The effect of the superhelicity on the double helix twist angle in DNA

Belintsev, B. N.; Gagua, A. V.; Nedospasov, Sergei A.

doi:10.1093/nar/6.3.983

Cited by 10 publications

(13 citation statements)

References 15 publications

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“…This variance, though not very significant, may play its role in the interaction of DNA with regulatory proteins or in DNA wrapping around the nucleosome cores. The calculated values of A'I are in reasonable agreement with the other estimations of fluctuation of the -T angle based on the experimental data: &V7 =3.3-5.90 (16)(17)(18)(19)(20)(21)(22).…”

Section: Resultssupporting

confidence: 88%

“…In this case <(& t )t.> = N -<(,-)'> = IV .R T/9 since A tw = E& 'A and all AZN, vary independently (17). Fluctuation of the winding angle found according to the above equation: T = >= , proved to be 3.30-5.90 (16)(17)(18)(19)(20)(21)(22).…”

Section: Introductionmentioning

confidence: 92%

“…Recently the torsional stiffness of DNA in the standard environment was estimated on the basis of experimental data by several groups of authors (16)(17)(18)(19)(20)(21)(22). These findings make it possible to compare the results of conformational analysis with the data found independently.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Resultssupporting

confidence: 88%

Section: Introductionmentioning

confidence: 92%

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Torsional flexibility of DNA as revealed by conformational analysis

Zhurkin¹,

Lysov²,

Florentiev³

et al. 1982

Nucl Acids Res

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“…Moreover, as the bonds of the chains of Vologodskii et a1.26 are parallel to one of the eight vectors of components f l , f l , f l , the writhing number is always the ratio of an integer to 3, as may be shown using Eq. (17), and this might introduce a systematic error.…”

Section: Radius Of Gyration and Sedimentation Constantmentioning

confidence: 99%

“…Using circular dichroism, Belintsev et al 17 have measured 3 -00 for various values of c and found 0.7 for the ratio A. The fluorescence anisotopy decay of the ethidium cation intercalated into a linear double-stranded DNA19,20 has been theoretically related to the torsional constant K of DNA.15,21 Our elementary theory15 gives a value for X between 0.8 and 1.…”

Section: Introductionmentioning

confidence: 98%

Monte carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA

Bret

1980

Biopolymers

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SynopsisClosed random Gaussian polygonal chains of N (6 < N < 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w , the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types-0,31,41,51, and 52-the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw 2/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N1I4 WIN)^, and therefore depends on the writhing density and on the length of the DNA.

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Aminomethylanthracene Dyes as High‐Ionic‐Strength DNA‐Photocleaving Agents: Two Rings are Better than One

et al. 2018

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This paper compares the DNA interactions of a bis 9‐aminomethylanthracene dye (2) vs. a mono‐anthracene (4) under high ionic strength conditions similar to those in the cell nucleus (∼150 mM NaCl and 260 mM KCl). The chloride salts triggered an enhancement in anthracene‐sensitized DNA photocleavage, where bis‐anthracene 2 exhibited superior DNA binding affinity, faster reaction kinetics, and higher levels of DNA damage at low‐ to sub‐micro molar dye concentrations (350 nm hν, pH 7.0). While spectroscopic and viscometric data suggested that the chloride salts reduced DNA intercalation in favor of a non‐intercalative binding mode in which 2 and 4 were better able to generate hydroxyl radicals, there was evidence of persistent intercalation of the second anthracene ring of 2. We propose that such an interaction anchored the bis‐anthracene to DNA under the high ionic strength conditions, increasing its binding affinity and photocleaving capabilities relative to the mono analog (4).

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The effect of the superhelicity on the double helix twist angle in DNA

Cited by 10 publications

References 15 publications

Torsional flexibility of DNA as revealed by conformational analysis

Torsional flexibility of DNA as revealed by conformational analysis

Monte carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA

Aminomethylanthracene Dyes as High‐Ionic‐Strength DNA‐Photocleaving Agents: Two Rings are Better than One

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