Sedimentation-viscosity studies of high molecular weight DNA

Size and average density spectra of macromolecules obtained from hydrodynamic data

It is proposed to normalize the Mark-Kuhn-Houwink-Sakurada type of equation relating the hydrodynamic characteristics, such as intrinsic viscosity, velocity sedimentation coefficient and translational diffusion coefficient of linear macromolecules to their molecular masses for the values of linear density M(L) and the statistical segment length A. When the set of data covering virtually all known experimental information is normalized for M(L), it is presented as a size spectrum of linear polymer molecules. Further normalization for the A value reduces all data to two regions: namely the region exhibiting volume interactions and that showing hydrodynamic draining. For chains without intachain excluded volume effects these results may be reproduced using the Yamakawa-Fujii theory of wormlike cylinders. Data analyzed here cover a range of contour lengths of linear chains varying by three orders of magnitude, with the range of statistical segment lengths varying approximately 500 times. The plot of the dependence of [eta]M on M represents the spectrum of average specific volumes occupied by linear and branched macromolecules. Dendrimers and globular proteins for which the volume occupied by the molecule in solution is directly proportional to M have the lowest specific volume. The homologous series of macromolecules in these plots are arranged following their fractal dimensionality.

Studies on the fluorescence reaction between nucleic acid and the complex of cobalt(II) with 5-(3-fluoro-4-chlorophenylazo)-8-sulfonamidoquinoline and its applications

Based on the enhancement of the fluorescence intensity of the complex of 5-(3-fluoro-4-chlorophenylazo)-8-sulfonamidoquinoline (FCPBSQ) with Co(2+) by nucleic acid in the presence of Tween 80 and in the weakly basic medium, a fluorescence method for the determination of nucleic acid was proposed. The calibration graphs for the determination of denatured calf thymus DNA (ct DNA), fish sperm DNA (fs DNA), and yeast RNA (yt RNA) were obtained in concentration ranges 0.050-4.0, 0.10-3.0, and 0.050-3.0 microg/ml with limits of detection of 0.010, 0.030, and 0.020 microg/ml, respectively. The method has been satisfactorily used for the determination of DNA in wheat cell extraction and ct DNA, fs DNA, and yt RNA in synthetic samples. Investigations on the binding mode by the Scatchard plots method suggested that both intercalation and electrostatic binding modes existed in this system.

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.

Comparsion of the oxygen-enhancement ratio for gamma-ray-induced double-strand breaks in the DNA of bacteriophage T7 as determined by two different methods of analysis

Bacteriophage T7 was irradiated in a protecting medium under nitrogen and oxygen with 60Co gamma-rays. Double-strand breaks were measured by sucrose-gradient sedimentation and by boundary-sedimentation analysis. Both methods showed that the presence of oxygen during irradiation enhanced the production of double-strand breaks. This is at variance with a recent report which suggests that boundary-sedimentation analysis does not show an effect of oxygen. The discrepancy must be ascribed to differences in interpretation of the sedimentation data.

Metallointercalation reagents. 2-hydroxyethanethiolato(2,2',2'-terpyridine)-platinum(II) monocation binds strongly to DNA by intercalation

The red, cationic complex 2-hydroxy-ethanethiolato(2,2',2''-terpyridine)platinum(II), [(terpy)-Pt(SCH(2)CH(2)OH)](+), binds strongly to DNA by a mechanism involving intercalation. By means of fluorescence spectroscopy, the platinum complex was shown to inhibit competitively the binding of the intercalating dye ethidium bromide to calf thymus DNA. This platinum complex increases the viscosity of calf thymus DNA, raises the melting temperature by up to 5 degrees , and exhibits induced circular dichroism when bound to the DNA. The closed circular viral DNA from bacteriophage PM2 is unwound by the complex in a manner that is similar to that of ethidium bromide and with an unwinding angle that appears to be slightly less than that of ethidium. Studies of the related complex [(terpy)PtCl](+), which has a substitutionally more labile chloride ligand, suggest that it also intercalates, especially at [DNA-P]:[Pt] ratios greater than 2. The potential utility of these new metallointercalation reagents as heavy atom probes in fiber diffraction or electron microscopic studies of the interaction process is discussed.

Chromatography of transforming deoxyribonucleic acid on methylated albumin and by gel filtration

1. Native DNA from two strains of Bacillus subtilis was chromatographed by stepwise elution from MAK (methylated albumin on kieselguhr). 2. Transforming activity was confined to two out of the three main fractions, activity being distributed between the two peaks differently for DNA from the different strains. 3. Fractionation of DNA from both strains on 2% agarose gel gave two components. Approx. 75% of the material was eluted within the void volume of the column. Approx. 25% of the material consisted of degradation products of lower molecular weight. 4. Chromatography on MAK of the material of high molecular weight eluted from agarose gel gave a number of peaks differing in molecular weight, indicating that degradation of the DNA takes place during chromatography on MAK. 5. The distribution of transforming activity among the fractions from MAK suggests that degradation occurs preferentially in certain regions of the DNA.

A comparison of the number of nucleotides per unit length in Escherichia coli and phage T4 chromosomes

The grain density produced in radioautographs by fully labeled bacteriophage T(4) chromosomes was compared with the grain densities produced by fully labeled and half-labeled exponential phase Escherichia coli chromosomes. Taking into account the differing molar proportions of thymidine in E. coli and T(4) chromosomes, it was seen that the two types of chromosomes have approximately equal numbers of nucleotides per unit length, indicating that their structures are the same. Using molecular weight estimates in the literature for the T(4) and related T(2) chromosomes, and the lengths obtained in the radioautographs, the T(4) chromosome was estimated to have between 1.9 and 3.6 nucleotides/3.4 A. On the basis of these values alone, the E. coli and T(4) chromosomes could be either one Watson-Crick helix in a form about equal to or more condensed than the B form, or two helices more stretched out than the B form. The length of the T(4) chromosome was 48.7 +/- 4.1 mu when dried on the dull side of Millipore membranes and 42.3 +/- 4.8 mu on the shiny side, under the conditions used. Thus, the supporting surface apparently affects the configuration of a chromosome. Further evidence is also presented in support of the conclusion that the E. coli chromosome undergoes semi-conservative replication.