4F8G

Three-dimensional DNA lattices with non-canonical base pairs

4F8G の概要

• エントリーDOI: 10.2210/pdb4f8g/pdb
• 関連するPDBエントリー: 4F8I
• 分子名称: DNA (5'-D(*G*CP*GP*AP*AP*AP*GP*GP*GP*CP*AP*CP*GP*TP*GP*CP*CP*CP*T)-3'), COBALT HEXAMMINE(III) (3 entities in total)
• 機能のキーワード: non-canonical dna, dna nanotechnology, crystal design, parallel dna, dna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 6178.02

構造登録者

Paukstelis, P.J.,Muser, S.E. (登録日: 2012-05-17, 公開日: 2012-07-25, 最終更新日: 2024-02-28)

主引用文献

Muser, S.E.,Paukstelis, P.J.
Three-Dimensional DNA Crystals with pH-Responsive Noncanonical Junctions.
J.Am.Chem.Soc., 134:12557-12564, 2012

PubMed Abstract: Three-dimensional (3D) DNA crystals have been envisioned as programmable biomaterial scaffolds for creating ordered arrays of biological and nonbiological molecules. Despite having excellent programmable properties, the linearity of the Watson-Crick B-form duplex imposes limitations on 3D crystal design. Predictable noncanonical base pairing motifs have the potential to serve as junctions to connect linear DNA segments into complex 3D lattices. Here, we designed crystals based on a template structure with parallel-stranded noncanonical base pairs. Depending on pH, the structures we determined contained all but one or two of the designed secondary structure interactions. Surprisingly, a conformational change of the designed Watson-Crick duplex region resulted in crystal packing differences between the predicted and observed structures. However, the designed noncanonical motif was virtually identical to the template when crystals were grown at pH 5.5, highlighting the motif's predictability. At pH 7.0 we observed a structurally similar variation on this motif that contains a previously unobserved C-G•G-C quadruple base pair. We demonstrate that these two variants can interconvert in crystallo in response to pH perturbations. This study spotlights several important considerations in DNA crystal design, describes the first 3D DNA lattice composed of A-DNA helical sheets, and reveals a noncanonical DNA motif that has adaptive features that may be useful for designing dynamic crystals or biomaterial assemblies.

PubMed: 22768973
DOI: 10.1021/ja3025033

実験手法

X-RAY DIFFRACTION (1.93 Å)