Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition

Abstract

The backbone states of B-DNA influence its helical parameters, groove dimensions, and overall curvature. Therefore, detection and fine characterization of these conformational states are desirable. Using routine NMR experiments on a nonlabeled B-DNA oligomer and analyzing high-resolution X-ray structures, we investigated the relationship between interproton distances and backbone conformational states. The three H2′i-H6/8 i+1, H2″i-H6/8i+1, and H6/8 i-H6/8i+1 sequential distances were found cross-correlated and linearly coupled to ε-ζ values in X-ray structures and 31P chemical shifts (δP) in NMR that reflect the interconversion between the backbone BI (ε-ζ < 0°) and BII (ε-ζ > 0°) states. These relationships provide a detailed check of the NMR data consistency and the possibility to extend the set of restraints for structural refinement through various extrapolations. Furthermore, they allow translation of δP in terms of BI/BII ratios. Also, comparison of many published δP in solution to crystal data shows that the impact of sequence on the BI/BII propensities is similar in both environments and is therefore an intrinsic and general property of B-DNA. This quantification of the populations of BI and BII is of general interest because these sequence-dependent backbone states act on DNA overall structure, a key feature for DNA-protein-specific recognition. © 2006 American Chemical Society.