Probing the statistics of sequence-dependent DNA conformations in solution using SAXS.

IF 4.3 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Acta Crystallographica. Section D, Structural Biology Pub Date : 2026-02-01 Epub Date: 2026-01-19 DOI:10.1107/S2059798325011556

Heidar J Koning, Anuradha Pullakhandam, Andrew E Whitten, Charles S Bond, Michel Peyrard

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引用次数: 0

Abstract

SAXS studies of four 60-base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein binding. We show that the SAXS data can be analysed using a simple polymer model, which nevertheless quantitatively describes the average persistence length and torsional rigidity of the DNA double helix, to determine the statistical distribution of local conformations of the DNA in solution to high accuracy. Although the SAXS data are averaged over time and all spatial orientations of the molecules, for sequences which have some asymmetry in the data we show that the conformations can be oriented with respect to the sequence. This allows specific features detected by the analysis to be precisely related to the DNA sequence, opening up new opportunities for SAXS to investigate the properties of DNA in solution. The biological implications of these results are discussed.

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利用SAXS探测溶液中序列依赖性DNA构象的统计。

对与GAGE6 （g -抗原6）启动子部分密切相关的4个60碱基对DNA双链进行了SAXS研究，以研究溶液中DNA构象的作用及其与DNA-蛋白结合的潜在关系。我们表明，SAXS数据可以使用简单的聚合物模型进行分析，该模型定量描述了DNA双螺旋的平均持续长度和扭转刚度，以高精度确定溶液中DNA局部构象的统计分布。虽然SAXS数据随时间和分子的所有空间方向平均，但对于数据中有一些不对称的序列，我们表明构象可以相对于序列定向。这使得分析检测到的特定特征与DNA序列精确相关，为SAXS研究溶液中DNA的特性开辟了新的机会。讨论了这些结果的生物学意义。

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, Structural Biology BIOCHEMICAL RESEARCH METHODSBIOCHEMISTRY &-BIOCHEMISTRY & MOLECULAR BIOLOGY

CiteScore

4.50

自引率

13.60%

发文量

216

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.