Rolf Brandes

Interaction of water with oriented DNA in the A- and B-form conformations

High resolution 2H nuclear magnetic resonance (NMR) was used to investigate the interaction of D2O with solid samples of uniaxially oriented Li-DNA (B-form DNA) and Na-DNA (A- and B-form DNA). At low levels of hydration, 0 approximately 4 D2O/nucleotide, the 2H spectra shows a very weak (due to short T2) broad single resonance, suggestive of unrestricted rotational diffusion of the water. At approximately 5 or more D2O/nucleotide, the Li-DNA (B-form) spectra suddenly exhibit a large doublet splitting, characteristic of partially ordered water. With increasing hydration, the general trend is a decrease of this splitting. From our analysis we show that the DNA water structure reorganizes as the DNA is progressively hydrated. The D2O interaction with Na-DNA is rather different than with Li-DNA. Below 10 D2O/nucleotide Na-DNA is normally expected to be in the A-form, and a small, or negligible splitting is observed. In the range 9-19 D2O/nucleotide, the splitting increases with increasing hydration. Above approximately 20 D2O/nucleotide Na-DNA converts entirely to the B-form and the D2O splittings are then similar to those found in Li-DNA. We show that the complex Na-DNA results obtained in the range 0-20 D2O/nucleotide are caused by a mixture of A- and B-DNA in those samples.

Static disorder and librational motions of the purine bases in films of oriented Li-DNA☆

Solid-state 2H nuclear magnetic resonance line shapes have been obtained from folded films of oriented Li-DNA molecules with the purine bases selectively labeled with deuterium at the 8-position. From line shape simulations, the static base tilts as well as the anisotropic motional amplitudes were determined as a function of hydration level and temperature. It was found that the average tilt angle of the bases is close to 0 degrees and at a hydration of ten water molecules per nucleotide the distribution width of tilt angles about this average cannot be larger than 9 degrees (standard deviation). A slightly increased distribution width is observed at low hydration levels. The motional amplitudes are hydration dependent, with the tilting motion ranging from 4 degrees for the driest, up to 15 degrees for the wettest sample, and slightly larger amplitudes are observed for the twisting motion. The amplitude of the twisting motion is unaffected by a temperature decrease down to -60 degrees C, in contrast to the tilting motion that is suppressed at low temperatures.

Generation of tailored radiofrequency pulses by a simple audiofrequency filter method. II. Analysis

Abstract In an earlier paper, a novel method was presented for obtaining frequency-selective excitation in NMR. In this paper, the pulse shape of the rf pulse is calculated from the transfer function of common low-frequency filters and the response of the magnetization to these pulses is then solved by a numerical solution of the Bloch equations. As an example, the response of the spins to a pulse that is selective within a band of frequencies is calculated and compared with experimental results.

Effects of Hydration on the DNA Base Motion

The conformational flexibility of native deoxyribonucleic acid (DNA) is studied using 2H nuclear magnetic resonance (NMR) at two frequencies. By selective labeling of the adenine (A) and the guanine (G) bases with deuterium, a probe of the purine dynamics is obtained. When the DNA hydration is increased, the NMR spectrum shows a slightly reduced spectral width because of an increased amplitude of purine motion. Simultaneously, the spin-lattice relaxation time T1 decreases, indicating increased frequency of the motion. This motion cannot be explained in terms of a random local motion with a single correlation time. Instead, the relaxation data suggest that the DNA purine bases execute a pseudo-coherent motion involving several bases (1).