Statistical analysis of DNA duplex structures in solution derived by high resolution NMR

Abstract

An initial statistical analysis has been performed on the helical parameters for the solution structures of three DNA duplexes recently solved in this laboratory by proton NMR. Local conformations in these structures belong to the B family of forms; nevertheless they display a strong sequence-dependent heterogeneity akin to that found in single crystals and by theoretical calculations. However, average helical parameters as well as their variations are quite different for short DNA fragments in solution and in crystal. Average helical twist in three NMR-refined oligonucleotides is 34.6°, in remarkable agreement with independent solution-state data, while helical twist is 36° for DNA in crystals. Other characteristic features of solution DNA conformations are negative slide, systematically open minor groove (for almost all sequences), and decreased helical rise. The latter, rather unexpected finding, is correlated with a surprisingly strong non-flatness of Watson-Crick base pairs. Deviations of base pairs from planarity proved to be a significant source of conformational variability; of particular importance is base stagger, which is often missed in structural analysis of DNA. Several new structural parameters have been introduced for dinucleotide steps, characterizing non-planar geometries of constituent base pairs; these parameters show a significant degree of correlation with traditional step parameters (twist, tillt roll, shift, slide, rise). Many sequence-dependent features are observed in solution structures; variation of roll and slide parameters occurs according to “Calladine’s rules”, while variation of helical twist appears to oppose them. However, a larger set of solution structures is needed to complete the analysis of sequence dependence of DNA conformation.