Fluorescence Studies of Nucleic Acids: Dynamics, Rigidities, and Structures

Schurr, J. Michael; Fujimoto, Bryant S.; Wu, Pengguang; Lu, Song

doi:10.1007/0-306-47059-4_4

Cited by 22 publications

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References 210 publications

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“…After accounting for the contribution of excitation transfer to the depolarization process, the measured torsion elastic constant did not vary with the amount of bound of ethidium from 1 per 300 bp to 1 per 10 bp . That strongly implies that bound ethidium up to 1 per 10 bp does not significantly decrease the intrinsic torsion elastic constants of the springs associated with the individual bps of the DNA. , Values of C eff comparable to the values of C app reported by Celedon et al for DNAs in the presence of ethidium were observed only for DNAs that were temporarily trapped in a metastable state with low torsion elastic constant that forms immediately upon sufficient relaxation of the torsional stress in native supercoiled DNAs. ,− However, if the DNAs of Celedon et al were trapped in such a metastable state, the bare DNA also should have displayed an anomalously low value, contrary to observation. Hence, the anomalously low value for 3.4 × 10 –9 M ethidium is most unlikely to be a manifestation of that metastable state with low torsional rigidity.…”

Section: Introductionsupporting

confidence: 56%

Theory of Ethidium Binding to DNA under Tension and Torque: Possible Role of Cruciforms at Inverted Repeat Sequences

Schurr

2023

J. Phys. Chem. B

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Celedon et al. reported an unexpectedly low slope of applied torque vs turns (or apparent torsional rigidity) for a long DNA subject to 0.8 pN tension and modest negative torques (up to approximately −5 pN nm) in 3.4 × 10–9 M ethidium (J. Phys. Chem. B 2010, 114, 16929–16935). Extrusion of inverted repeat sequences to create cruciforms with anomalously large association constants for binding 4 ethidiums to the cruciform arms is investigated as a possible explanation for this observation and also for its compatibility with other observations of Celedon et al. The equilibrium between the linear main chain and cruciform states of an inverted repeat sequence under the prevailing tension, torque, and ethidium concentration is treated by first computing the free energy per bp of the linear main chain. This is done for a complex model, wherein every bp in the linear main chain participates in both the recently reviewed cooperative two-state a ⇔ b equilibrium (Quarterly Reviews of Biophysics 2021, 54, e5, 1–25) and in ethidium binding with a modest relative preference for either the a- or b-state. Plausible assumptions are made concerning the relative populations of the cruciform and linear main chain states of an inverted repeat, and also the relative populations of cruciform states with and without 4 bound ethidiums in the presence of tension, torque, and 3.4 × 10–9 M ethidium. Besides a large drop in slope (or apparent torsional rigidity) from 10–9 to 10–8 M ethidium, this theory also predicts maxima between 6.4 × 10–8 and 2.0 × 10–7 M ethidium, a region where no measurements were made. Overall agreement between theoretical and experimental values of the slope (or apparent torsional rigidity), and also the number of negative turns due to bound ethidium at zero torque, is fairly good for all of the ethidium concentrations studied by Celedon et al., provided that there is a modest preference for binding to the b-state. When there is a modest preference for binding to the a-state, the theory significantly underestimates experimental values at the higher ethidium concentrations, likely ruling out that possibility.

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Section: Introductionsupporting

confidence: 56%

Theory of Ethidium Binding to DNA under Tension and Torque: Possible Role of Cruciforms at Inverted Repeat Sequences

Schurr

2023

J. Phys. Chem. B

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The question of long-range allosteric transitions in DNA

et al. 1997

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Dynamic twisting correlations in a model DNA with uniform torsion elastic constant

Schurr¹,

Fujimoto²

1999

Biopolymers

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The extent to which the twisting motions of two separate subunits (base pairs) in an elastic filament are correlated is discussed in terms of the two‐point correlation function of their azimuthal angular displacements C(Δ,t) ≡ 〈(ϕm(t) − ϕm(0))(ϕn(t) − ϕn(0))〉, where m,n are the sequential subunit indices and Δ = |m − n| is their absolute difference. An approximate expression is derived for C(Δ,t) for an infinitely long model DNA from the analytical theory developed previously to treat the decay of the fluorescence polarization anisotropy of intercalated ethidium. C(Δ,t) is numerically evaluated as a function of Δ for a range of times (20, 40, 60, 80, 100, and 120 ns) for a model DNA with a typical torsion elastic constant. By t = 120 ns, significant dynamic correlations are observed to extend over a domain (Δ) several hundred base pairs. © 1999 John Wiley & Sons, Inc. Biopoly 49: 355–359, 1999

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Fluorescence Studies of Nucleic Acids: Dynamics, Rigidities, and Structures

Cited by 22 publications

References 210 publications

Theory of Ethidium Binding to DNA under Tension and Torque: Possible Role of Cruciforms at Inverted Repeat Sequences

Theory of Ethidium Binding to DNA under Tension and Torque: Possible Role of Cruciforms at Inverted Repeat Sequences

The question of long-range allosteric transitions in DNA

Dynamic twisting correlations in a model DNA with uniform torsion elastic constant

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