Characterization of acid-denatured DNA by low-angle light scattering

Crystal structure of the DNA-bound VapBC2 antitoxin/toxin pair from Rickettsia felis

Besides their commonly attributed role in the maintenance of low-copy number plasmids, toxin/antitoxin (TA) loci, also called ‘addiction modules’, have been found in chromosomes and associated to a number of biological functions such as: reduction of protein synthesis, gene regulation and retardation of cell growth under nutritional stress. The recent discovery of TA loci in obligatory intracellular species of the Rickettsia genus has prompted new research to establish whether they work as stress response elements or as addiction systems that might be toxic for the host cell. VapBC2 is a TA locus from R. felis, a pathogen responsible for flea-borne spotted fever in humans. The VapC2 toxin is a PIN-domain protein, whereas the antitoxin, VapB2, belongs to the family of swapped-hairpin β-barrel DNA-binding proteins. We have used a combination of biophysical and structural methods to characterize this new toxin/antitoxin pair. Our results show how VapB2 can block the VapC2 toxin. They provide a first structural description of the interaction between a swapped-hairpin β-barrel protein and DNA. Finally, these results suggest how the VapC2/VapB2 molar ratio can control the self-regulation of the TA locus transcription.

Molecular weight and polydispersity of calf-thymus DNA: static light-scattering and size-exclusion chromatography with dual detection

Plausible calf-thymus DNA molecular weight distribution can be obtained by size-exclusion chromatography with dual low-angle light scattering/refractometric detection at sufficiently low flow rate. The distribution extends over three decades of molecular weight and is characterized by weight average molecular weight M(w) = 8418000 and polydispersity index M(w)/M(n) = 5.2. After strongly scattering impurities had been removed from the sample using adsorption properties of the 3 mum mixed-cellulose-ester filter membranes, static light-scattering measurement in flow injection mode was feasible and gave M(w) = 8580000, corroborating the veracity of SEC results.

Low angle light scattering studies on whole, half, and quarter molecules of T2 bacteriophage DNA

Static light scattering measurements have been made at angles as low as 8 degrees on whole, half, and quarter molecules of native, T2 bacteriophage DNA in 0.195 M Na+. The fragments were obtained by high-speed stirring of the native DNA, and fractionated on methylated-albumin-kieselguhr columns. Accompanying measurements of sedimentation coefficients and intrinsic viscosities were made. Because linear extrapolations of light scattering data above 8 degrees for these samples were suspect, the measurements were analyzed by fitting curves calculated from the theory of wormlike coils to experimental curves at c = 0. Results showed that the excluded volume parameter, epsilon, must be used in analyzing the scattering curves; a reasonable value of epsilon was 0.08, in agreement with that found for T7 DNA (Harpst, J. A. 1980. Biophys. Chem. 11:295-302). The persistence length of all three DNAs in this paper was 50 +/- 5 nm, showed no dependence on molecular weight, but was somewhat below that reported previously for T7 DNA (60 nm). Theoretical curves calculated with the preceding parameters had a clear upward curvature in scattering envelopes below 8 degrees for quarter and half molecules, but such curvature was minimal for whole T2 DNA, so that linear extrapolations of experimental data above 8 degrees gave a molecular weight and root-mean-square radius which were nearly the same as those from theory. The molecular weight and radius for whole T2, derived from the comparison of theory and experiment, were 115 X 10(6) and 1,224 nm, respectively. The measurements on T2 DNA were clearly at the upper limit of current techniques.

Analysis of low angle light scattering results from T7 DNA

Selected light scattering data, obtained in earlier studies on T7 DNA in 0.195 M Na+, are analyzed by comparison with calculations from the theory of wormlike coils, both with and without excluded volume effects. The results confirm the conclusion from an earlier criticism, that linear extrapolations of data from the 10 degrees to 20 degrees angular range give incorrect values for the limiting molecular weight, MT, and for the limiting root-mean-square radius, RT. Further, it is shown that the excluded volume parameter, epsilon, must be used to provide a proper fit of calculated curves to experimental data. The revised analysis gives the following parameters for T7 DNA:MT = 25.5 X 10(6); RT = 587 nm; epsilon = 0.08; and the statistical segment length, 1/lambda' = 120 nm. These parameters agree well with other values in the literature. The method of analysis, therefore, provides reliable results from light scattering data on high-molecular-weight, native DNA.