Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements

Abstract

ABSTRACT:The dynamics of three synthetic oligonucleotides d(CG)4, d(CG)6, and d(CGCGTTGTTCGCG) of different length and shape were studied in solution by depolarized dynamic light scattering (DDLS) and time-resolved nuclear Overhauser effect cross-relaxation measurements. For cylindrically symmetric molecules the DDLS spectrum is dominated by the rotation of the main symmetry axis of the cylinder. The experimental correlation times describe the rotation of the oligonucleotides under hydrodynamic stick boundary conditions. It is shown that the hydrodynamic theory of Tirado and Garcia de la Torre gives good predictions of the rotational diffusion coefficients of cylindrically symmetric molecules of the small axial ratios studied here. These relations are used to calculate the solution dimensions of the DNA fragments from measured correlation times. The hydrodynamic diameter of the octamer and dodecamer is 20.5 f 1.0 A, assuming a rise per base of 3.4 A. The tridecamer, d(CGCGTTGTTCGCG), adopts a hairpin structure with nearly spherical dimensions and a diameter of 23.0 f 2.0 A. The DDLS relaxation measurements provide a powerful method for distinguishing between different conformations of the oligonucleotides (e.g., DNA double-helix versus hairpin structure). Furthermore, the rotational correlation times are a very sensitive probe of the length of different fragments. The N M R results reflect the anisotropic motion of the molecules as well as the amount of local internal motion present. The experimental correlation time from N M R is determined by the rotation of both the short and long axes of the oligonucleotide. The contributions of the various correlation times are given by the relative orientation of the internuclear vector with respect to the main axis and the correlation function for internal motion, if it is assumed that the librational motions decay much faster than the overall reorientational motion. Our results are compared with those from N M R relaxation measurements on other short oligonucleotides with lengths of up to 20 base pairs. Various dynamic models for the reorientation of the internuclear vector are applied to their interpretation. The extent of local internal motion is apparently independent of the length and base sequence of the DNA fragments and gives a significant contribution to the effective correlation time measured by the cross-relaxation rate.

NMR studies of dynamics in RNA and DNA by 13C relaxation

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Spin-Labeled Psoralen Probes for the Study of DNA Dynamics

“…NMR results have been interpreted in terms of motions over a time range of 10 orders of magnitude (Opella et al, 1981;Eimer et al, 1990;Borer et al, 1994;Nuutero et al, 1994). However, no good estimates of the time required for either local or collective angular motions of the bases are available, except that they are rapid relative to the tumbling times.…”

Exploring Metal Ion Coordination to Nucleic Acids by NMR

“…Depending on the theoretical ratio q (q = L/d) between the length L and the diameter d of the RNA sequences the molecules can be either modeled as a spherical particle (q < 2) or as a symmetrical cylinder (2 < q <3 0). [73,74] The apparent hydrodynamic radius r H can then be calculated according to Eqn. (4) and (5), respectively.…”