DNA persistence length revisited

Publisher Website
Google Scholar
Abstract
DNA restriction fragments ranging from 79 to 789 base pairs in length have been characterized by transient electric birefringence (TEB) measurements at various temperatures between 4 and 43°C. The DNA fragments do not contain runs of four or more adenine residues in a row and migrate with normal electrophoretic mobilities in polyacrylamide gels, indicating that they are not intrinsically curved or bent. The low ionic strength buffers used for the measurements contained 1 mM Tris Cl, pH 8.0, EDTA, and variable concentrations of Na+ or Mg2+ ions. The rotational relaxation times were obtained by fitting the TEB field‐free decay signals with a nonlinear least‐squared fitting program; the decay of the birefringence was monoexponential for fragments ≤ 241 base pair (bp) in length and multiexponential for larger fragments. The terminal relaxation times, characteristic of the end‐over‐end rotation of the DNA molecules, were then used todetermine the persistence length (p) and hydrodynamic radius (r) of DNA as a function of temperature and ionic strength, using several different hydrodynamic models. The specific values obtained for p and r are model dependent. The wormlike chain model of P. J. Hagerman and B. H. Zimm (Biopolymers 1981, Vol. 20, pp. 1481–1502) combined with the revised Broersma equation (J. Newman et al., Journal of Mol Biol 1997, Vol. 116, pp. 593–606) appears to be the most suitable for describing the flexibility of DNA in low ionic strength solutions. The values of p and r obtained from the global least squares fitting of this equation are independent of DNA length, and the deviations of the individual values from the average are reasonably small. The consensus r value calculated for DNA in various low ionic strength solutions containing 1 mM Tris buffer is 14.7 ± 0.4 Å at 20°C. The consensus p values decrease from 814 ∼ 564 Å in solutions containing 1 mM Tris buffer plus 0.2–1 mM NaCl and decrease still further to 440 Å in solutions containing 0.2 mM Mg2+ ions. The persistence length exhibits a shallow maximum at 20°C and decreases slowly upon either increasing or decreasing the temperature, regardless of the model used to fit the data. By contrast, the consensus values of the hydrodynamic radius are independent of temperature. The calculated persistence lengths and hydrodynamic radii are compared with other data in the literature. © 2002 Wiley Periodicals, Inc. Biopolymers 61: 261–275, 2002