Internal motions in DNA.

Abstract

We have measured the 31P and 1H NMR parameters of fractionated double-stranded DNA fragments 600, 300, and 150 base pairs long. The results indicate that, inside an intact double helix, both the deoxyribose and the sugarphosphate backbone of the helix fluctuate substantially from their equilibrium geometry. The time constant for those coupled motions is of the order of 1 nsec.The DNA structure proposed from x-ray diffraction studies is rigid. In that structure, nucleotide components of B-form DNA are locked into a 10-fold helix with base pairs oriented perpendicular to the helix axis (1).Although this DNA structure has served as an important tool in the practice of molecular biology, it is now evident that in solution B-form DNA is not rigid. The time-averaged flexibility of the DNA helix in solution approximates that of a uniform elastic wormlike coil. Recently, Barkley and Zimm have calculated the dynamic properties of the wormlike coil model (2). Their calculations predict that the average fluctuation in the twist angle between bases in DNA is about 50. The corresponding fluctuation in bending of the helix axis between bases is calculated to be about 40. Although nonexponential, both bending and twisting motions have major components with time constants between 1 and 100 nsec.NMR is a powerful tool for detecting structural fluctuations. If the motions suggested from the J3arkley-Zimm calculations involve substantial changes in DNA geometry in the time range from 1 to 100 nsec, then these motions should be detectable by both 1H and 31P NMR. Several authors have reported 31p NMR measurements on DNA (3-7). In general, it was found that when the DNA is shorter than the persistence length, it displays a 31p linewidth of about 20-30 Hz and a alp T1 relaxation time near 3 sec (8-10).Klevan et al. (4) have suggested that the 31P NMR properties (Ti, T2, nuclear Overhauser enhancement) of DNA must result from an internal motion of phosphate, independent of the overall motion of the helix. They have modeled that motion as being a rotation of backbone phosphate about C4'-C5' and P-O (w) bonds with a time constant of about 0.4 nsec. Independently, Bolton and James (5) have proposed a similar model to explain the 31P NMR properties of their DNA and RNA preparations. The two models are alike in that they consider motion within the phosphate backbone to be the only motion in the helix.Here we present a NMR study of well-defined doublestranded DNA fragments, 150-600 base pairs long. We show that, in addition to 31P NMR spectra, 1H spectra can be observed for DNA. The NMR properties of both nuclei suggest that a B-form helix experiences large fast internal motions, the best fit to the data specifying that at room temperature both the deoxyribose and the phosphate backbone of the helix fluctuate in a concerted fashion from their equilibrium geometries with a time constant near 1 nsec.The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "adverti...

Temperature dependence of fast fluctuations in single- and double-stranded DNA molecules: a neutron scattering investigation

“…These structural slow motions, like those involving bending and twisting of the double helix, allow and control the accessibility of the structure to host molecules such as nucleases and polymerases. Through nuclear magnetic resonance (NMR) studies [2], it has been shown that, inside an intact double helix, the deoxyribose and the sugar-phosphate backbone fluctuate from their equilibrium geometry, and bases undergo libration motions with correlation times of the order of nanoseconds or longer. Electronic spin resonance measurements [3] have revealed the existence of base motions on the nanosecond timescale in RNA and DNA single-and double-stranded systems.…”

Molecular motion of DNA as measured by triplet anisotropy decay.

“…For that reason, we assayed the DNA preparations by redigesting the samples analytically with nuclease SI, using the protocol described in ref. 2. Under these assay conditions, any single-stranded DNA is digested completely (2).…”

“…Recently, however, evidence has accumulated suggesting that the structure ofthe helix fluctuates substantially (1)(2)(3)(4)(5)(6)(7)(8). It has been shown by NMR techniques (1)(2)(3)(4) that the helix experiences large fast motions in the nanosecond time range. Fast motions in the 1-to 100-ns time range have also been seen by fluorescence anisotropy methods (5-7), using as a probe ethidium bromide intercalated in DNA, and by measuring the ESR line shapes of spin-labeled intercalated dyes (8).…”

“…Data were stored on a Biomation 6500 transient recorder with a maximum sample rate of2 ns per point. A microcomputer was used to control the transient recorder and to signal average.The computer analyzed the two files stored to compute the time-resolved anisotropy decay [1] I~t = AI 11(t) -Wl (W)AIII(t) + 2W (t) and the isotropic absorbance decay a(t) = AII(t) + 2A11(t), [2] where AIII(t) and AI(t) refer to monitoring beam intensity changes for polarization parallel and perpendicular, respectively, to the excitation pulse polarization. Since typical transmission changes were 5% or less (20 mV out of 500 mV), intensity changes were directly proportional to changes in absorbance.…”

Propagation of elastic waves in DNA

“…This constantly exchanges energy and motion with solvent molecules; thus, internal motions within the structure are set up. These are evidenced from spectroscopic probes: fluorescence depolarization measurements of DNA bound drug molecules [7], changes of NMR spectral line widths [8], light scattering studies of DNA [9], and hydrogen ion-exchange reaction of DNA bases with solvent molecules [i0]. These are sufficient to show that the DNA double helix possessesa d?amic structure.…”