The origins of the back-mutation assay method: a personal recollection.

The back-mutation assay method for determining the mutagenicity of various treatments was first developed a little over 50 years ago and has been in continuous use ever since. Shortly after the method was first used it became evident that certain factors of cell density, composition of media, etc., had to be carefully controlled to preserve an acceptable reliability of the method. A factor of particular importance was the suppression of growth of back-mutant prototrophic cells by the large number of auxotrophic cells present, a phenomenon which later became known as the "Grigg Effect." This review describes the origins of the back-mutation method and of the confounding competitive suppression phenomenon, the cause of competitive suppression, methods of diagnosing whether it is likely to bias the interpretation of a particular back-mutation experiment, and an experimental design which removes it entirely as a possible source of error. A number of other phenomena, such as phenotypic lag and coincident mutation associated with back-mutation, are also discussed as possible sources of error.

Urea improves efficiency of bisulphite-mediated sequencing of 5'-methylcytosine in genomic DNA.

The detection of 5'-methylcytosine by the bisulphite-mediated genomic sequencing method has considerably aided study of the role of methylation in areas such as X chromosome inactivation, genomic imprinting and cancer research. However on occasion difficulty has been experienced in obtaining complete conversion of cytosine to uracil in regions of the target DNA. We report here a simple improvement to the method involving addition of urea to the bisulphite reaction, a step which greatly improves the reaction efficiency, presumably by maintaining the target DNA in single stranded form, thereby allowing complete and reliable conversion.

Hypotensive effects of peptide T in conscious rats.

1. The present study investigated the effects of peptide T on mean arterial blood pressure (MAP) in conscious normotensive Sprague-Dawley (SD) rats, spontaneously hypertensive rats (SHR) and two-kidney one-clip (2K1C) hypertensive rats. 2. Peptide T was infused via the left jugular vein at a rate of 1 mg/kg per h in SD, SHR and 2K1C rats and then at doses of 0.1, 0.25, 0.5, 1 and 5 mg/kg per h in SHR, with 0.9% saline as a sham control in SHR and 2K1C. Mean arterial pressure was measured directly before, during and after infusion. 3. Peptide T (1 mg/kg per h) decreased blood pressure in both SHR (P < 0.01) and 2K1C (P < 0.05). In normotensive SD rats the fall in MAP approached statistical significance (P = 0.06). The effect of peptide T was not significantly different in normotensive compared with hypertensive rats. Saline infusion had no effect. The blood pressure lowering effect of peptide T appeared to be dose-dependent in SHR.

Sequencing 5-methylcytosine residues by the bisulphite method.

Measuring patterns of cytosine methylation in genomic DNA is most efficiently accomplished by use of the bisulphite method. This method depends on the large difference in reactivity of cytosines relative to 5-Methyl cytosines in genomic DNA to bisulphite. The chemistry and history of the method and recent developments which greatly increase its sensitivity, simplicity and reliability are described. An updated protocol to guide users is appended.

DNA methylation and mutation.

5-Methylcytosine (5mC) in DNA is produced by post-synthetic modification of cytosine residues, and it occurs primarily in CpG doublets in the mammalian genome. 5mC is a mutable site, because it can undergo spontaneous deamination to thymine. There is a repair mechanism which specifically recognises G.T mispairs, and replaces thymine with cytosine. However, this repair is not fully efficient, because the 5mC-->T transition mutation occurs about 10 times as frequently as other transitions. Such mutations are frequently seen in inherited diseases, and mutations in the p53 gene in tumours are also very commonly in 5mCpG doublets. As well as mutations, there can also be heritable changes in DNA methylation, known as epimutations, which may be of particular significance in somatic cells. Whereas the pattern of DNA methylation is very constant for any one cell type, the pattern becomes very variable in tumour cells. The breakdown of the normal controls of DNA methylation in tumorigenesis can lead to increased gene expression or to gene silencing. DNA damage increases not only mutation, but also heritable changes in methylation. At present, little is known about the ability of DNA repair to preserve the normal pattern of methylation in somatic cells.

A general method for selecting strains of Escherichia coli having altered spontaneous or induced mutabilities.

A simple method is described for selecting mutant strains of E. coli differing from their parent in the ability to spontaneously mutate via any mechanism. The method detects hypo- and hyper-mutators. It relies on the detection as papillae on thy colonies of second mutations either at the dra or drm locus.

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.

The modulation of DNA-protein interactions by methylation of protein-binding sites in DNA and the occurrence in genomic imprinting, X chromosome inactivation, and fragile X syndrome of different methylation patterns in DNA of different chromosomal origin have underlined the need to establish methylation patterns in individual strands of particular genomic sequences. We report a genomic sequencing method that provides positive identification of 5-methylcytosine residues and yields strand-specific sequences of individual molecules in genomic DNA. The method utilizes bisulfite-induced modification of genomic DNA, under conditions whereby cytosine is converted to uracil, but 5-methylcytosine remains nonreactive. The sequence under investigation is then amplified by PCR with two sets of strand-specific primers to yield a pair of fragments, one from each strand, in which all uracil and thymine residues have been amplified as thymine and only 5-methylcytosine residues have been amplified as cytosine. The PCR products can be sequenced directly to provide a strand-specific average sequence for the population of molecules or can be cloned and sequenced to provide methylation maps of single DNA molecules. We tested the method by defining the methylation status within single DNA strands of two closely spaced CpG dinucleotides in the promoter of the human kininogen gene. During the analysis, we encountered in sperm DNA an unusual methylation pattern, which suggests that the high methylation level of single-copy sequences in sperm may be locally modulated by binding of protein factors in germ-line cells.

An Escherichia coli mutant resistant to phleomycin, bleomycin, and heat inactivation is defective in ubiquinone synthesis.

A mutant of Escherichia coli, selected for resistance to the antibiotic and antitumor agent phleomycin, has been characterized, and the phleomycin resistance determinant has been identified. The mutant is equally resistant to bleomycins. The resistance to phleomycin is strongly dependent on the nature of the C-terminal amine of the drug, with the greatest resistance being shown to phleomycins and bleomycins with the most basic terminal amines. The mutation also confers resistance to the lethal effects of heating at 52 degrees C. Other characteristics of the phleomycin-resistant strain include a slow growth rate, an inability to grow on succinate as the sole carbon source (Suc- phenotype), cross resistance to aminoglycoside antibiotics, and a slight sensitivity to hydrogen peroxide, methyl methanesulfonate, and gamma-irradiation. Some of these characteristics, together with mapping data, suggested that the phleomycin resistance and Suc- determinant probably lies within the ubiF gene coding for an enzyme effecting a step in the biosynthesis of ubiquinone. The phenotypes of known mutants defective in this and other steps of the ubiquinone pathway were found to be closely similar to those of the original phleomycin-resistant strain.

Diethylpyrocarbonate and permanganate provide evidence for an unusual DNA conformation induced by binding of the antitumour antibiotics bleomycin and phleomycin.

DNA structural changes induced by bleomycin have been investigated using diethylpyrocarbonate and permanganate as probes under conditions in which the antibiotic binds to, but does not cut the DNA. Diethyl-pyrocarbonate shows an enhanced reaction with adenines in the presence of the antibiotic in the sequences GTA greater than GCA greater than GAA, on the 3' side of the drug cutting site (GPy). Permanganate ions display an enhanced reactivity at the second pyrimidine of the sequence GPyPy. The results are consistent with a model in which bleomycin distorts the structure of the base pair on the 3' side of its binding site.

Breakage of double-stranded DNA due to single-stranded nicking.

Enzymes such as pancreatic deoxyribonuclease (DNase I) nick the single strands of double-stranded DNA. Two nicks sufficiently close on opposite strands will lead to breakage of the DNA molecule. This paper gives a mathematical model for the breakage of circular, supercoiled DNA under the action of an enzyme which nicks at random sites (or at preferred sites, these being in abundance and randomly positioned around the circle). After the first nick the DNA loses its supercoiled structure; after many nicks it breaks to become topologically linear; further nicks lead to fragmentation of this linear form. Formulae are given for the proportions of DNA molecules in each of the four classes: supercoiled; nicked but still circular; linear; fragmented. Formulae are also presented for the case when there is, in addition to nicking, simultaneous action of an endonuclease which produces direct double-stranded breaks in the DNA. Finally, a general theory is given for the case where a third type of enzyme, topoisomerase I, is operative, with all three DNA modifications taking place simultaneously.

Sequence-selective binding of phleomycin to DNA.

The binding of phleomycin and bleomycin to DNA has been investigated by studying their effects on cleavage by DNAase I and micrococcal nuclease. In the presence of cobalt, cleavage of DNA by the antibiotics is suppressed, yet they still provide protection from nuclease attack in regions surrounding the drug cleavage sites. We conclude that cleavage by phleomycin occurs at bonds around which the antibiotic is already selectively bound.

Enhancement of frameshift mutagenesis in Salmonella typhimurium derivatives of hisC3076 by 5-azacytidine and other agents.

The yield of frameshift revertants of Salmonella typhimurium strain hisC3076 on plates containing the mutagen 9-aminoacridine (9AA) is enhanced by the addition to the selection medium of a number of chemical agents. These include 5-azacytidine (5-azaC), naladixic acid, ethyl methanesulphonate; pre-treatment of cells with u.v. light or gamma-radiation is also effective. With the exception of u.v. which is detected as a poor mutagen in strain hisC3076, all other enhancing agents are not usually detected as mutagens in this strain. The observed synergism between 9AA and 5-azaC in recA and uvrB derivatives of hisC3076 eliminates the possibility that recA-dependent repair or excision repair is necessary. However a lack of synergism in a uvrD derivative suggests that helicase II is involved. It is suggested that the presence of 9AA in the plating medium enables the synergistic agents to be detected as mutagens.

Amplification of the antitumor activity of phleomycins and bleomycins in rats and mice by caffeine.

While having no antitumor effect per se, caffeine substantially enhanced the antitumor effects of the phleomycins PLM-CHP and PLM-PEP, and the bleomycins BLM-CHP and Blenoxane in rats carrying Walker 256 carcinosarcoma and/or mice carrying Ehrlich ascites tumor, even at doses of phleomycin and bleomycin below the minimum effective level. Positive but less conclusive results were also obtained with PLM-A4A4G and PLM-G.

Amplification of the antibiotic effects of the bleomycins, phleomycins and tallysomycins: its dependence on the nature of the variable basic groups.

The bleomycins, phleomycins and tallysomycins are structurally similar glycopeptide antibiotics. Within each class, individual members differ only in the structure of a basic group. The antibiotic effect of phleomycin (Bristol batch A9331-648) against Escherichia coli is amplified substantially by a number of simple heterocyclic and aromatic compounds. In this paper a sample of 26 such compounds were tested for this property with 25 different phleomycins, bleomycins and tallysomycins. The nature of the variable basic group of the phleomycins, bleomycins and tallysomycins determined the response obtained with all amplifiers, although variation of response was much less marked with caffeine which potentiated the cytotoxic effects of all the phleomycins, bleomycins and tallysomycins tested. Phleomycins and bleomycins having two or three guanidino groups in the variable basic group, or phleomycins having a secondary amino group within a methylene chain and a terminal 2-phenylethyl substituent, were amplified by most compounds, whereas the cytotoxicity of others was enhanced little or not at all. Similar phleomycins, having a secondary amino and a terminal guanidino group and no 2-phenylethyl substituent showed little enhancement, and in these cases the inclusion of a 2-phenylethyl substituent had a major influence in determining amplifiability. Bleomycins and phleomycins having identical basic groups were amplified to similar extents by the sample of 26 amplifying agents used.

Inhibition and enhancement of phleomycin-induced DNA breakdown by aromatic tricyclic compounds.

Cationic aromatic tricyclic compounds including triphenylmethane dyes, phenazines, phenoxazines, acridines, phenothiazines, phenanthridinium compounds, anthracenes and xanthene dyes, which amplify cell killing in phleomycin-treated Escherichia coli B cells also modified phleomycin-induced breakdown of DNA to acid-soluble fragments. A plot of DNA breakdown as a function of concentration was bell-shaped for each of the active compounds, i.e. as the concentration increased, DNA breakdown was enhanced initially, but above a certain concentration, the proportion of DNA degraded declined, often to zero. One of the compounds, acriflavine, when tested also inhibited DNA breakdown following ultraviolet irradiation. A study, by sedimentation methods, of DNA single-strand breakage in phleomycin-treated E. coli cells, using 3 representative compounds, Crystal Violet, 3,6-diaminoacridine and Methylene Blue, revealed a consistent increase in DNA strand breaks as concentration of compound increased. In similar experiments with ethidium bromide the breakage yield/concentration curve exhibited a maximum. In general, however, it seems that the inhibition of DNA-breakdown observed at higher concentrations of these amplifying compounds is not explicable by an effect on the primary breakage event, but is due to suppression of exonucleolytic activity in the cells.

Amplification of the antitumor activity of phleomycins in rats and mice by heterocyclic analogues of purines.

Significant and often substantial enhancement of the antitumor properties of several individual phleomycins , by co- administration via intraperitoneal injection of a number of purine analogues, is demonstrated in rats and mice having three diverse tumors. It is evident that the dose levels of both the phleomycin and the amplifier are very significant and that optimal levels vary widely with the actual agents used. Constant serum levels of amplifier can be maintained for several days by administration via silastic-pellet implantation rather than injection, and this route of administration is an effective alternative for amplifiers of low solubility.