Light scattering studies of supercoiled and nicked DNA

作者：D. M. Fishman, G. D. Patterson · 发表于：Biopolymers · 年份：1996 · DOI：10.1002/(sici)1097-0282(199604)38:4<535::aid-bip9>3.3.co;2-h · 被引用次数：22 · 研究领域：DNA and Nucleic Acid Chemistry、Spectroscopy and Quantum Chemical Studies、Electrostatics and Colloid Interactions

Static and dynamic light scattering measurements were made of solutions of pGem1a plasmids (3730 base pairs) in the relaxed circular (nicked) and supercoiled forms. The static structure factor and the spectrum of decay modes in the autocorrelation function were examined in order to determine the salient differences between the behaviors of nicked DNA and supercoiled DNA. The concentrations studied are within the dilute regime, which is to say that the structure and dynamics of an isolated DNA molecule were probed. Static light scattering measurements yielded estimates for the molecular weight M, second virial coefficient A2, and radius of gyration RG. For the nicked DNA, M = (2.8 ± 0.4) × 106g/mol, A2 = (0.9 ± 0.2) × 10−3 mol cm3/g2, and RG = 90 ± 3 nm were obtained. For the supercoiled DNA, M = (2.5 ± 0.4) × 106 g/mol, A2 = (1.2 ± 0.2) × 10−3 mol cm3/g2, and RG = 82 ± 2.5 nm were obtained. The static structure factors for the nicked and supercoiled DNA were found to superpose when they were scaled by the radius of gyration. The intrinsic stiffness of DNA was evident in the static light scattering data. Homodyne intensity autocorrelation functions were collected for both DNAs at several angles, or scattering vectors. At the smallest scattering vectors the probe size was comparable to the longest intramolecular distance, while at the largest scattering vectors the probe size was smaller than the persistence length of the DNA. Values of the self-diffusion coefficients D were ob...