DNA ORIENTATION IN SHEAR-FLOW

The linear dichroism (LD) has been measured for DNA molecules 239-164, 000 base pairs long oriented in shear flow over a large range of veloc ity gradients (30-3,000 s-1) and ionic strengths (2-250 mM). At very l ow gradients, the degree of DNA orientation increases quadratically wi th the applied shear as predicted by the Zimm theory [J. Zimm, (1956) Chemical Physics, Vol. 24, p. 269]. At higher gradients, the orientati on of fragments greater-than-or-equal-to 7 kilobase pairs (kbp) increa ses linearly with increasing shear, whereas the orientation of fragmen ts greater-than-or-equal-to 15 kbp shows a more complicated dependence . In general, the orientation decreases with increasing ionic strength throughout the studied ionic strength interval, owing to a decrease i n the persistence length of the DNA. The effect is most dramatic at io nic strengths below 10 mM, and is more pronounced for longer DNA fragm ents. For fragments greater-than-or-equal-to 15 kbp and velocity gradi ents greater-than-or-equal-to 100 s-1, the orientation can be adequate ly described by the empirical relation: LD(r) = - (k1 . G)/(k2 + G), w here k1 is a linear function of the square root of the ionic strength and k2 depends on the DNA contour length. Since the DNA persistence le ngth can be represented as a linear function of the reciprocal square root of the ionic strength [D. Porschke, (1991) Biophysical Chemistry, Vol. 40, p. 169], extrapolation of the empirical relation provides in formation about the stiffness of the DNA fibers. (C) 1993 John Wiley & Sons, Inc.