3UBI

The Absence of Tertiary Interactions in a Self-Assembled DNA Crystal Structure

3UBI の概要

• エントリーDOI: 10.2210/pdb3ubi/pdb
• 分子名称: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3'), DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3'), ... (4 entities in total)
• 機能のキーワード: nanotechnology, dna crossover, designed crystal lattice, dna
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 18977.34

構造登録者

Nguyen, N.,Birktoft, J.J.,Sha, R.,Wang, T.,Zheng, J.,Constantinou, P.E.,Ginell, S.L.,Chen, Y.,Mao, C.,Seeman, N.C. (登録日: 2011-10-24, 公開日: 2012-05-16, 最終更新日: 2024-02-28)

主引用文献

Nguyen, N.,Birktoft, J.J.,Sha, R.,Wang, T.,Zheng, J.,Constantinou, P.E.,Ginell, S.L.,Chen, Y.,Mao, C.,Seeman, N.C.
The absence of tertiary interactions in a self-assembled DNA crystal structure.
J.Mol.Recognit., 25:234-237, 2012

PubMed Abstract: DNA is a highly effective molecule for controlling nanometer-scale structure. The convenience of using DNA lies in the programmability of Watson-Crick base-paired secondary interactions, useful both to design branched molecular motifs and to connect them through sticky-ended cohesion. Recently, the tensegrity triangle motif has been used to self-assemble three-dimensional crystals whose structures have been determined; sticky ends were reported to be the only intermolecular cohesive elements in those crystals. A recent communication in this journal suggested that tertiary interactions between phosphates and cytosine N(4) groups are responsible for intermolecular cohesion in these crystals, in addition to the secondary and covalent interactions programmed into the motif. To resolve this issue, we report experiments challenging this contention. Gel electrophoresis demonstrates that the tensegrity triangle exists in conditions where cytosine-PO(4) tertiary interactions seem ineffective. Furthermore, we have crystallized a tensegrity triangle using a junction lacking the cytosine suggested for involvement in tertiary interactions. The unit cell is isomorphous with that of a tensegrity triangle crystal reported earlier. This structure has been solved by molecular replacement and refined. The data presented here leave no doubt that the tensegrity triangle crystal structures reported earlier depend only on base pairing and covalent interactions for their formation.

PubMed: 22434713
DOI: 10.1002/jmr.2183

実験手法

X-RAY DIFFRACTION (6.8046 Å)