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D E Pulleyblank

Publications and source records attributed to D E Pulleyblank.

29 records · Page 2Linked to original sources
PubMed1982

A topoisomerase from chicken erythrocyte nuclei which does not assemble nucleosome core particles in vitro.

We have examined the ability of a topoisomerase purified from chicken erythrocyte nuclei to mediate nucleosome core assembly in vitro at physiological ionic strength (0.15 M NaCl). Although we have detected limited amounts of spontaneously assembled nucleosome cores at this salt concentration, the addition of this topoisomerase does not increase the amount of assembly observed. Nucleosome assembly was assayed by quantitating the amount of core particle length DNA accumulated with time upon the nuclease digestion of histone-DNA complexes. In addition, the amount of negative supercoils introduced into relaxed closed circular DNA upon nucleosome core particle assembly was determined. Correctly assembled complexes do not protect more DNA from nuclease digestion than random histone-DNA complexes but shift the heterogeneous size distribution of protected fragments to a more homogeneous distribution centred around 145 base pairs. Under our conditions of nucleosome assembly, a second histone-DNA complex which is distinct from the nucleosome core can be detected under physiological ionic strength conditions. This particle does not form in high salt assembly experiments. Similarly, the assembly of this particle is unaffected by the presence or absence of topoisomerase.

Animals↗
PubMed1981

Improved methods for the fluorographic detection of weak beta-emitting radioisotopes in Agarose and acrylamide gel electrophoresis media.

The use of acetic acid as a solvent for diphenyloxazole (PPO) in fluorographic procedures has been investigated. It is demonstrated to be superior to both dimethyl sulfoxide and methanol with respect to its suitability in both agarose and acrylamide gel electrophoresis systems. In addition, a method has been developed for impregnating fragile gels such as those used for immunodiffusion with PPO in preparation for fluorography.

Carbon Radioisotopes↗
PubMed1979

Review: ethidium fluorescence assays. Part 1. Physicochemical studies.

DNA and RNA can be assayed rapidly and very sensitively by exploiting the enhanced fluorescence of ethidium intercalated into duplex regions. By assaying at different pHs and introducing a heating/cooling cycle, a great many physicochemical aspects of DNA and RNA can be studied avoiding the use of radiolabels, and often giving information not otherwise readily obtainable. Studies are described on duplex DNA which involve measurement of extinction coefficients, cross-linking by chemicals, Cot curve analysis as well as estimation of drug-DNA binding constants. The assays can be adapted to investigate multi-stranded nucleic acid structures. The use of covalently closed circular DNA also allows rapid and extremely sensitive measurements of nicking caused by irradiation or drugs.

Animals↗
PubMed1979

Review: ethidium fluorescence assay. Part II. Enzymatic studies and DNA-protein interactions.

Almost all DNA and RNA metabolizing enzymes can be assayed rapidly and very sensitively by exploiting the enhanced fluorescence of ethidium intercalated into duplex DNA or RNA. Denatured DNA and natural RNAs contain duplex regions due to intramolecular hydrogen-bonding and can also be sensitively measured. Where the product is truly single-stranded (e.g. dTn) it can be assayed by adding the appropriate complementary strand (e.g. dAn or rAn). Some of the assays described provide information not readily obtained by other assay procedures. Among the enzymes readily assayed are DNA and RNA polymerases, terminal deoxynucleotidyl transferases, nucleases of all varieties (e.g. single-strand specific, endonucleases including for example AP endonucleases, exonucleases, RNase H, etc.), ligases, topoisomerases including gyrases, and indirectly enzymes such as proteases and superoxide dismutase. DNA binding proteins such as histones and helix destablizing proteins can also be quantitatively assayed.

DNA↗
PubMed1977

The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity.

Systems for gel electrophoresis in the presence of one of the intercalative unwinding ligands, ethidium or chloroquine, have been developed which permit the resolution of highly supercoiled closed circular DNA molecules differing by unit values of the topological winding number, alpha. All native closed circular DNAs examined, including the viral and intracellular forms of SV40 and polyoma DNA, bacterial plasmid DNAs, and the double stranded closed circular DNA genome of the marine bacteriophage, PM2, are more heterogeneous with respect to the number of superhelical turns present than are the thermal distributions observed in the limit products of the action of nicking-closing (N-C) enzyme on the respective DNAs. In the cases of SV40 and polyoma, where it has been shown that the supercoiling is a combined consequence of the binding of the four nucleosomal histones, H2a, H2b, H3 and H4, and the action of N-C enzyme, the breadth of the distributions within the form I DNAs poses specific problems since the work of other laboratories indicates that the number of nucleosomes on the respective minichromosomes falls within a narrow distribution of 21. If it is assumed that all nucleosomes have identical structures, and that the DNA within a nucleosome is not free to rotate, the native DNA would be anticipated to be less heterogeneous than the thermal equilibrium mixtures present in N-C enzyme relaxed SV40 and polyoma DNAs. The absolute number of superhelical turns (at 37 degrees C in 0.2 M NaCl) in virion polyoma DNA has been determined to be 26 +/- 1, which is the same value obtained for virion SV40 DNA. This is consistent with the observations that polyoma DNA has a higher molecular weight, a lower superhelix density, but the same number of nucleosomes as SV40 DNA. In addition, the distributions within the virion and intracellular form I DNAs of both SV40 and polyoma were found to be indistinguishable.Images

Bacteriophages↗
PubMed1977

The quantitation of fluorescence by photography.

A method based on theory has been developed for the photographic quantitation of fluorescent substances. DNA stained with ethidium in agarose gels is used as an example of an application of this method. In the course of developing this method we have demonstrated that the empirical methods employed by others authors can give rise to large systematic errors. We have also developed an approximate method based on photographic theory, avoiding the use of digital integration which is required by the rigorous method.

Bacteriophages↗
PubMed1975

Partial purification of "omega" protein from calf thymus.

Proteins which relax supercoiled DNA, called "omega" proteins, are thought to be involved in DNA replication. Calf thymus is a plentiful source of "omega" protein activity. It has been extensively purified and has been characterized as behaving similarly to other eukaryotic "omega" proteins in completely relaxing either positively or negatively supercoiled DNA, requiring a salt concentration of about 0.2 M NaCl or KCl, and not requiring Mg2+. A transient nick must occur but could not be detected. A new assay for "omega" activity is described which is rapid and sensitive, and depends on the fluorescence enhancement of ethidium intercalating duplex DNA.

Animals↗
PubMed1975

Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers.

Highly purified nicking-closing enzyme from mouse cells in 20-fold enzyme/substrate excess converts closed circular native PM2, ColE1, and Minicol DNA into limit product sets of DNAs. Each set has a mean degree of supercoiling of approximately zero. The individual species in the sets differ by deltatau = +/-1, +/-2, etc., and the relative masses fit a Boltzmann distribution. It was also demonstrated that "nonsupercoiled" closed circular duplex molecules serve as substrates for the nicking-closing enzyme, and that a distribution of topological isomers is generated. Polynucleotide ligase, acting on nicked circular DNA, forms under the same conditions, the same set of closed DNAs. The latter enzyme freezes the population into sets of molecules otherwise in configurational equilibrium in solution.

Animals↗
PubMedDate not supplied

Yeast plasmids have fewer superhelical turns than predicted by the nucleosome repeat of yeast DNA.

The superhelical density of three Saccharomyces cerevisiae plasmids was determined with respect to a defined reference state during vegetative growth and stationary phase. The levels of supercoiling determined were approximately 20% lower than predicted by comparisons with SV40 DNA and reconstituted minichromosomes using histones from higher eukaryotes. In two different plasmids with the ARS1 origin of replication, the level of supercoiling changed substantially as the host cells entered stationary phase. Supercoiling of the endogenous 2-microns plasmid during vegetative growth was lower than in the ARS1-containing plasmids but did not change significantly upon entry of the cells into stationary phase.

Cell Cycle↗