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Rotational dynamics of DNA from 10 −10 to 10 −5 seconds: Comparison of theory with optical experiments
Author(s) -
Shibata John H.,
Fujimoto Bryant S.,
Schurr J. Michael
Publication year - 1985
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.360241006
Subject(s) - chemistry , chromophore , birefringence , torsion (gastropod) , amplitude , molecular physics , persistence length , rotational diffusion , relaxation (psychology) , isotropy , physics , anisotropy , atomic physics , optics , molecule , medicine , psychology , social psychology , surgery , organic chemistry
Optical anisotropy data spanning a very wide time range are analyzed using a recently developed theory for filamentous macromolecules that can bend, twist, and also admit overdamped local libration (or wobble) of the chromophore. A rapid relaxation in the fluorescence polarization anisotropy (FPA) near 10 −10 s is fitted well by superimposing isotropic wobble of the chromophore (7° rms polar and azimuthal amplitude) on the long‐wavelength twisting and bending motions that characterize the relaxation at longer times but not by the latter alone. Moreover, the decay of the FPA from 0.5 to 150 ns cannot be satisfactorily fitted by chromophore wobble in an otherwise rigid DNA and must be assigned primarily to twisting, as noted previously. Data from 26 ns to 20 μs for 600 base‐pair DNA are accurately fitted with only a single adjustable scaling factor when the tumbling correlation function is taken to be the empirical electric birefringence decay function of Elias and Eden. The Barkley‐Zimm (BZ) tumbling correlation for very long filaments appears to decay too rapidly and results in significant overestimation of the depolarization for t ≤ 300 ns. In the range of the FPA experiments ( t ≥ 150 ns), equally good fits with equally uniform torsion constants are obtained for long DNAs, whether one assumes the BZ tumbling correlation function or neglects tumbling entirely, but the best‐fit torsion constant (actually the product of the torsion constant and friction factor) is increased by the factor 1.9 when the BZ result is used with a persistence length of a = 500 Å. The BZ bending theory is compared with other experimental data, and also with a simulation at very short times with mixed results. Present uncertainties regarding the tumbling dynamics and the friction factor for azimuthal rotation allow the torsion constant to be as much as 3.8 times larger than the initial estimate of Thomas et al. Apparent torsion constants obtained from relative ligase kinetics measurements are also briefly discussed.