Excision repair of O6-methylguanine synthesized at the rat H-ras N-methyl-N-nitrosourea activation site and introduced into Escherichia coli

O6-methylguanine (O6-methylG) is believed to be the premutagenic lesion responsible for mutational activation of the H-ras proto-oncogene in rats treated with N-methyl-N-nitrosourea (MNU). Research on the repair of O6-methylG has primarily focused on the methyltransferases. Potentially, other repair proteins may be involved in repair of O6-methylG. We have investigated the effect of Escherichia coli UvrABC excision repair on O6-methylG synthesized at the rat H-ras MNU activation site in a partial rat H-ras sequence constructed in an M13mp vector. An oligonucleotide self-selection technique was used to identify progeny phage containing DNA replicated from the O6-methylG-containing strand. We found that excision repair can help protect against mutation by O6-methylG at the rat H-ras MNU activation site.

Insertion and extension of acyclic, dideoxy, and ara nucleotides by herpesviridae, human alpha and human beta polymerases. A unique inhibition mechanism for 9-(1,3-dihydroxy-2-propoxymethyl)guanine triphosphate

The ability of human alpha and beta DNA polymerases and herpes simplex virus type 2 (HSV-2) and human cytomegalovirus (HCMV) DNA polymerases to insert and extend several nucleotide analogs has been investigated using a variation of Sanger-Coulson DNA sequencing technology. The analogs included the triphosphates of two antiviral nucleosides with incomplete sugar rings: 9-(1,3-dihydroxy-2-propoxymethyl)guanine (dhpG) and 9-(2-hydroxyethoxymethyl)guanine (acyG or acyclovir), as well as dideoxy and arabinosyl nucleoside triphosphates. Three pairs of contrasting behaviors were found, each pair distinguishing the two human polymerases from the two viral ones: first, extension behavior with araNTPs; second, insertion/extension behavior with dhpGTP; and third, the relative preference for insertion of ddGTP versus acyGTP. The relative level of insertion of the nucleotide analogs by HCMV and HSV-2 DNA polymerases was dhpGTP greater than (acyGTP and araNTP) greater than ddGTP, whereas by human alpha polymerase it was araATP greater than ddGTP much greater than (acyGTP and dhpGTP) and by human beta polymerase it was (araATP and ddGTP) much greater than (acyGTP and dhpGTP). Evidence is presented for three mechanisms of inhibition by extendible nucleotides (of dhp and ara types) exhibiting frequent internalization: araATP acted as a simple pseudoterminator of alpha and beta polymerases, but was easily extended past singlet sites by Herpesviridae polymerases and only stalled at sites requiring two or more araATP insertions in a row. Herpesviridae polymerases stalled after adding dhpGMP and one additional nucleotide, suggesting that polymerase translocation problems may be a factor in polymerase inhibition by modified sugar nucleotide analogs. The amino acid sequence of the human alpha DNA polymerase, which is acyGTP resistant, was found to vary by one amino acid from the amino sequences of the Herpesviridae polymerases in a region of significant similarity and probable functional homology. Amino acid differences at that same site differentiate acyclovir-resistant HSV-1 mutants from the acyclovir-sensitive HSV-1 wild type.

DNA damage at thymine N-3 abolishes base-pairing capacity during DNA synthesis

3-Methylthymine was synthesized into DNA copolymers and deoxynucleoside triphosphate to study its effect on DNA synthesis by the Klenow fragment of Escherichia coli polymerase I and avian myeloblastosis virus reverse transcriptase. Both polymerases were greatly inhibited by template 3-methylthymine. In response to 3-methylthymine, misincorporation of dTTP increased slightly, but occurred only at low levels consistent with spontaneous misincorporation in vitro. Surprisingly, template 3-methylthymine resulted in a striking decrease in background misincorporation, relative to normal incorporation by the Klenow fragment, of dGTP and, to a lesser extent, of dATP and dCTP. The incorporation of 3-methyl-dTTP into DNA was studied using DNA sequencing technology. The Klenow fragment failed to incorporate 3-methyl-dTTP even at 1 mM. Reverse transcriptase incorporated 3-methyl-dTTP opposite adenine, cytosine, and thymine, but at only about 1/40,000th the efficiency of complementary deoxynucleoside triphosphate incorporation. Furthermore, synthesis generally stalled at sites of 3-methyl-thymine incorporation. From these results, we conclude that damage at the central hydrogen-bonding position of thymine abolishes its base-pairing capabilities during DNA synthesis.

Induction of deletion and insertion mutations by 9-aminoacridine. An in vitro model

The ability of 9-aminoacridine to induce mutagenic lesions during DNA replication in vitro was investigated. The ampicillinase gene of pBR322 was replicated in vitro in the presence of 9-aminoacridine. Transfection of the replicated DNA into Escherichia coli gave Amps mutants. Determination of the base changes in 76 of these mutants indicated that the spectrum of mutations induced by 9-aminoacridine was consistent with its action in vivo. Both large (407-base) and small (1- and 2-base) deletions were induced at repetitive sequences. The frequency of deletion mutations depended on the identity of the base deleted and sequences surrounding the deletions. The characteristics of the frameshift mutations induced were consistent with the interactions of 9-aminoacridine with DNA. These results establish that 9-aminoacridine can induce frameshift mutations during the replication process and provide an in vitro model of frameshift induction for mechanistic studies.

O6-methylguanine mutation and repair is nonuniform. Selection for DNA most interactive with O6-methylguanine

Mutations were induced in the ampicillinase gene of a bacteriophage f1/pBR322 chimera both by incorporation of O6-methyl-dGTP opposite T during DNA replication in vitro and by site-directed mutagenesis using O6-methylguanine-containing oligonucleotides. After passage of the DNA through Escherichia coli, analysis of 151 O6-methyl-dGTP-induced mutations indicated a significantly greater number of unmutated mutation sites than expected, whereas the mutated sites generally fit a Poisson distribution. The unmutated sites are assumed to be caused by the inability of some sequences to tolerate the presence of a tetrahedral methyl group within the confines of a Watson-Crick helix (Toorchen, D., and Topal, M.D. (1983) Carcinogenesis 4, 1591-1597). A consensus of the DNA sequences surrounding unmutated mutation sites was derived. The consensus sequence had significant similarity to the region of the rat Harvey ras oncogene containing the N-methyl-N-nitrosourea activated site for transformation (Zarbl, H., Sukumar, S., Arthur, A. V., Dionisio, M.-Z., and Barbacid, M. (1985) Nature 315, 382-385). We propose that direct alkylation at O6 of a guanine present within the consensus sequence may produce a DNA conformation less subject to repair. Mutation by O6-methylguanine-containing oligonucleotides demonstrated that repair of the O6-methylguanine lesions varied at least 3-4-fold with position of the lesion.

Mutagenesis by incorporation of alkylated nucleotides

The cellular DNA precursor pool was shown to be a target for N-methyl-N-nitrosourea, a potent mutagen and carcinogen. O6medGTP, a product of this interaction, was chemically synthesized and shown to be incorporated into DNA in vitro by Klenow E. coli pol I and phage T4 DNA polymerases. O6medGTP incorporated predominantly opposite T template residues and to a lower extent opposite C. At some loci incorporation of O6medGTP caused DNA synthesis arrest. The significance of the behavior of O6medGTP for mutagenesis in vivo is discussed.

O6-Methylguanine-DNA transmethylase converts O6-methylguanine thymine base pairs to guanine thymine base pairs in DNA

O6-Methylguanine lesions in natural and synthetic DNAs were studied as substrates for the O6-methylguanine-DNA methyltransferase in vitro. The results indicate that O6-methylguanine is repaired by this protein when base paired to T as well as to C in double-stranded DNA. The results also indicate that O6-methylguanine is less subject to repair than previously reported when it is in single-stranded DNA and suggest that O6-methylguanine may not be repaired when it is at the 3' terminus.

Molecular mechanisms of chemical mutagenesis: 9-aminoacridine inhibits DNA replication in vitro by destabilizing the DNA growing point and interacting with the DNA polymerase

9-Aminoacridine was found to inhibit dNTP incorporation into DNA homopolymer duplexes by phage T4 DNA polymerase in vitro. Systematic variation of the molar ratio of 9-aminoacridine to DNA, to DNA polymerase, and to DNA precursors demonstrated that this inhibition at 9-aminoacridine concentrations below 10 microM was mainly due to interaction of 9-aminoacridine with the DNA and suggested that the basis for the preferential inhibition of incorrect precursor incorporation was destabilization of the DNA growing point. Consistent with destabilization, 9-aminoacridine stimulated the hydrolysis of correctly base paired DNA by the 3'-5' exonuclease activity of phage T4 DNA polymerase. This is the first indication to my knowledge that an intercalating dye destabilizes the DNA growing point, whereas it raises the overall Tm of the DNA. At 9-aminoacridine concentrations above 10 microM overall incorporation of dNTPs was inhibited by 9-aminoacridine interaction with the DNA polymerase. A possible explanation for the induction of both deletion and addition frameshift mutations by 9-aminoacridine during DNA biosynthesis is discussed in light of growing-point destabilization.

Mechanism of mutagenesis by O6-methylguanine

O6-methylguanine (O6meG) lesions of double-stranded DNA have been associated with mutation and neoplastic transformation. These lesions can, in principle, be produced by at least three different mechanisms: direct alkylation of G X C base pairs in double-stranded DNA; alkylation of guanine residues in single-stranded regions of DNA associated with replication forks; and alkylation of the DNA precursor pool followed by incorporation of O6-methyl deoxyguanosine triphosphate (O6-medGTP) during DNA replication. DNA biosynthesis subsequent to all three events will generate predominantly O6-meG X T base pairs as O6meG preferentially pairs with T. We show here that O6meG X T base pairs are mutagenic; that transalkylase repair has a direct role in the generation of mutations induced by alkylated pool nucleotides; and that the Escherichia coli mismatch repair system is capable of repairing mutagenic G X T intermediates.

Mechanisms of chemical mutagenesis and carcinogenesis: effects on DNA replication of methylation at the O6-guanine position of dGTP

The incorporation of O6-methyl-dGTP during DNA replication in vitro by 'Klenow' E. coli pol I was determined. O6-Methyl-dGTP was found to: (i) incorporate opposite T and C template residues, with a greater than 20-fold preference for T, and (ii) arrest DNA synthesis when incorporated in place of dATP at all but pyrimidine-rich growing-strand sequences. The significance of O6-methyl-dGTP incorporation during DNA biosynthesis in vivo for mutagenesis and carcinogenesis is discussed.

Products of bacteriophage T4 genes 32 and 45 improve the accuracy of DNA replication in vitro

The six "accessory" proteins of the bacteriophage T4 specified by replication genes 32, 41, 44, 45, 61, and 62 were studied for their ability to enhance the accuracy with which phage T4 DNA polymerase (product of gene 43) replicates synthetic homopolymer duplexes in vitro. Two of these proteins, gene 32-protein (helix-destabilizing protein) and gene 45-protein, inhibited the selection of incorrect, but not correct, precursors, at the growing strand end. Gene 32-protein is shown to enhance replication fidelity by interacting with the DNA, whereas gene 45-protein exerts its fidelity-enhancing effect by interacting with the DNA polymerase. This is the first example to our knowledge of a DNA polymerase's accuracy being altered through interaction with another protein. Possible mechanisms by which gene 32- and gene 45-protein act to enhance replication fidelity are discussed.

Reaction of dATP with N-methyl-N-nitrosourea in vitro

Extensive methylation was found upon reaction of N-methyl-N-nitrosourea with dATP. The products of this reaction were purified by repeated anion exchange column chromatography and were found to consist of adenine deoxyribonucleotides methylated on the base moiety, terminal phosphate, or both. Products methylated on the adenine ring were identified by co-migration of acid-hydrolyzed samples with authentic standards on reverse phase high pressure liquid chromatography. Products methylated on the sugar phosphate moiety were identified by digestion with snake venom phosphodiesterase, alkaline phosphatase, or both followed by polyethyleneimine cellulose thin layer chromatography. The results demonstrate production of gamma-phosphate-methyldATP, beta-phosphate-methyl-dADP, 1-methyldATP, and gamma-phosphate-methyl-1-methyldATP as well as the relatively unstable products 3-methyldATP and gamma-phosphate-methyl-3-methyl-dATP. The identities and amounts of products formed during this reaction in vitro are consistent with our finding that cellular deoxyribonucleotide pools are a significant target for N-methyl-N-nitrosourea (Topal, M. D., and Baker, M. S. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 2211-2215).

DNA precursors in chemical mutagenesis: a novel application of DNA sequencing

Recently, we have shown that deoxyribonucleoside residues in the cellular DNA precursor pool are generally more susceptible to methylation than are residues within the DNA duplex. The N-1 position of adenosine, for example, was found to be at least 13,000 times more susceptible to methylation by N-methyl-N-nitrosourea (MNU) than the same site in the DNA. These results suggest that potential sites for alkylation in the double-strand duplex are relatively inaccessible to direct alkylation in vivo. Many of these sites are probably protected from alkylation not only by their position in the interstices of the DNA helix, but also by further in vivo 'packaging' of the DNA in chromatin. We have now used DNA sequencing to demonstrate the incorporation properties of products of the reaction of MNU with dATP and of deoxy-N4-hydroxycytidine triphosphate during DNA replication in vitro by phage T4 DNA polymerase and the 'Klenow' fragment of Escherichia coli pol I. The results suggest that DNA precursor nucleotides due to their greater availability for alkylation, may offer routes for the introduction of alkylated residues into double-stranded DNA.

DNA precursor pool: a significant target for N-methyl-N-nitrosourea in C3H/10T1/2 clone 8 cells

Synchronized C3H/10T1/2 clone 8 cells were treated in vitro with a nontoxic dose of N-methyl-N-nitrosourea during their S phase. Chromatographic isolation of the deoxyribonucleotide DNA precursor pool and measurement of the precursor content per cell showed that a nucleic acid residue in the precursor pool is 190-13,000 times more susceptible to methylation than a residue in the DNA duplex, depending on the site of methylation. This conclusion comes from measurements indicating that, for example, the N-1 position of adenine in dATP is 6.3 times more methylated than the same position in the DNA, even though the adenine content of the pool is only a fraction (0.0005) of the adenine content of the DNA helix. The comparative susceptibility between pool and DNA was found to vary with the site of methylation in the order the N-1 position of adenine greater than phosphate greater than the N-3 position of adenine greater than the O6 position of guanine greater than the N-7 position of guanine. The significance of these results for chemical mutagenesis and carcinogenesis is discussed.

DNA in proximity to the site of replication is preferentially alkylated in S phase 10T1/2 cells treated with N-methyl-N-nitroso-urea

Replicating DNA is more susceptible to modification by N-methyl-N-nitrosourea (MNU), a spontaneously active methylating agent, than bulk DNA. This conclusion is supported by results from two different experimental approaches. First, synchronized C3H 10T1/2 clone 8 cells were treated in S phase with MNU and DNA replicated during the period of treatment was separated from bulk DNA. This was done by digesting the purified DNA with restriction enzymes and retaining the replication fork-associated DNA in nitro-cellulose filters. Second, synchronized C3H 10T1/2 clone 8 cells were exposed to 5-bromodeoxyuridine and [3H]MNU and the density-labelled, replicated DNA was separated in CsCl gradients. Both methods show 2.6 to 5.0 times more [3H]methyl adducts per nucleotide residue associated with replicating DNA than that expected from random methylation. These experiments were done at low MNU concentrations (0.018-0.115 mM) that did not cause any detectable inhibition of DNA synthesis or stimulation of repair replication in 10T1/2 cells.

Molecular basis for substitution mutations. Effect of primer terminal and template residues on nucleotide selection by phage T4 DNA polymerase in vitro

The DNA-dependent conversion of incorrect deoxynucleoside triphosphate precursors to monophosphates (turnover) by bacteriophage T4 DNA polymerase was determined using either poly(dA) x (dT) or poly(dG) x (dC) homopolymer templates. Competition between correct and incorrect triphosphates for incorporation into DNA, and the use of chain-terminating dideoxynucleoside triphosphates enabled us to determine the amount of turnover occurring at the end of each strand of the homopolymer duplex (e.g. amount of turnover of dATP occurring at the 3'-OH of poly(dG) and the 3'-OH of poly(dC)). These determinations suggest that nearest neighbor interactions between incoming dNTPs and the growing strand terminal residue play a major role in the occurrence of substitution errors during DNA synthesis in vitro byDNA polymerase. When considered together with existing evidence from studies of turnover (Gillin, F. D., and Nossal, N. G. (1976) J. Biol. Chem. 251, 5225-5232) and direct incorporation (Hall, Z. W., and Lehman, I. R. (1968) J. Mol. Biol. 36, 321-333) these results demonstrate that pyrimidine-pyrimidine and purine-purine as well as purine-pyrimidine oppositions have a role in error production at least during DNA replication in vitro. The implications of these results for the role of the "accessory" replication proteins in maintaining accuracy during the DNA biosynthetic process are discussed.

Fluorescence of terbium ion-nucleic acid complexes: a sensitive specific probe for unpaired residues in nucleic acids

The interaction of the lanthanide cation Tb3+ with the phosphate moieties of non-hydrogen-bonded residues of nucleic acids has been shown to result in substantial enhancement of the fluorescence of this cation. The excitation spectrum for this fluorescence is characteristic of the base moiety of the residue to which the Tb3+ is bound, while the emission spectrum is characteristic of the cation itself. The intensity of the fluorescence enhancement, however, is dependent upon the base of the ligand moiety, with G inducing the strongest enhancement, C and T rather less, and A very little. Base-paired residues of nucleic acids induce no such fluorescence enhancement, even though the cation is more tightly bound to double helical regions than to residues in single strands. The enhancement of Tb3+ fluorescence upon binding to non-hydrogen-bonded residues therefore provides a highly specific conformational probe for such residues. This probe has been exploited successfully for the purpose of analyzing the kinetics of reassociation of DNAs (C0t analysis) and as a specific stain for single-strand DNA bands on polyacrylamide gels.

Base pairing and fidelity in codon-anticodon interaction

Base pairing in codon-anticodon interaction has been investigated in order to understand the basis on which particular base pairs have been selected for or against participation at the wobble position and the basis for codon-anticodon infidelity.

Complementary base pairing and the origin of substitution mutations

On the basis of chemical considerations and model building, the Watson-Crick concept of complementary base pairing is extended to a wider range of DNA pairs that A-T and G-C (including A-C, G-T, A-A, G-G and G-A) by invoking imino or enol tautomers (or protonated species) and synisomers. The virtual absence of these additional base pairs from DNA is explained in terms of the low frequency with which these unfavoured forms occur and the two-step mechanism of DNA synthesis, whereby residues are first incorporated by the DNA polymerase and then checked. This base-pairing hypothesis is used to explain the origin, nature and level of spontaneous substitution mutations, their enhancement by base analogues, and the unique effects of certain mutator alleles.