4RIM

Native structure of intercalation-locked DNA tetraplex

4RIM の概要

• エントリーDOI: 10.2210/pdb4rim/pdb
• 関連するPDBエントリー: 4RIP
• 分子名称: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*TP*GP*AP*T)-3') (1 entity in total)
• 機能のキーワード: dna, homo-duplex, intercalation-locked dna tetraplex
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 3373.22

構造登録者

Tripathi, S.K.,Zhang, D.,Paukstelis, P. (登録日: 2014-10-06, 公開日: 2015-02-11, 最終更新日: 2024-02-28)

主引用文献

Tripathi, S.,Zhang, D.,Paukstelis, P.J.
An intercalation-locked parallel-stranded DNA tetraplex.
Nucleic Acids Res., 43:1937-1944, 2015

PubMed Abstract: DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC(Br)UCGGA(Br)UGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. (1)H-(1)H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.

PubMed: 25628357
DOI: 10.1093/nar/gkv033

実験手法

X-RAY DIFFRACTION (2.3 Å)