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L S Ripley

Publications and source records attributed to L S Ripley.

34 records · Page 2Linked to original sources
PubMed1986

Frameshift mutations produced by proflavin in bacteriophage T4: specificity within a hotspot.

Frameshift mutations were induced by proflavin in the rIIB gene of bacteriophage T4. rIIB DNA from each of 48 independent frameshifts was inserted into M13mp8 and sequenced. Two-thirds of the frameshifts (33/48) lie contiguous to one another in 10 base pairs of the rIIB sequence. This hotspot differs markedly from previously characterized mutagen-induced frameshift hotspots. Distinctive features of the hotspot include the absence of locally repetitive sequences, particularly G X C runs, and the fact that many different sequence changes are induced within the hotspot sequence at appreciable frequencies. Among the 33 mutants at the hotspot, 8 distinguishable DNA sequence changes were seen. All of the mutations were deletions of a single base or duplications of one or more bases. Duplications were more frequent than deletions. The patterns of the base sequence changes suggest that two specific phosphodiester bonds within the hotspot sequence are sites at which proflavin-induced mutation is initiated.

Acridines↗
PubMed1984

Bacteriophage T4 particles are refractory to bisulfite mutagenesis.

Bisulfite-induced deamination of cytosine produces uracil, a thymine analog reported to be mutagenic both in vitro and in vivo. Although deamination of cytosine in DNA should produce G:C----A:T transitions, treating bacteriophage T4 particles with 0.9 M bisulfite at pH 5 at 37 degrees C produced no more mutations than did the equivalent buffer without bisulfite. Lack of bisulfite mutagenicity is fully consistent with the reported resistance of 5-substituted cytosines to bisulfite-induced deamination, since T4 DNA contains glucosylated 5-hydroxymethylcytosine. However, bisulfite also failed to induce mutations in T4 particles whose DNA contained unmodified cytosine. The lack of mutagenesis persisted in E. coli hosts deficient in uracil glycosylase, an enzyme expected to participate in the repair of the putative bisulfite-generated uracil. Cytosine in T4 DNA may be largely protected from bisulfite attack within phage particles.

Hydrogen-Ion Concentration↗
PubMed1984

Demonstration of the production of frameshift and base-substitution mutations by quasipalindromic DNA sequences.

The in vivo production of frameshift and base-substitution mutations predicted as a consequence of the metabolic processing of misaligned quasipalindromic DNA sequences has been confirmed. Spontaneous frameshift mutations of the T4 rII gene that had been genetically mapped to quasipalindromic DNA sequences were sequenced. Some of the mutant sequences are exactly those predicted by a mutational model based on misaligned quasipalindromes. Furthermore, these sequences are distinct from those predicted by the classical frameshift model based on misaligned repeated sequences. The rII frameshift mutant sequences reported here result from the deletion of a specific base or bases that would remain looped out should the quasipalindromes assume a hairpin secondary structure. One hairpin predicted not only the deletion of two bases (a frameshift) but the concomitant production of nearby but noncontiguous base substitutions. The substitution of as many as three bases as well as the frameshift were predicted to arise as a consequence of a single mutational event in the palindrome. Two independent examples of the predicted deletion frameshift were found among the small sample of sequenced spontaneous frameshifts examined and both were associated with the predicted transversion and transition base substitutions.

Base Sequence↗
PubMed1984

Structural intermediates of deletion mutagenesis: a role for palindromic DNA.

A model is presented for deletion mutations whose formation is mediated by palindromic and quasipalindromic DNA sequences. It proposes that the self-complementarity of palindromes allows the formation of DNA secondary structures that serve as deletion intermediates. The structures juxtapose the end points of the deletion and thus direct deletion specificity. While misaligned DNA intermediates that explain deletion termini occurring in repeated DNA sequences have been described, no explanations have been offered for deletion termini occurring in other sequences. The DNA secondary structures whose formation is mediated by palindromic sequences appear to explain many of these. In this paper, secondary-structure intermediates are described for a series of spontaneous deletions of known sequence in the lacl gene of Escherichia coli. The model is supported by its failure to predict structures that can juxtapose simulated deletion termini in the lacl gene. We have found a strong association between palindromic sequences and repeated sequences at lacl deletion termini that suggests the joint participation of repeated and palindromic DNA sequences in the formation of some deletions. Sequences of deletions in other organisms also suggest the participation of palindromic DNA sequences in the formation of deletions.

Base Sequence↗
PubMed1983

Mutator versus antimutator activity of a T4 DNA polymerase mutant distinguishes two different frameshifting mechanisms.

Classical "antimutator" DNA polymerases of bacteriophage T4 were examined for their effects upon frameshift mutation rates at a number of positions within rII cistrons. Their antimutagenic activities reduced frameshift frequencies at a number of sites, but at other sites the opposite occurred: the mutant polymerases exhibited clear mutator activities. This dichotomy reveals the operation of two distinct mechanisms of frameshift mutagenesis that are correlated with the DNA sequences at the frameshift sites. Frameshift mutants subject to the antimutator effects of the mutant polymerase lie in A: T-run DNA sequences, where mutations presumably arise by means of the interstrand DNA misalignments postulated by classical theory. The frameshift mutants produced by the mutator activity of these same polymerases lie in quasipalindromic DNA sequences, where mutations are postulated to arise by aberrant metabolism of DNA secondary structures such as hairpins.

Alleles↗
PubMed1983

A major role for bacteriophage T4 DNA polymerase in frameshift mutagenesis.

T4 DNA polymerase strongly influences the frequency and specificity of frameshift mutagenesis. Fifteen of 19 temperature-sensitive alleles of the DNA polymerase gene substantially influenced the reversion frequencies of frameshift mutations measured in the T4 rII genes. Most polymerase mutants increased frameshift frequencies, but a few alleles (previously noted as antimutators for base substitution mutations) decreased the frequencies of certain frameshifts while increasing the frequencies of others. The various patterns of enhanced or decreased frameshift mutation frequencies suggest that T4 DNA polymerase is likely to play a variety of roles in the metabolic events leading to frameshift mutation. A detailed genetic study of the specificity of the mutator properties of three DNA polymerase alleles (tsL56, tsL98 and tsL88) demonstrated that each produces a distinctive frameshift spectrum. Differences in frameshift frequencies at similar DNA sequences within the rII genes, the influence of mutant polymerase alleles on these frequencies, and the presence or absence of the dinucleotide sequence associated with initiation of Okazaki pieces at the frameshift site has led us to suggest that the discontinuities associated with discontinuous DNA replication may contribute to spontaneous frameshift mutation frequencies in T4.

Base Sequence↗
PubMed1982

Model for the participation of quasi-palindromic DNA sequences in frameshift mutation.

A model is described for the templated production of frameshift and base-substitution mutations mediated through aberrant DNA structures arising as a consequence of quasi-palindromic DNA sequences. Two general mechanisms are considered. One evokes the formation and processing of imperfect DNA secondary structures (hairpins) for the production of mutations. The other evokes a "strand switch" during DNA synthesis which, in a manner unique to quasi-palindromic sequences, may be resolved to produce frameshift or base-substitution mutations, or both. It is the unique combination of symmetrical and asymmetrical elements of the quasi-palindromic sequence itself that provides the basis for both models. Through the mechanisms described, the symmetrical elements permit unusually paired DNA substrates, and the asymmetrical elements permit templated insertions, deletions, and base substitutions. The model predicts a class of mutations--simultaneously frameshifts and base substitutions--whose sequences can be predicted from a local quasi-palindromic sequence. This prediction appears to be met by a significant fraction (more than 15%) of frameshift mutations in the iso-1-cytochrome c gene of Saccharomyces cerevisiae.

Base Sequence↗
PubMed1981

Mutagenic specificity of nitrosomethylurea in bacteriophage T4.

In contrast to alkylating agents such as ethyl methanesulphonate which can induce mutation after treatment of free phage particles, nitrosamides induce mutations only when phage are treated intracellularly during infection of the host. The basis of this intracellular dependence is not currently understood. In this study the mutational specificity of nitrosomethylurea (NMU) in bacteriophage T4 was investigated by measuring the reversion of well-characterized mutants in the rII genes. While no mutation was produced after in vitro treatments of free phage, in vivo treatments strongly induced G:C leads to A:T transitions and substantially induced A:T leads to G:C transitions. Transversions and frameshift mutations were rarely induced. Although methyl methanesulfonate mutagenesis of T4 depends upon a phage-encoded error-prone repair system, NMU-induced mutagenesis is independent of this repair system. Similarities in mutagen specificity of nitrosamides and differences in DNA metabolism in T4 when compared to its host, Escherichia coli, suggest that T4 is well-suited for the study of mechanisms of nitrosamide mutagenesis.

Base Composition↗
PubMed1976

Heat mutagenesis in bacteriophage T4: the transversion pathway.

Heat induces transversions (as well as transitions) at G-C base pairs in bacteriophage T4. The target base for transversions is guanine,which is converted to a product which is sometimes replicated and transcribed as a pyrimidine.A model for this process is proposed in which the deoxyguanosine glycosidic bond migrates from N9 to N2: the resulting deoxyneoguanosine may pair with normal guanine to produce G-C leads to C-G transversions.

Base Sequence↗
PubMed1975

Transversion mutagenesis in bacteriophage T4.

Transversion mutations can be distinguished from transition mutations by the use of special tauII mutants of bacteriophage T4. Methyl methanesulfonate did not induce reversion of the tester mutants along transversion or transition pathways from A:T1 base pair sites, nor along transversion pathways from G:C base pair sites. Ethyl methanesulfonate and N-methyl-N-nitrosourea, however, induced both transversions and transitions at an A:T base pair site; no transversions were detected at G:C-sites. Mn++ induced transversions and transitions at both A:T-and G:C-sites. The influence of temperature-sensitive gene-43 DNA polymerase mutator and antimutator mutations on the reversion of the tauII tester mutants was measured: some gene-43 mutants differentially influenced different pathways of reversion. Studies of thymineless mutagenesis demonstrated A:T-site transversion mutations. A synergistic interaction between thymineless mutagenesis and the gene-43 mutator, tsL56, was used to demonstrate thymineless mutagenesis at one site where it was not detected in the presence of the wild type polymerase.

Base Sequence↗
PubMed1973

Thymineless mutagenesis in bacteriophage T4.

Thymine deprivation can be achieved in bacteriophage T4 either by the use of the thymidylate synthetase inhibitor FUdR, or by an appropriate combination of genetic blocks; both methods produce marked mutagenesis. Extensive tests of the specificity of thymineless mutagenesis reveal that only A:T base pairs are affected, and that transitions and possibly transversions are produced. This system therefore constitutes the first example of an A:T-specific mutagen. Thymineless mutagenesis in bacteriophage T4 exhibits a marked dependence upon the functional state of the DNA polymerase gene, but is largely independent of the px-y misrepair system.

Adenine Nucleotides↗