DNA orientation during gel electrophoresis and its relation to electrophoretic mobility.
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DNA, Viral↗
Biomedical subjects
I Hurley
Publications and source records attributed to I Hurley.
Sequence-determined DNA separations.
The variation in electrophoretic mobility of DNA under conditions of marginal helix stability provides a useful means for investigation of the relation between the helix-random chain transition and base sequence in natural DNA and a powerful procedure for separation of DNA molecules according to sequence. The use of statistical mechanical theory for analysis of the transition equilibria together with new, simplified theoretical considerations on the effect of strand unravelling on mobility have shown that the gel behavior is predictable for known sequences. A number of the distinctive consequences of the theory and their correspondence with the properties of real molecules have been demonstrated. These include the extremely close cooperative linkage of large blocks of bases into domains, the existence of sharp boundaries between domains, the major role of nearest-neighbor interaction in determining stability, the dependence of domain structures on neighboring and more remote sequences, and the depression of domain melting temperature if the sequence lies at the end of a molecule. New and unusual applications derive from the possibility of separating DNA molecules by properties of their sequence. Exceedingly complex mixtures, such as the sum of all fragments produced by the action of a sixbase specific restriction endonuclease on a complete bacterial genome, can be resolved completely. Additional inserted sequences are easily discerned. The difference of a single base pair in a molecule permits detection and isolation of mutant sequences. The need for full sequential analysis of long molecules for characterization of mutants can be reduced by localizing a change within a small fragment.
Bacteriophage lambda↗
Torsional motion and elasticity of the deoxyribonucleic acid double helix and its nucleosomal complexes.
Torsional thermal oscillations of the DNA double helix within the electron paramagnetic resonance (EPR) time scale (10(-10)-10(-3) s) as indicated by a rigid, intercalating probe are much smaller in the spacer segment between nucleosomes in chromatin than in long, free DNA molecules. Still smaller DNA oscillation is indicated in intact nuclei and yet smaller if the nuclei have been treated with glutaraldehyde. The values of EPR measurements are not affected by the loading density of probe. If the probe were capable of substantial oscillations or movement different from that of the helix, those oscillations would be expected to dominate the spectra when movement of the helix is restrained. We conclude that the correlation time for torsional movement of free DNA inferred from EPR spectra is characteristic of the double helix and that there is no significant independent motion of the probe. The correlation time for the DNA double helix in molecules longer than approximately 500 base pairs is close to 30 ns, corresponding to an elastic constant of 1.5 X 10(-19) ergs cm for deformation by twisting. The motions observed in chromatin are consistent with a model in which spheres of 50-60-A radius are connected by simple elastic rods with the length of spacer DNA and the same elastic constant. The spin-labeled ethidium probe has been characterized in detail by nuclear magnetic resonance, infrared, fluorescence, and visible light spectroscopy. The binding equilibria are consistent with the hypothesis that strongly immobilized probe molecules are preferentially bound to spacer DNA.
Animals↗