Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-12-01 DOI:10.1107/S1399004715019598

M. Saoji, P. Paukstelis

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引用次数: 5

Abstract

DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson-Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg(2+) through a combination of Watson-Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson-Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A-G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G-A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson-Crick duplex region. These results provide important new insights into the sequence-structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson-Crick and noncanonical base pairs that is responsible for crystallization fate.

查看原文本刊更多论文

自组装DNA寡核苷酸的序列依赖性结构变化。

由于互补的沃森-克里克碱基配对提供的可编程性和结构可预测性，DNA已被证明是构建复杂的二维和三维结构的重要分子。然而，DNA寡核苷酸可以表现出大量的局部结构多样性。DNA构象与环境条件和寡核苷酸序列中固有的核碱基身份密切相关，但序列与局部结构之间的确切关系尚不完全清楚。本研究探讨了在相同的结晶条件下，单核苷酸添加到一类自组装DNA 13-mers中如何导致显着不同的整体结构。DNA 13-mers通过沃森-克里克和非规范碱基配对相互作用的组合在Mg(2+)存在下自组装。这里描述的晶体结构表明，所有预测的沃森-克里克碱基对都存在，主要区别在于非规范碱基对的显著重排。这包括剪切a - g碱基对的形成，碱基三重相互作用形成的链结，以及产生类似于串联剪切G-A碱基对的三级相互作用的结构特征。这种交替非规范结构的采用部分取决于沃森-克里克双相区的序列。这些结果为短DNA寡核苷酸的序列-结构关系提供了重要的新见解，并证明了沃森-克里克和非规范碱基对之间独特的相互作用是结晶命运的原因。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Acta Crystallographica Section D: Biological Crystallography 生物-晶体学

自引率

13.60%

发文量

审稿时长

3 months

期刊介绍： Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.