THE AMPLITUDE OF LOCAL ANGULAR MOTION OF PURINES IN DNA IN SOLUTION

Nuclear magnetic resonance and optical experiments are combined to det ermine the rms amplitude of local angular motion of purines in DNA in solution. A 12 base-pair duplex DNA with the sequence d(CGCGAATTCGCG)( 2) is deuterated at the H8 positions of adenine and guanine by exchang e with solvent at 55 degrees C. The deuterium nmr spectrum of this DNA is measured at 30 mg/mL at 30 degrees C in an 11.76 Tesla magnet (76. 75 MHz). The time-resolved fluorescence polarization anisotropies (FPA ) of this same sample and also a greatly diluted sample (0.215 mg/mL) were measured after addition of ethidium. FPA measurements of the dilu te sample yield the hydrodynamic radius, R(H) = 9.94 +/- 0.2 Angstrom, while those at the nmr concentration are employed to characterize the collective motions in terms of either an enhanced viscosity or dimer formation. The rms amplitude of local angular motion was determined by analyzing the H-2-nmr spectrum, in particular the line width, using r ecently developed theory for the transverse relaxation rate (R(2)(Q)) together with essential information about the collective motions from these and other optical studies. When the principal-axis frame of the electric field gradient tenser is assumed to undergo overdamped librat ion around each of its three body-fixed axes in an isotropic deflectio n potential, then the rms amplitude of local angular motion around any single axis is found to lie in the range 10 degrees-11 degrees, provi ded the high DNA concentration acts to enhance the viscosity, and is a bout 9 degrees-11 degrees, if it acts to produce end-to-end dimers. Th e proton nmr relaxation data of Eimer et al. are reanalyzed and shown to yield an rms amplitude of angular motion of the cytosine H5-H6 inte rnuclear vector of 9 degrees-10 degrees, depending upon its orientatio n with respect to the helix axis. In all of these analyses, full accou nt is taken of the collective twisting and bending deformations, which have a small but significant effect on the results. It is shown that the rms amplitudes of local angular motion do not depend strongly on t he model (potential), provided that isotropic rotation around the same number of axes is allowed and that one compares rms angles of the sam e dimensionality. The rms amplitudes of local angular motion in soluti on are comparable to those observed for the same sequence at low level s of hydration in the solid state. (C) 1994 John Wiley & Sons, Inc.