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The spatial configuration of ordered polynucleotide chains. I. Helix formation and base stacking
Author(s) -
Olson Wilma K.
Publication year - 1976
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1976.360150505
Subject(s) - polynucleotide , stacking , chemistry , crystallography , helix (gastropod) , base pair , base (topology) , stereochemistry , dna , biochemistry , mathematics , organic chemistry , biology , ecology , mathematical analysis , snail
A single virtual bond scheme set forth previously for the treatment of average properties of randomly coiling polynucleotides is here applied to the calculation of helical parameters which characterize a regularly repeating polynucleotide molecule. Only a fraction of the enormous number of conformationally feasible helixes fulfill the geometric criteria of vertical base stacking usually associated with ordered polynucleotide chains. Detailed examination of the nature and mode of base stacking feasible in a single helical backbone structure indicates that the handedness of a base stacking arrangement does not correlate either quantitatively or qualitatively with the handedness of the polymer backbone. A number of polynucleotide chains which exhibit lefthanded base stacking patterns in nmr and CD studies may, in fact, be righthanded helixes.