Nucleic Acids Research

The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, Band Z-DNA forms, we have also identified combined A+B backbone-deformed conformers, e.g. with a/c switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of Aand B-like conformers show a close relationship between the Aand B-form double helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the Aand Bforms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail.