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

TL;DR

This study uses SAXS to analyze sequence-dependent conformations of DNA in solution, revealing how DNA flexibility and structure relate to sequence and potential protein interactions.

Contribution

It introduces a simple polymer model to accurately describe DNA conformations and demonstrates sequence-specific orientation analysis using SAXS data.

Findings

Quantitative description of DNA persistence length and torsional rigidity

Sequence-dependent orientation of DNA conformations in solution

Potential for SAXS to investigate DNA-protein interactions

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 a high accuracy. Although the SAXS data is 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.