1978
DOI: 10.1002/bip.1978.360170209
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Different families of double‐stranded conformations of DNA as revealed by computer calculations

Abstract: SynopsisAn 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 atomatom 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 th… Show more

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Cited by 82 publications
(62 citation statements)
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“…The set of internal coordinates was designed specifically for nucleic acid structures, and it includes generalized helical parameters defining the relative positions of nucleic bases in space; aromatic bases are treated as rigid bodies with idealized geometry. The conformations of backbones connecting adjacent bases are calculated with a specialized chain closure algorithm (38), which ensures that bond lengths and bond angles have standard values. The conformational energy is calculated in vacuo with a distance-dependent dielectric constant, using an empirical force field optimized for nucleic acids (22,39).…”
Section: Methodsmentioning
confidence: 99%
“…The set of internal coordinates was designed specifically for nucleic acid structures, and it includes generalized helical parameters defining the relative positions of nucleic bases in space; aromatic bases are treated as rigid bodies with idealized geometry. The conformations of backbones connecting adjacent bases are calculated with a specialized chain closure algorithm (38), which ensures that bond lengths and bond angles have standard values. The conformational energy is calculated in vacuo with a distance-dependent dielectric constant, using an empirical force field optimized for nucleic acids (22,39).…”
Section: Methodsmentioning
confidence: 99%
“…These parameters define relative positions of idealized aromatic bases and sugars, as well as internal conformations of sugar moieties. The atomic coordinates of the sugar-phosphate backbone are then calculated by a chain closure algorithm (28). The force field used in miniCarlo was optimized specifically for nucleic acids (29).…”
Section: Methodsmentioning
confidence: 99%
“…In all, the system has 160 independent variables. Geometry of the sugar-phosphate backbone was found with the use of the chain-closure algorithm, developed in this laboratory (18). All The energies were calculated with the use of the atomatom potentials (19,20).…”
Section: Methodsmentioning
confidence: 99%