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ABSTRACT:The ultrasonic scission was studied for deoxyribonucleic acid (DNA) and five polyribonucleotide duplexes; three antiparallel-stranded helices (Poly(G) · Poly(C), Poly(A) · Poly(U), Poly(!)· Poly(C)) and two parallel-stranded helices (Poly(C) · Poly(C+) and Poly(A) · Poly(A +)). The sonication was carried out in 0.1---0.2 M NaCl solutions at 0°C and 200 watts for totally 20 minutes under helium gas atmosphere. The sonicated sample was fractionated by successive precipitation with acetone as the precipitant. For each duplex, several fractions were obtained in large quantities. The weight-average molecular weight M w• the degree of polydispersity M w! M., and the molecular weight distribution were determined for unsonicated, sonicated, and fractionated samples by the gel-permeation-chromatography/low-angle-laser-light-scattering method. The Mw values were reduced to a limit of 10 5 and the Mw/M. values were narrowed to a 2-1.5 range by sonication. These values were further refined by fractionation. The molecular weight distribution profiles of well-defined fractions could be fitted by the logarithmic-normal function. The relationship between intrinsic viscosity and Mw was evaluated for each duplex. The result showed that the rigidity or flexibility of polymer chain depends on the molecular weight of fractionated samples and the kind of duplex examined.KEY WORDS Sonicated DNA and Polynucleotides / Molecular Weights / Molecular Weight Distribution / Intrinsic Viscosity / Precipitational Fractionation / GPC/LALLS / It is well-known that the hydrodynamic and electric properties of the double-stranded helices of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are sensitive to the chain length or molecular weight. 1 -5 In order to study the dependence of these physical quantities on the chain length, a large quantity of respective polymer is needed. In addition, the sample should be fractionated in such a way that the molecular weight and the weight distribution of each fraction are well-defined. The technique of sonication has been employed in the past to prepare fairly large batches of DNA samples, each of which was irradiated for a different period of time and at a varied power level to reduce molecular weights. 2 • 6 • 7 Recently, a preparative technique was developed for narrowing the molecular weight and weight distribution of a sonicated DNA sample by successive precipitational fractionation with

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Changes of weight-average molecular weights (M w) and the molecular weight distributions in terms of weight fraction (g w) 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 M w 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 g w 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 M w 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 M w for the sonicated but unfractionated nucleic acid samples under the present conditions.

The effect of polydispersity on transient electric birefringence (EB) was examined for a dilute solution which contains like macromolecules of varying lengths. The molecules were assumed to be rigid rods of cylindrical symmetry, so that the molecular weight is linearly proportional to length. Polydispersity was expressed by the ratio of the weight-average to the number-average lengths lw/ln. A logarithmic-normal type continuous length distribution was generally used. Calculations were performed for the birefringence-average relaxation time 〈τ〉EB and initial slope 〈S〉EB as a function of the electric field strength E, which is applied prior to the start of the decay process, with the electric parameter (βw)2/2γw, which is related to the weight-average permanent dipole moment (the βw-term) and polarizability anisotropy (the γw-term). Both 〈τ〉EB and 〈S〉EB are very sensitive to E, lw/ln, and (βw)2/2γw. A convenient method was devised for determining the polydispersity parameters (lw/ln and lw) from the weight-averages of relaxation time and initial slope, which are free from the mechanism of field orientation. Examples are given for a polydisperse, rigid rodlike sonicated DNA sample in aqueous solution.