62

構造登録者

Evich, M.,Spring-Connell, A.M.,Storici, F.,Germann, M.W. (登録日: 2016-06-16, 公開日: 2016-08-24, 最終更新日: 2024-05-01)

主引用文献

Evich, M.,Spring-Connell, A.M.,Storici, F.,Germann, M.W.
Structural Impact of Single Ribonucleotide Residues in DNA.
Chembiochem, 17:1968-1977, 2016

PubMed Abstract: Single ribonucleotide intrusions represent the most common nonstandard nucleotide type found incorporated in genomic DNA, yet little is known of their structural impact. This lesion incurs genomic instability in addition to affecting the physical properties of the DNA. To probe for structural and dynamic effects of single ribonucleotides in various sequence contexts-AxC, CxG, and GxC, where x=rG or dG-we report the structures of three single-ribonucleotide-containing DNA duplexes and the corresponding DNA controls. The lesion subtly and locally perturbs the structure asymmetrically on the 3' side of the lesion in both the riboguanosine-containing and the complementary strand of the duplex. The perturbations are mainly restricted to the sugar and phosphodiester backbone. The ribose and 3'-downstream deoxyribose units are predominately in N-type conformation; backbone torsion angles ϵ and/or ζ of the ribonucleotide or upstream deoxyribonucleotide are affected. Depending on the flanking sequences, the C2'-OH group forms hydrogen bonds with the backbone, 3'-neighboring base, and/or sugar. Interestingly, even in similar purine-rG-pyrimidine environments (A-rG-C and G-rG-C), a riboguanosine unit affects DNA in a distinct manner and manifests different hydrogen bonds, which makes generalizations difficult.

PubMed: 27504600
DOI: 10.1002/cbic.201600385

実験手法

SOLUTION NMR