4J2I

Multiple crystal structures of an all-AT DNA dodecamer stabilized by weak interactions

4J2I の概要

• エントリーDOI: 10.2210/pdb4j2i/pdb
• 分子名称: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3' (2 entities in total)
• 機能のキーワード: dna, oligonucleotides, weak interactions, at-rich dna
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 29275.52

構造登録者

Acosta-Reyes, F.J.,Subirana, J.A.,Pous, J.,Sanchez, R.,Condom, N.,Baldini, R.,Malinina, L.,Campos, J.L. (登録日: 2013-02-04, 公開日: 2014-02-05, 最終更新日: 2024-02-28)

主引用文献

Acosta-Reyes, F.J.,Subirana, J.A.,Pous, J.,Sanchez-Giraldo, R.,Condom, N.,Baldini, R.,Malinina, L.,Campos, J.L.
Polymorphic crystal structures of an all-AT DNA dodecamer.
Biopolymers, 103:123-133, 2015

PubMed Abstract: In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed.

PubMed: 25257185
DOI: 10.1002/bip.22565

実験手法

X-RAY DIFFRACTION (2.98 Å)