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A R Morgan

Publications and source records attributed to A R Morgan.

At least 91 records · Page 5Linked to original sources

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↗

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↗

Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded.

(Pyrimidine)n . (purine)n DNAs of repeating sequences form a distinctive complex on lowering the pH below 6. Previously this complex was thought to be tetra-stranded. The present work is inconsistent with this view, and four lines of evidence show that the complex consists of a triplex together with a poly d(purine) possessing secondary structure. Formula: (see text). (a) S1 nuclease digestion leads to degradation of 50% of the poly d(purine) content of the pH 5-induced complex. (b) Buoyant density studies demonstrate that there is no interaction between the triplex and added free poly d(purine) and also that the complex formed from duplex DNA contained poly d(purine) which is free to form a triplex on addition of an appropriate poly d(pyrimidine) in the correct stoichiometry. (c) The hyperchromic shifts of the triplex and poly d(purine), upon melting, are mutually independent. (d) The circular dichroism spectrum of the complex is simply the weighted average of a triplex together with a free poly d(purine). The triplexes have tm's approximately 20 degrees higher than the corresponding duplexes under comparable conditions and they are extremely resistant to various deoxyribonucleases; properties which may prove useful for their isolation from natural sources.

Base Sequence↗

A novel assay for endonucleases acting at apurinic sites and its use in measuring AP endonuclease activity in repair-deficient mutants of Saccharomyces cerevisiae.

A quick and convenient assay for depurination and AP endonuclease activities has been developed. (The term 'AP endonuclease' refers to a nuclease that acts on apurinic and probably apyrimidinic sites on DNA.) It is based on the observation that different topological forms of DNA, such as open circular DNA and covalently closed circular DNA, bind different amounts of the fluorescent intercalator ethidium bromide, and can therefore be distinguished by their fluorescence. This assay has been used to measure AP endonuclease activity in 22 repair-deficient mutants of Saccharomyces cerevisiae. All 22 had normal or nearly normal AP endonuclease activity. The AP endonuclease activity was partially characterized.

Apurinic Acid↗

Analysis of DNA structure by hydroxyapatite columns and ethidium bromide fluorescence techniques. A comparative study and effect on DNA binding.

Seven duplex DNA preparations have been structurally analyzed by hydroxyapatite column chromatography and an ethidium bromide fluorescence technique. Significant contamination of one preparation with single-stranded DNA was detected by hydroxyapatite column chromatography. Five of the other six preparations were found to contain significant single-stranded regions by the ethidium bromide fluorescence technique. Synthetic poly dAT was found to be duplex in structure. The presence of single-stranded regions considerably influenced DNA binding results in a radioimmunoassay.

Antibodies↗

Unique structures formed by pyrimidine-purine DNAs which may be four-stranded.

Pyrimidine-purine DNAs with repeating sequences can be made to undergo a reversible transition to possibly a tetra-stranded complex. Physicochemical characterization of the new structures and model building are consistent with, in the case of d(TC)n-d(GA)n, a tetra-stranded complex forming by the addition of d(GA)n to the remaining space in the major groove of the triple-stranded complex d(TC)n-d(GA)n-d(CT)n. A possible role for tetra-stranded complexes in chromosome condensation is suggested by the natural occurrence of repeating sequence pyrimidine-purine DNAs and the properties of condensed chromosomes.

Base Sequence↗

A comparison of the circular dichroism spectra of synthetic DNA sequences of the homopurine . homopyrimidine and mixed purine- pyrimidine types.

We have obtained the ultraviolet circular dichroism spectra of two repeating trinucleotide DNAs, poly [d(A-G-G).d(C-C-T)] and poly[d(A-A-G).d(C-T-T)], that have all purines on one strand and all pyrimidines on the other. These spectra, together with spectra of other synthetic polymers, can be combined to give 3 first-neighbor calculations of the spectrum of poly[d(A).d(T)] and 2 first-neighbor calculations of the spectrum of poly [d(G).d(C)]. The results show (1) that first-neighbor calculations utilizing only spectra of homopurine.homopyrimidine DNA sequences are no more accurate than are similar calculations that involve spectra of mixed purine-pyrimidine sequences, demonstrating that double-stranded homopurine.homopyrimidine sequences do not obviously belong to a special class of secondary conformations, and (2) that the wavelength region above 250 nm in the CD spectra of synthetic DNAs is least predictable from first-neighbor equations, probably because this region is especially sensitive to sequence-dependent conformational differences.

Base Sequence↗

A rapid method for the measurement of the unwinding angle of intercalating agents and the superhelix density of circular DNAs.

By incubating covalently-closed circular DNA in the presence of calf thymus topoisomerase and unwinding ligands (intercalating drugs and proteins) DNAs of different superhelix density can be produced. These changes in superhelix density can be monitored by an ethidium fluorescence assay, since the level of ethidium binding varies with the superhelix density of a DNA. Thus the equivalence point, in a titration between an unwinding ligand and a supercoiled DNA, can be found. This forms the basis for an extremely rapid method for measuring unwinding angles and superhelix densities. Results are presented which agree well with those reported by previous authors using different techniques. The present method compares very favourably with others when evaluated in terms of rapidity, cost of materials, cost of equipment, accuracy and also applicability.

Acridines↗

DNA nicking--closing activity from salmon testis.

Salmon testis is a good source of DNA nicking--closing (N--C) enzyme, as expected for rapidly proliferating cells. Partial purification was obtained but it resulted in an unstable form of N--C enzyme. Cruder fractions are useful for relaxing supercoiled DNA under conditions where other N--C enzymes are inactive. The enzyme is very tolerant of salt concentration, with activity still detectable at 0.6 M NaCl. It is also active at low temperatures with reasonable activity at 0 degrees C. However, at temperatures greater than 25 degrees C it is rapidly inactivated. Otherwise, its properties are similar to other eucaryotic N--C enzymes.

Animals↗

The purification and characterization of a DNA nicking-closing enzyme from Bacillus megaterium.

Although several eucaryote DNA nicking--closing (N--C) enzymes have been characterized, only the Escherichia coli enzyme has been extensively studied amongst procaryotes. The latter enzyme is distinctly different from the eucaryotic enzymes and we have therefore purified the N--C enzyme from Bacillus megaterium to determine if procaryotes form a distinctive class of N--C enzymes. The purified B. megaterium N--C enzyme has a molecular weight of 120,000, only partly relaxes negative supercoils, does not affect positive supercoils, requires Mg2+, and is inhibited by 0.2 M KCl. The enzyme is also inhibited by 1 mM nalidixic or oxolinic acids but unaffected by novobiocin. A crude N--C enzyme preparation from Micrococcus luteus shows very similar properties.

Bacillus megaterium↗

Evaluation of a standardised assay for the measurement of antibodies to double-stranded (native) DNA.

A standardised commercially available radioimmunoassay kit for the detection of antibodies to native DNA (N-DNA) has been evaluated in clinical practice. This test system is shown to be a reliably reproducible method of detecting these antibodies. In addition, evaluation of the purity of the radiolabelled test antigen in this assay has shown it to be almost entirely double stranded (native) DNA with virtually no contamination with single stranded (denatured) DNA, and with few areas of single stranded breaks or ends in the duplex molecule. The inclusion of known standards and precise characterisation of the DNA has partially overcome variability in results and provides for interlaboratory standardisation which is lacking in the techniques used at present.

Antibodies, Antinuclear↗

Studies on the mechanism of DNA cleavage by ethidium.

Ethidium causes the cleavage of DNA via a light and oxygen dependent process. Using covalently closed circular DNA as a substrate, the saturation kinetics and the dependence on superhelical density of the cleavage indicate that intercalated ethidium is mainly responsible for nicking DNA. Superoxide dismutase has little effect on the reaction and catalase none. Lowering the pH inhibited the reaction. The reaction mechanism and its use in determining superhelical densities of covalently closed circular DNA's are discussed.

Binding Sites↗

Studies related to antitumor antibiotics. Part V. Reactions of mitomycin C with DNA examined by ethidium fluorescence assay.

The cytotoxic action of the antitumor antibiotic mitomycin C occurs primarily at the level of DNA. Using highly sensitive fluorescence assays which depend on the enhancement of ethidium fluorescence only when it intercalates duplex regions of DNA, three aspects of mitomycin C action on DNA have been studied: (a) cross-linking events, (b) alkylation without necessarily cross-linking, and (c) strand breakage. Cross-linking of DNA is determined by the return of fluorescence after a heat denaturation step at alkaline pH's. Under these conditions denatured DNA gives no fluorescence. The cross-linking was independently confirmed by S1-endonuclease (EC 3.1.4.-) digestion. At relatively high concentrations of mitomycin the suppression of ethidium fluorescence enhancement was shown not to be due to depurination but rather to alkylation, as a result of losses in potential intercalation sites. A linear relationship exists between binding ratio for mitomycin and loss of fluorescence. The proportional decrease in fluorescence with pH strongly suggests that the alkylation is due to the aziridine moiety of the antibiotic under these conditions. A parallel increase in the rate and overall efficiency of covalent cross-linking of DNA with lower pH suggests that the cross-linking event, to which the primary cytotoxic action has been linked, occurs sequentially with alkylation by aziridine and then by carbamate. Mitomycin C, reduced chemically, was shown to induce single strand cleavage as well as monoaklylation and covalent cross-linking in PM2 covalently closed circular DNA. The inhibition of this cleavage by superoxide dismutase (EC 1.15.1.1) and catalase (EC 1.11.1.6), and by free radical scavengers suggests that the degradation of DNA observed to accompany the cytotoxic action of mitomycin C is largely due to the free radical O2. In contrast to the behavior of the antibiotic streptonigrin, mitomycin C does not inactivate the protective enzymes superoxide dismutase or catalase. Lastly, mitomycin C is able to cross-link DNA in the absence of reduction at pH 4. This is consistent with the postulated cross-linking mechansims.

Animals↗

The mechanism of the degradation of DNA by streptonigrin.

The production of single strand cleavage in covalently-closed circular-DNA by the antitumour agent streptonigrin (reduced in situ by NADH) is demonstrated using the ethidium bromide fluorescence assay described previously. The degradation dependent on oxygen is completely inhibited by superoxide dismutase (EC 1.15.1.1) suggesting the intermediacy of the superoxide radical anion in the degradation. However similar complete inhibition of DNA strand breakage by catalase (EC 1.11.1.6) indicates that the hydroxyl radical (formed by interaction of superoxide with hydrogen peroxide) is the primary reactive species. Cupric ion stimulates the cleavage reaction and cobaltous ion has no effect in keeping with model studies using quinolinequinones.

Binding Sites↗

The purification from Escherichia coli of a protein relaxing superhelical DNA.

The Escherichia coli omega protein was first described by Wang (Wang J.C.: J. Mol. Biol. 55, 523-533 (1971)) as having the ability to relax supercoiled covalently-closed circular DNA by changing the topological winding number, alpha. We have developed a rapid assay for omega activity which has allowed us to purify the protein to homogeneity. It appears to be an alphabeta-type subunit protein with a molecular weight of the intact protein of about 80,000 (determined by gel filtration) and of the individual subunits of 56000 and 31000 (sodium dodecyl sulfate polyacrylamide gels). We have confirmed Wang's observation that it only partly relaxes negative supercoils, and is not active on a positive supercoils. Its characteristics with respect to pH, salts, temperature and chromatography are described. A method for rapid screening of E. coli for omega mutants is described.

Bacterial Proteins↗