Changes in Molecular Weights and Molecular Weight Distributions of Differently Stranded Nucleic Acids after Sonication: Gel Permeation Chromatography/Low Angle Laser Light Scattering Evaluation and Computer Simulation

Abstract

Changes of weight-average molecular weights (Mw) and the molecular weight distributions in terms of weight fraction (gw) were evaluated in the course of sonication for three nucleic acids in different conformations by the gel permeation chromatography/low angle laser light scattering (GPC/LALLS) method. High Mw samples used were single-stranded poly(uridylic acid), (U)n, double-stranded DNA, and triple-stranded poly(adenylic acid)·2poly(inosinic acid), (A)n·2(I)n, in 0.2−0.1 M NaCl at 0 °C. The experimental gw vs M curves were computer-simulated for different chain-scission mechanisms: (1) random, (2) midpoint, (3) Gaussian, (4) classical partially random, and (5) newly proposed partially random scission models. In comparison with the GPC/LALLS data, the middle portion of each single- or multiple-stranded chain was sheared randomly, whereas the adjacent end portions of the chain resisted sonic scission. The Mw value of each intact end portion was 1.0 × 105 for (U)n, 1.5 × 105 for DNA, and 1.7 × 105 for (A)n·2(I)n, corresponding to the lowest possible Mw for the sonicated but unfractionated nucleic acid samples under the present conditions.