4ZYM

Structural implications of homo-pyrimidine base pairs on the parallel-stranded d(GAY) motif.

4ZYM の概要

• エントリーDOI: 10.2210/pdb4zym/pdb
• 分子名称: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*CP*GP*AP*T)-3'), MAGNESIUM ION (3 entities in total)
• 機能のキーワード: tetraplex, homo-base pair, pyrimidine substitution., dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 13530.06

構造登録者

Tripathi, S.K.,Paukstelis, P. (登録日: 2015-05-21, 公開日: 2015-12-16, 最終更新日: 2023-09-27)

主引用文献

Tripathi, S.,Paukstelis, P.J.
Structural Implications of Homopyrimidine Base Pairs in the Parallel-Stranded d(YGA) Motif.
Chembiochem, 17:1177-1183, 2016

PubMed Abstract: DNA can adopt many other structures beyond the canonical B-form double helix. These alternative DNA structures have become increasingly significant as new biological roles are found for them. Additionally, there has been a growing interest in using non-canonical base pairs to provide structural diversity for designing DNA architectures for nanotechnology applications. We recently described the crystal structure of d(ACTCGGATGAT), which forms a tetraplex through parallel-stranded homo-base pairs and nucleobase intercalation. The homoduplex region contains a d(YGA⋅YGA) motif observed in crystal and solution structures. Here, we examine the structural implications of the homopyrimidine base pair within this motif. We determined crystal structures of two variants that differ from the original structure in the homopyrimidine base pairs and number of d(YGA) motifs. Our results show that the intercalation-locked tetraplex motif is predictable in these different sequence contexts and that substituting C⋅C base pairs for T⋅T base pairs introduces asymmetry to the homoduplex. These results have important implications for utilizing d(YGA) motifs in DNA crystal design and could provide a basis for understanding how local structures could be associated with repeat expansions.

PubMed: 26629965
DOI: 10.1002/cbic.201500491

実験手法

X-RAY DIFFRACTION (2.53 Å)