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

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)-H6/8(i+1), and H6/8(i)-H6/8(i+1) sequential distances were found cross-correlated and linearly coupled to epsilon-zeta values in X-ray structures and P-31 chemical shifts (delta P) in NMR that reflect the interconversion between the backbone BI (epsilon-zeta < 0 degrees) and BII (epsilon-zeta > 0 degrees) 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 delta P in terms of BI/BII ratios. Also, comparison of many published delta P 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.