Effects of Na+ on the persistence length and excluded volume of T7 bacteriophage DNA.

Total intensity, Rayleigh light scattering has been used to measure the rms radius, second virial coefficient, persistence length, and excluded volume of homogeneous T7 bacteriophage DNA as a function of Na+ concentration (0.005 to 3.0 M). All parameters decrease sharply as [Na+] increases, and tend to level off at high Na+. The variation of persistence length with [Na+] is consistent with predictions from counterion condensation theory.

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.

Column purification of adenovirus cores.

A simple and efficient technique for purifying adenoviral chromatin (nucleoprotein cores) with Sephacryl S-1000 is described. This method is significantly faster than previous methods and gives a higher degree of purity with an increased recovery of the nucleoprotein. In addition, the structural integrity of the cores is maintained.

Ionic effects on the structure of nucleoprotein cores from adenovirus.

Nucleoprotein cores, prepared from adenovirus type 5 with a deoxycholate/heat treatment, consist of the viral DNA and two major internal proteins. The core particles exhibit structural characteristics that are highly reproducible and dependent on their ionic environment. In low-ionic-strength buffer, the cores had a sedimentation coefficient of 180 S and appeared in the electron microscope as homogeneous particles with distinct centers from which numerous arms and loops radiated. Condensation of the cores was induced by Mg2+ or Ca2+ over the range 0 to 1 mM. The sedimentation coefficient increased monotonically with divalent cation concentration, reaching a maximum of 405 S in 1 mM Mg2+. A corresponding condensation in the core structure was observed by electron microscopy. Increasing concentrations of NaCl also produced a conformational change in the cores, with an almost linear increase in sedimentation velocity up to 274 S in 0.04 M NaCl. Between 0.05 and 1.0 M NaCl, the cores were insoluble. In 2.0 M NaCl, the cores were again soluble with an s20,w of 228 S. Under all ionic strength conditions in which the cores were soluble, both core proteins remained bound to the DNA.

In vitro replication directed by a cloned adenovirus origin.

A 5.7-kb recombinant plasmid, called XD-7, contains the terminal XbaI-E fragment from the left end of type 2 adenovirus cloned into the EcoRI site of pBR322. An average of 9% +/- 1% of input supercoiled, protein-free XD-7 DNA replicated as rolling circles with single-stranded tails ranging up to unit length and longer in reaction mixtures containing nuclear and cytoplasmic extracts from adenovirus-infected, but not uninfected, HeLa cells. The adenovirus origin was mapped on XD-7 by electron microscopy at the left boundary of the cloned adenovirus segment. Since replication proceeded rightwards, we conclude that the adenovirus l strand was displaced during replication. No origin was located at or near the EcoRI site on pBR322. Reversing the orientation of the adenovirus origin reversed the direction of replication, and deletion of the adenovirus origin abolished replication.

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.

Physical properties of nucleoprotein cores from adenovirus type 5.

Analytical ultracentrifugation, thermal denaturation, and electron microscopy have been used to study nucleoprotein core particles, obtained from disrupted type 5 adenovirus and partially purified on glycerol density gradients. Electron microscopy at low salt concentrations has shown that the cores are homogeneous particles with characteristic structures, which vary with conditions of observation from a fairly loose network of fibers to a highly condensed, compact particle. Sedimentation measurements in the analytical ultracentrifuge, both by boundary and by band techniques, show that the cores are relatively homogeneous in solution and have sedimentation coefficients near 185 S at low salt concentrations, about 243 S in 1 or 2 M NaCl, and 376 S in 1 mM MgCl2. Correlation of sedimentation data with electron microscopic observations suggests that the 185 S particle has a loose, fibrous structure, while the faster species are more highly condensed particles. The melting temperature of the cores in 5 mM Tris/HCl is 79 degrees C, which is 10 degrees C higher than the Tm for purified, viral DNA. This indicates that the protein enhances the stability of DNA in the nucleoprotein complex.

Electron microscopy of adenovirus cores.

Adenovirus type 5 'cores' prepared by heating in the presence of deoxycholate and partially purified on a glycerol density gradient could be visualized as roughly isometrical particles with a condensed centre from which twisted filaments or loops of DNA emanated. This compact structure was readily dispersed by spreading on distilled water or by treatment with EDTA, Nonidet, DNase or trypsin. Spreading with Nonidet was particularly effective in unfolding the cores and revealing long filaments about 100 A thick presumably of the virus nucleoprotein. Subunits (about 30 to 60 A in diam.) could be seen free in the DNase-treated cores, suggesting a particulate nature of one or both of the core proteins.