The amplitude of local angular motion of purines in DNA in solution

Abstract

Nuclear magnetic resonance and optical experiments are combined to determine 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 exchange 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 dilute sample yield the hydrodynamic radius, RH = 9.94 +/- 0.2 A, 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 2H-nmr spectrum, in particular the line width, using recently developed theory for the transverse relaxation rate (RQ2) together with essential information about the collective motions from these and other optical studies. When the principal-axis frame of the electric field gradient tensor is assumed to undergo overdamped libration around each of its three body-fixed axes in an isotropic deflection potential, then the rms amplitude of local angular motion around any single axis is found to lie in the range 10 degrees-11 degrees, provided the high DNA concentration acts to enhance the viscosity, and is about 9 degrees-11 degrees, if it acts to produce end-to-end dimers. The 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 internuclear vector of 9 degrees-10 degrees, depending upon its orientation with respect to the helix axis. In all of these analyses, full account 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 the model (potential), provided that isotropic rotation around the same number of axes is allowed and that one compares rms angles of the same dimensionality. The rms amplitudes of local angular motion in solution are comparable to those observed for the same sequence at low levels of hydration in the solid state.

Water molecule binding and lifetimes on the DNA duplex d(CGCGAATTCGCG)2

“…The values of the correlation time in Tables 1 and 2 are larger suggesting that there is some aggregation. Light-scattering and NMR studies on the dodecamer used in the present study also have reported rotational correlation times that are shorter by as much as a factor of three than the present data suggest (Eimer et al, 1990;Nuutero et al, 1994). The concentrations of DNA used in these studies are very high and aggregation is likely (Nuutero et al, 1994); however, aggregation does not change the arguments because the magnetic relaxation dispersion experiment reports both the strength and the correlation time for the relaxation coupling.…”

Kinetics of DNA hydration

“…The second simpli®cation is the neglect of the anisotropy in the rotational diffusion of the DNA duplex. This motion is well described by hydrodynamic theory (Tirado & Garcia de la Torre, 1980), modeling the duplex as a rigid cylinder of radius 10 A Ê and length 12 Â 3.4 A Ê (Nuutero et al, 1994). Using the viscosity of H 2 O at 10 C, we obtain for the three second-rank rotational correlation times of a symmetric top (Woessner, 1962): 8.1, 6.7 and 4.4 ns.…”

DNA persistence length revisited

“…The average hydrodynamic radius obtained using the Hagerman-Zimm/Newman model (14.7 Ϯ 0.4 Å) is somewhat larger than the values of 10 -12.5 Å determined by fitting dynamic light scattering (DLS) 31 and fluorescence polarization anisotropy (FPA) [47][48][49] data (see Bloomfield et al for a review of various hydrodynamic methods of characterizing DNA conformation 1 ). A hydrodynamic radius of 14.7 Å would imply that the DNA helix in solution is surrounded by a relatively immobile layer of water molecules approximately 5 Å thick.…”