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Virtual bond probe to study ordered and random coil conformations of nucleic acids
Author(s) -
Malathi R.,
Yathindra N.
Publication year - 1981
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560200122
Subject(s) - random coil , polynucleotide , chemistry , nucleotide , nucleic acid , crystallography , side chain , macromolecule , hydrogen bond , stereochemistry , chemical physics , molecule , circular dichroism , biochemistry , organic chemistry , gene , polymer
Recognition of the stereochemical features inherent to a nucleotide, viz., the preferred trans character of the two CO bonds and the approximate chemical and conformational symmetry, has facilitated the representation of a nucleotide in terms of two nearly equal blocks or two virtual bonds spanning the atoms P to C4' on the 5' side and C4' to P on the 3' side. The scheme, by virtue of its unique ability to account for the main sources of flexibility and to incorporate their interdependence, could be effectively applied to probe ordered, as well as random coil conformations of polynucleotide chains. Using this scheme, conformations of nucleotide, dinucleotides, helices, and yeast t RNA Phe have been characterized by virtual bond parameters. The two blocks of nucleotide have also been described in terms of two approximate planes similar to peptides. Unperturbed end‐to‐end dimensions and persistence lengths of random coil polynucleotides have been computed by considering short‐range as well as near‐neighbor bond long‐range correlations and are in excellent agreement with the experimentally determined values. A striking finding of these studies is the relevation that random coils comprise of a large proportion of stacked A ‐type helical segments in sharp contrast to earlier interpretations which invoked a high fraction of unstacked extended conformations.