[4] Statistical analysis of DNA duplex structural features

Publisher Summary This chapter discusses the emerging picture of the DNA duplexes in solution as seen by the modern nuclear magnetic resonance (NMR) methods. Commonly available experimental NMR data alone are not sufficient to determine an accurate average structure of a DNA duplex in solution with high definition. A theoretical force field must be employed in the refinement process, together with experimental restraints, to produce solution structures in agreement with independent data. Importantly, the nature of a force field does not appear to be essential; using different empirical force fields but the same experimental restraints during the refinement has led to practically the same DNA conformations. The overall average conformation of DNA oligonucleotides in solution is B-form. At the same time, modern NMR methods are able to detect a strong sequence-dependent local heterogeneity of the solution DNA structure similar to the high-resolution X-ray methods for DNA in solid state.

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