Spatial configuration of ordered polynucleotide chains. V. Conformational energy estimates of helical structure

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Abstract
Semiempirical potential energy functional used previously to account successfully for the mean‐square unperturbed dimensions and nmr coupling constants of randomly coiling polynucleotides are used, after modifications, to account for base stacking and interstrand hydrogen bonding, and to evaluate the conformational energies of single‐ and double‐stranded polynucleotide helices. Attention is focused upon the variety of A‐genus helices with local backbone conformations resembling the known double‐helical structures of RNA. Distinct structural differences between single‐ and double‐stranded helices are predicted from the energy calculations. A second point of interest is the apparent failure of two conformationally identical left‐handed polynucleotide chains to form a left‐handed duplex. The third major observation of the study is the wide morphological variety of theoreticaly allowed right‐handed polynucleotide duplexes. In addition to the familiar double helix stabilized by horizontal base stacking and hydrogen bonding, an unusual vertical double helix is predicted to form between complementary bases fixed in the unusual but not energetically forbidden high anti glycosyl conformation. Experimental results bearing upon the theoretical predictions are discussed.