Construction and expression of a chimeric gene encoding human terminal deoxynucleotidyltransferase and DNA polymerase beta.

A domain substitution experiment was carried out between the structurally related DNA-polymerizing enzymes Pol beta and TdT to investigate the region of Pol beta required for template utilization. Site-directed mutagenesis and recombinant DNA procedures were used for construction of a gene encoding a chimeric form of the two enzymes and termed TDT::POLB, in which the DNA region encoding amino acids (aa) 154-212 of TdT was replaced by the corresponding region encoding aa 1-60 of POL beta. The construction was confirmed by restriction analysis and DNA sequencing. Since this region of POL beta represents most of the N-terminal domain of the enzyme possessing single-stranded DNA (ssDNA)-binding activity, it was hypothesized that the chimeric protein, unlike TdT, might possess template-dependent DNA polymerase activity. The chimeric gene product was produced in Escherichia coli, purified and subjected to preliminary enzymological characterization. The finding that the chimeric TdT::Pol beta protein possessed significant template-dependent polymerase activity suggests that aa 1-60 of Pol beta are involved in template utilization during the polymerization reaction, as suggested by the previous finding that the 8-kDa N-terminal domain of Pol beta possesses ssDNA-binding activity [Kumar et al., J. Biol. Chem. 265 (1990a) 2124-2131; Kumar et al., Biochemistry 29 (1990b) 7156-7159; Prasad et al., J. Biol. Chem. 268 (1993) 22746-22755].

Mutagenic consequences of the incorporation of 6-thioguanine into DNA.

6-Thioguanine (S6G) has been used in the treatment of acute leukemias because of its cytotoxic effect on proliferating leukemic cells. The cytotoxicity of S6G is thought to derive from its incorporation into DNA in place of guanine. The deoxyribonucleoside triphosphate of S6G, SdGTP, is a good substrate for bacterial and human DNA polymerases (Ling et al., Mol Pharmacol 40: 508-514, 1991). Since SdGTP was observed to misincorporate in place of adenine at a greater frequency than did dGTP, it appeared plausible that this analog could produce more subtle effects (mutations) due to mispairing with thymine. To assess whether such mutations occur, SdGTP was incorporated into the lacI gene of phage M13lacISaXb in reactions that omitted dGTP (-G) or dATP (-A). LacI mutation frequency was determined by beta-galactosidase colorimetric staining (inactivation of the lac repressor results in blue plaques in the absence of inducer). When a high concentration of SdGTP (24 microM) was used in the DNA polymerase reaction, phage infectivity was inhibited. When a relatively low concentration (2.4 nM) was added to the -G and -A reactions, mutagenic effects were observed. DNA sequencing of mutant progeny arising from the -G + S6G reaction revealed C-to-T base transitions and some C-to-A transversions. Similarly, the presence of SdGTP in the -A reactions led to mutants with T-to-C transitions. No insertions or deletions were observed. These data indicate that mispairing of S6G with thymine leads to mutagenic effects in this assay.

Hybridization of glass-tethered oligonucleotide probes to target strands preannealed with labeled auxiliary oligonucleotides.

In this article we introduce a strategy of preannealing labeled auxiliary oligonucleotides to single-stranded target DNA, prior to hybridization of the DNA target to oligonucleotide arrays (genosensors) formed on glass slides for the purpose of mutation analysis. Human genomic DNA samples from normal individuals and cystic fibrosis (CF) patients (including homozygous delta F508 and heterozygous delta F508/wild type (wt) in the region examined) were used. A PCR fragment of length 138 bp (wt) or 135 bp (mutant) was produced from exon 10 in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, using a new pair of polymerase chain reaction (PCR) primers. This fragment contains four of the most frequent mutation sites causing the disease (Q493X, delta I507, delta F508, and V520F). Each of these mutations was tested using a pair of nonamer (9-mer) probes covalently attached to glass slides, representing the normal (wt) and the mutant alleles. Single-stranded target DNA was isolated from the PCR fragment using one PCR primer labeled with biotin and a streptavidin minicolumn to capture the biotin-labeled strand. Prior to hybridization to the 9-mer array on a glass slide, the unlabeled target strand was preannealed with one, three, or four auxiliary oligonucleotides, at least one being labeled with 32P. As observed previously in several laboratories, the discrimination between normal (wt) and mutant alleles at each site using oligonucleotide array hybridization ranged from very good to poor, depending on the number and location of mismatches between probe and target. Terminal mismatches along the probe were difficult to discriminate, internal mismatches were more easily discriminated, and multiple mismatches were very well discriminated. An exceptionally intense hybridization signal was obtained with a 9-mer probe that hybridized contiguously (in tandem) with one auxiliary oligonucleotide preannealed to the target DNA. The increased stability is apparently caused by strong base stacking interactions between the "capture probe" and the auxiliary oligonucleotide. The presence of the delta F508 mutation was detected with this system, including discrimination between homozygous and heterozygous conditions. Base mismatch discrimination using the arrayed 9-mer probes was improved by increasing the temperature of hybridization from 15 to 25 degrees C. Auxiliary oligonucleotides, preannealed to the single-stranded template, may serve several purposes to enable a more robust genosensor-based DNA sequence analysis: 1. A convenient means of introducing label into the target DNA molecule. 2. Disruption of interfering short-range secondary structure in the region of analysis. 3. Covering up of redundant binding sites in the target strand (i.e., where a given probe has more than one complement within the target). 4. Tandem hybridization with the capture probe (providing contiguous stacking) as a means for achieving efficient mismatch discrimination at the terminal position of the capture probe (adjacent to the auxiliary oligonucleotide). By use of multiple auxiliary oligonucleotides, all of the above benefits can be derived simultaneously.

Mutation detection by stacking hybridization on genosensor arrays.

A new strategy for analysis of point mutations using oligonucleotide array (genosensor) hybridization was investigated. In the new approach, a single-stranded target strand is preannealed with a labeled "stacking oligonucleotide," and then the partially duplex labeled target molecule is hybridized to an array of glass-tethered oligonucleotide probes, targeted to the region on the target immediately adjacent to the stacking oligomer. In this configuration, the base-stacking interactions between the "capture probe" and the contiguously stacking oligomer stabilize the binding of the target molecule to its complementary probe on the genosensor array. The temperature of hybridization can be adjusted so that the target molecule will bind to the glass-tethered probe only in the presence of the stacking oligomer, and a single mismatch at or near the terminal position ol the capture probe disrupts the stacking interactions and thereby eliminates or greatly reduces the hybridization. This stacking hybridization approach was investigated using a collection of synthetic targets, probes, and stacking oligonucleotides, which permitted identification of conditions for optimal base mismatch discrimination. The oligonucleotide probes were tethered to the glass using a simple, improved attachment chemistry in which a 3'-aminopropanol function introduced into the probe during chemical synthesis binds covalently to silanol groups on clean, underivatized glass. "Operating parameters" examined in the stacking hybridization system included length of capture probe, position, type and number of mismatches between the probe and the target, temperature of hybridization and length of washing, and the presence of terminal phosphate group in the probe, at its junction with the stacking oligomer. The results suggest that in the stacking hybridization configuration: 1. Optimal mismatch discrimination with 9-mer probes occurs at 45 degrees C, after which little or no improvement in mispair rejection occurred on lengthy continued washing at 45 degrees C. 2. At 25 degrees C optimal mismatch discrimination occurred with 7- or 8-mer probes, or with 9-mer probes containing an additional internal mismatch. 3. The presence of a phosphate group on the 5'-end of the glass-tethered probe had no general effect on mismatch discrimination, but influenced the relative stability of different mismatches in the sequence context studied. These results provide a motivation for continued development of the stacking hybridization technique for nucleic acid sequence analysis. This approach offers several advantages over the traditional allele-specific oligonucleotide hybridization technique, and is distinct from the contiguous stacking hybridization sitrategy that the Mirzabekov laboratory has introduced (Yershov et al. (1996) Proc. Natl. Acad. Sci. USA 93, 4913-4918; Parinov et al. (1996) Nucleic Acids Res. 24, 2998-3004).

Mutagenic and lethal action of polychromatic near-ultraviolet (325-400 nm) on Haemophilus influenzae in the presence of nitrogen.

The lethal effect of polychromatic near-UV light (325-400 nm) on Haemophilus influenzae was 8 times higher under aerobic than anaerobic irradiation. This light increased the frequency of mutation to novobiocin resistance and ability to utilize protoporphyrin IX. The slope of mutagenic effect at low doses appeared greater for the aerobic than for the anaerobic group. We concluded that polychromatic near-UV mutation of H. influenzae under anaerobic irradiation was caused by direct oxygen-independent action on DNA.

Influence of neighboring base sequence on mutagenesis induced by in vitro misincorporation in the lacI gene of Escherichia coli.

Genetic and electrophoretic assays of misincorporation were used to assess the effect of DNA sequence on mutagenesis arising from in vitro DNA synthesis within the lacI gene of Escherichia coli. The viral strand of a derivative of phage M13 containing the entire lacI gene was annealed with a series of synthetic oligonucleotides complementary to the N-terminal region of the lacI gene. Each primer-template was incubated with E. coli DNA polymerase I (Klenow fragment) under conditions favoring misincorporation, wherein one of the 4 dNTPs was lacking ('minus' reaction) or present at very low concentration ('micro' reaction). The extent of elongation of each primer was assessed by gel electrophoresis, and lacI mutants arising during the misincorporation reactions were detected by a transfection assay in which i- base substitutions within the in vitro synthesized strand were selectively recovered by the use of uracil-containing templates. Direct dideoxy sequencing of the '-A' reaction products and sequence analysis of i- mutant progeny revealed a vast predominance of single and non-tandem multiple base transitions. The addition of small quantities of dATP to a '-A' reaction increased the mutation yield and broadened the distribution of base substitutions along the template. We detected a general bias towards increased base substitution at template positions flanked by G.C base pairs or 5'-pyrimidine, 3'-purine nearest neighbors, although considerable site-to-site variation in the occurrence of base substitutions was seen, even within identical nearest neighbor contexts.

Lethal and mutagenic action of black light (325 to 400 nm) on Haemophilus influenzae in the presence of air.

Near-ultraviolet (UV) light (325 to 400 nm), in the presence of air and the absence of exogenous photosensitizing compounds, is lethal and mutagenic for Haemophilus influenzae. The lethal effect is the same for both wild type and streptomycin-resistant mutants, indicating that the mutants are not selected by the irradiation. The inactivation and mutagenicity show a large shoulder, suggesting the existence of repair systems. Filters were used to eliminate the possibility of short-UV irradiation. The effective radiation is between 325 to 400 nm. The lethal and mutagenic effects are higher during mid and late log phase than during early log or stationary phase.

[Repair mechanisms of damaged deoxyribonucleic acid molecules]. / Mecanismos de reparación de daños a la molécula del ácido desoxirribonucleico.

The importance of the DNA-damage repair mechanisms comes from the fact that any chemical modification to the DNA molecule, no matter how small it is, very often causes cell death and sometimes it can produce mutations whose biological effects are unpredictable. Taking into account that in the last decade great advances have been reported for the understanding of these mechanisms, and this knowledge can be essential to reach the control of the mutagenesis, we give a current review of the main DNA-damage repair pathways, with special emphasis in its classification by the kind of mechanisms and in their main features. As a particular case, the error prone repair mechanism is included (SOS-REPAIR). Additionally the three inducible DNA repair systems are described. That is to say, those cases in which the cell treatment with sublethal doses of some physical or chemical agents, induces a cell response that increases its capacity to repair the DNA-damage causes by higher doses of the same agent. Finally some small general comments are made.

Mutagenic assessment of 1,N6-ethenodeoxyadenosine in DNA.

The mutagenic role of 1-N6-Ethenodeoxydenosine (epsilon A) was assessed by a genetic assay of mutations in the 5' coding region of the lacl gene of Escherichia coli. 1-N6-Etheno-2-deoxydadenosine 5'-triphosphate (epsilon dATP) was substituted for dATP during in vitro DNA synthesis on M13 recombinant uracil single stranded DNA bearing the lacl gene, catalyzed by the large fragment of E. coli DNA polymerase I. DNA products were transfected into a strain of E. coli lacking a chromosomal copy of the lacl gene, and i- phenotypic mutants were seen as blue plaques in the absence of inducer. Mutant progeny were characterized by dideoxy sequencing in the N-terminal region of the lacl gene where epsilon A had originally replaced A, and were found to have T-->C transitions. The frequency of base substitution mutation was different in each of three target sites tested. Taking into account the sequence changes and the coding properties at target sites, we conclude that in general, epsilon A increases the mutation frequency when compared with the control (transfection with unsubstituted DNA). This increase was similar to that produced by in vitro primer elongation in absence of dATP. The combined results of the electrophoretic assay of primer elongation, measurements of mutation frequency, and sequence analysis of mutant phage progeny support the proposal that epsilon A in template DNA can be mutagenic through epsilon AC mispairing during in vivo replication.

Estudio comparativo del efecto de 5-bromodesoxiuridina y de 5-hidroximetildesoxiuridina sobre el desarrollo de Escherichia coli auxotrofa a timidina. / Comparative study of the effect of 5-bromodeoxyuridine and 5-hidroxymethyldeoxyuridine on the development of thymidine auxotroph Escherichia coli

Actualmente contamos con una mutante de Escherichia coli sin actividad de fosforilasa de la timidina, por consecuencia, este microorganismo crece con timidina y no con timina siendo posible en esta cepa hacer los estudios del efecto de BrUdR y de otro analogo de la timidina la hmUdR sobre el crecimiento de E. coli. La adicion de cantidades limitadas de timidina en un medio minimo dio lugar a la aparicion de "muerte por falta de timidina". Los analogos se agregaron solos o mezclados en diferentes proporciones con timidina, observandose que hmUdR solo, no estimulo el crecimiento, pero al agregarse junto con timidina disminuyo la muerte de la bacteria por falta de timidina. La BrUdR por su parte aumento la viabilidad tanto cuando se agrego sola como cuando se anadio mezclada con timidina. Estos estudios sugirieron que la cepa utiliza de preferencia timidina