DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations

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Abstract
Sugar–phosphate backbone conformations are an important structural element for a complete understanding of specific recognition in nucleic acid–protein interactions. They can be involved both in early stages of target discrimination and in structural adaptation upon binding. In the first part of this study, we have analyzed high‐resolution structures of double‐stranded B‐DNA either isolated or bound to proteins, and explored the impact of both the standard BI and the unusual BII phosphate backbone conformations on neighboring sugar puckers and on selected helical parameters. Correlations are found to be similar for free and bound DNA, and in both categories, the possible facing backbone conformations (BI.BI, BI.BII, and BII.BII) define well‐characterized substates in the B‐DNA conformational space. Notably, BII.BII steps are characterized by specific, and sequence‐independent, structural effects involving reduced standard deviations for almost all conformational parameters. In the second part of this work, we analyze four 10 ns molecular dynamics simulations in explicit solvent on the DNA targets of NF‐κB and bovine papillomavirus E2 proteins, highlighting the multiplicity of backbone dynamical behavior. These results show sequence effects on the percentages of BI and BII conformers, the preferential state of facing backbones, the occurrence of coupled transitions. The backbone states can consequently be seen as a mechanism for transmitting information from the bases to the phosphate groups and thus for modulating the overall structural properties of the target DNA. © 2003 Wiley Periodicals, Inc. Biopolymers 73:356–368, 2004