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Different families of double‐stranded conformations of DNA as revealed by computer calculations
Author(s) -
Zhurkin V. B.,
Lysov Yu. P.,
Ivanov V. I.
Publication year - 1978
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.1978.360170209
Subject(s) - chemistry , helix (gastropod) , base (topology) , crystallography , atom (system on chip) , position (finance) , base pair , dna , double stranded , chemical physics , stereochemistry , mathematical analysis , ecology , biochemistry , mathematics , finance , snail , computer science , economics , biology , embedded system
An algorithm has been developed that permits one to find all possible conformations of the sugar‐phosphate backbone for any given disposition of DNA base pairs. For each of the conformations thus obtained, the energy of the helix was calculated by the method of atom‐atom potentials. Several isolated regions in the space of the bases′ parameters (Arnott's parameters) have been found for energetically favorable helical structures. Two parameters, the distance of a base pair from the helix axis, D , and the windling angle, τ, allow one to subdivide possible conformations into the families of closely related forms. Two regions (ravines) on the (D, τ) map correspond to the know A and B families. In the B family a continuous transition has been obtained in which the double helix undergoes increasing winding, while the base pairs are moving toward the major (nonglycosidic) groove. Interrelationships between the variables, characterizing the spatial structure of the double helix, D , τ, TL and χ, when going along the bottom of the B ravine, were also obtained. Besides the Known A and B families, several new ones were found to be energetically possible. Among these the strongly underwound helices with the negative D values, as well as the forms with the C4‐C5 angle in a trans position, should be mentioned. Biological roles of the different double‐stranded conformations, in particular, in protein‐nuclei acid interaction are discussed.