Structure factor calculations of various DNA duplexes

Abstract

Based upon a stereochemical guideline, both right- and left-handed duplexes were generated for A, B, and D forms of DNA using a mononucleotide as the repeat. Structure factor amplitudes were computed following two methods: (i) one employed an infinite helix as the motif and (ii) the other had an exact crystallographic repeat (e.g., 10 b.p. for B-DNA) as the motif. Both the procedures showed that DNA in either handedness for A, B, and D forms of DNA are consistent with the observed fiber data. This observation is attributed to the fact that fibre pattern (resolved only upto 3 Å ) only gives the image of the gross structure of the molecule. Thus, when the gross structure is suitably fitted to match the observed pattern, it is immaterial as to what the precise stereochemistry of the repeating unit (fine structure) and handedness of a model are. Sequence specific helical conformations were obtained using dinucleotide as the repeating unit. Helices fell into two classes: (i) right-handed uniform (RU) and (ii) left-handed zig-zag (LZ) structures. A few aspects concerning the scattering profile of these helices are discussed.