The intrinsic mechanics of B-DNA in solution characterized by NMR

Experimental characterization of the structural couplings in free B-DNA in solution has been elusive, because of subtle effects that are challenging to tackle. Here, the exploitation of the NMR measurements collected on four dodecamers containing a substantial set of dinucleotide sequences provides new, consistent correlations revealing the DNA intrinsic mechanics. The difference between two successive residual dipolar couplings (Delta RDCs) involving C6/8-H6/8, C'-H3' and C4'-H4' vectors are correlated to the P-31 chemical shifts (delta P), which reflect the populations of the BI and BII backbone states. The delta Ps are also correlated to the internucleotide distances (D-inter) involving H6/8, H2' and H2 '' protons. Calculations of NMR quantities on high resolution X-ray structures and controlled models of DNA enable to interpret these couplings: the studied Delta RDCs depend mostly on roll, while D-inter are mainly sensitive to twist or slide. Overall, these relations demonstrate how delta P measurements inform on key inter base parameters, in addition to probe the BI <-> BII backbone equilibrium, and shed new light into coordinated motions of phosphate groups and bases in free B-DNA in solution. Inspection of the 5' and 3' ends of the dodecamers also supplies new information on the fraying events, otherwise neglected.