Computer analysis of conformational possibilities of double‐helical DNA

Zhurkin, Victor B.; Lysov, Yu. P.; Иванов, В. И.

doi:10.1016/0014-5793(75)80337-1

Cited by 14 publications

(9 citation statements)

References 15 publications

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“…One more group of forms occupies a region where 7 = 40-50'; D = -5 to -7.5 A (Table Ia, line 4; Table IIa, lines [19][20]. Here we have also I = 2, J = 1.…”

Section: Noncanonical Overwound Formsmentioning

confidence: 92%

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Different families of double‐stranded conformations of DNA as revealed by computer calculations

1978

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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 the winding angle, 7, allow one to subdivide possible conformations into the families of closely related forms. Two regions (ravines) on the ( D , 7) map correspond to the known K 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, 7, TL, and x, when going along the bottom of the B ravine, were also obtained. Besides the known K and 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 proteinnucleic acid interaction are discussed.

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“…One more group of forms occupies a region where 7 = 40-50'; D = -5 to -7.5 A (Table Ia, line 4; Table IIa, lines [19][20]. Here we have also I = 2, J = 1.…”

Section: Noncanonical Overwound Formsmentioning

confidence: 92%

“…20 Recently, a similar approach has been used by Khutorsky and Poltev.21 A distinct feature of their work is the permission of rotation within the sugar ring. Such an unfreezing of the sugar greatly enlarges the number of independent variables and prevents a detailed examination of correlations between the parameters.…”

Section: Introductionmentioning

confidence: 96%

Different families of double‐stranded conformations of DNA as revealed by computer calculations

1978

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“…The first quantitative data on the torsional rigidity of DNA were provided by conformational analysis of the regular double helix, i.e. the helix in which all nucleotides have the same geometry (11)(12)(13)(14)(15). Such calculations imitate the uniform smooth deformation of the duplex under change of ionic strength, temperature etc.…”

Section: Introductionmentioning

confidence: 99%

Torsional flexibility of DNA as revealed by conformational analysis

Zhurkin¹,

Lysov²,

Florentiev³

et al. 1982

Nucl Acids Res

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The thermal fluctuations of a regular double helix belonging to the B-family were studied by means of atom-atomic potentials method. The winding angle fluctuation was found to be 2.4 degrees for poly(dA):poly(dT) and 3.0 degrees for poly(dG):poly(dC). The reasonable agreement of these estimations with those obtained experimentally reveals the essential role of the small-amplitude torsional vibrations of atoms in the mechanism of the double helix flexibility. The calculated equilibrium winding angle, tau 0, essentially depends on the degree of neutralization of phosphate groups, being about 35.5 degrees for the full neutralization. The deoxyribose pucker is closely related to the tau angle: while tau proceeds from 30 degrees to 45 degrees the pseudorotation phase angle, P, increases from 126 degrees to 164 degrees. Fluctuations of the angles TL and TW, which specify inclination of the bases to the helix axis, were evaluated to be 5 degrees-10 degrees. Possible correlation between conformational changes in the adjacent nucleotides is discussed.

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“…The presence of Na+ coordinated with the uracil 2-keto group in the double-helical crystal structure of ApU (66) implies that dA.dT-rich DNA in particular might be stabilized in the B but not the A conformation (67) by ion binding. Yet the homopo lymer pair and alternating copolymer could differ with respect to the stereochemical disposition of bound ions in the minor groove (68) and/or base-stacking interactions (46). Thus, both interstrand and intra strand base overlaps exist in A-type struc tures, whereas only the latter occur in B-DNA (46,55).…”

Section: Joyinmentioning

confidence: 99%

Recognition Mechanisms of DNA-Specific Enzymes

Jovin¹

1976

Annu. Rev. Biochem.

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Computer analysis of conformational possibilities of double‐helical DNA

Cited by 14 publications

References 15 publications

Different families of double‐stranded conformations of DNA as revealed by computer calculations

Different families of double‐stranded conformations of DNA as revealed by computer calculations

Torsional flexibility of DNA as revealed by conformational analysis

Recognition Mechanisms of DNA-Specific Enzymes

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