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At least 883 records · Page 49Linked to original sources
PubMed2000

Escherichia coli responses to a single DNA adduct.

To study the mechanisms by which Escherichia coli modulates the genotoxic effects of DNA damage, a novel system has been developed which permits quantitative measurements of various E. coli pathways involved in mutagenesis and DNA repair. Events measured include fidelity and efficiency of translesion DNA synthesis, excision repair, and recombination repair. Our strategy involves heteroduplex plasmid DNA bearing a single site-specific DNA adduct and several mismatched regions. The plasmid replicates in a mismatch repair-deficient host with the mismatches serving as strand-specific markers. Analysis of progeny plasmid DNA for linkage of the strand-specific markers identifies the pathway from which the plasmid is derived. Using this approach, a single 1, N(6)-ethenodeoxyadenosine adduct was shown to be repaired inefficiently by excision repair, to inhibit DNA synthesis by approximately 80 to 90%, and to direct the incorporation of correct dTMP opposite this adduct. This approach is especially useful in analyzing the damage avoidance-tolerance mechanisms. Our results also show that (i) progeny derived from the damage avoidance-tolerance pathway(s) accounts for more than 15% of all progeny; (ii) this pathway(s) requires functional recA, recF, recO, and recR genes, suggesting the mechanism to be daughter strand gap repair; (iii) the ruvABC genes or the recG gene is also required; and (iv) the RecG pathway appears to be more active than the RuvABC pathway. Based on these results, the mechanism of the damage avoidance-tolerance pathway is discussed.

Bacterial Proteins↗
PubMed2004

The repair of gamma-ray-induced chromosomal damage in human lymphocytes after exposure to extremely low frequency electromagnetic fields.

G(0) human blood lymphocytes were irradiated with 2.0 Gy gamma-rays and cultured to metaphase whilst held in a 50-Hz power frequency magnetic field of 0.23, 0.47 or 0.7 mT. No differences were found in the frequencies of gamma-induced chromosome aberrations observed in cells held in the EM fields compared with replicates held in a sham coil. Similar field conditions have been reported to increase the frequency of gamma-induced HPRT mutations, leading to a suggestion that the EM fields alter the fidelity of repair of genomic lesions. This was not confirmed by the chromosome aberration assay described here.

Adult↗
PubMedDate not supplied

[Mismatch repair].

Specific repair systems are activated in response to the DNA damage. Mismatch repair protects the genome of prokaryotic and eukaryotic cells from lesions that appear during process of DNA replication or are induced by mutagenic factors. The methyl directed mismatch repair distinguishes the new strand from the old strand by the hemi-methylated state of the DNA and controls the fidelity of genetic information after homologous recombination. The very short patch repair restores the mismatches at the sites with nucleotide sequence CC(W/T)GG. The "8-oxoG" pathway is independent of the hemi-methylated state of the DNA, and removes the oxidated nucleotides from the genome of prokaryotes and eukaryotes. Mutations in genes of mismatch repair enhance the process of mutagenesis in prokaryotic cell, and are the reason for the development of the colon cancer in humans. The mechanisms of mismatch repair and the role of defective repair proteins in mutagenesis and carcinogenesis are discussed in this review.

Animals↗
PubMed2006

Human replication protein A can suppress the intrinsic in vitro mutator phenotype of human DNA polymerase lambda.

DNA polymerase lambda (pol lambda) is a member of the X family DNA polymerases and is endowed with multiple enzymatic activities. In this work we investigated the in vitro miscoding properties of full-length, human pol lambda either in the absence or in the presence of the human auxiliary proteins proliferating cell nuclear antigen (PCNA) and replication protein A (RP-A). Our data suggested that (i) pol lambda had an intrinsic ability to create mismatches and to incorporate ribonucleotides at nearly physiological Mn++ and Mg++ concentrations; (ii) the sequence of the template-primer could influence the misincorporation frequency of pol lambda; (iii) pol lambda preferentially generated G:T and G:G mismatches; (iv) RP-A, but not PCNA, selectively prevented misincorporation of an incorrect nucleotide by pol lambda, without affecting correct incorporation and (v) this inhibitory effect required a precise ratio between the concentrations of pol lambda and RP-A. Possible physiological implications of these findings for the in vivo fidelity of pol lambda are discussed.

Base Pair Mismatch↗
PubMed2000

Transfer of research-based HIV prevention interventions to community service providers: fidelity and adaptation.

HIV prevention research interventions usually follow protocols with specific procedures. If a community-delivered intervention uses the same procedures with the same populations as those in the original research, the behavior change effects should be similar. However, community-based providers may not replicate an intervention exactly as it was conducted in the effectiveness study. Adaptation may be needed to better meet the needs of the clients, community, or organization. We propose that interventions can be defined in terms of core elements likely to be responsible for effectiveness. These core elements cannot be changed without fundamentally changing the intervention, whereas other characteristics may be modified without altering effectiveness. HIV prevention researchers and service providers can collaborate to develop interventions that not only are effective but can also be successfully implemented by service organizations. If researchers actively involve service providers and community members in intervention planning, technology transfer goals can be better achieved.

Community Health Services↗
PubMed1983

Subspecies of DNA polymerase alpha from calf thymus with different fidelity in copying synthetic template-primers.

Three different subspecies of DNA polymerase alpha from calf thymus sedimenting at 9 S, 7 S and 5.7 S have been investigated with respect to their accuracy of in vitro DNA synthesis on poly (dA) (dT)16 and poly d(AT) as template-primers. Our results indicate that the structure of DNA polymerase alpha has a strong influence on the accuracy of DNA synthesis. The 9 S enzyme shows a misincorporation frequency of about 1:100 000. An error rate of 1:15 000 is measured for the 7 S species. The 5.7 S enzyme for which an error rate of 1:3 000 is determined, has to be considered as error prone. Lowering the rate of DNA synthesis leads to a decrease in fidelity. The single stranded DNA binding protein from E.coli increases the accuracy of the 5.7 S and the 7 S enzyme by a factor of two. Mn2+ decreases the fidelity of all three subspecies in a concentration dependent manner.

Animals↗
PubMed2003

Expression of cyclins A, E and topoisomerase II alpha correlates with centrosome amplification and genomic instability and influences the reliability of cytometric S-phase determination.

BACKGROUND: The progression of normal cells through the cell cycle is meticulously regulated by checkpoints guaranteeing the exact replication of the genome during S-phase and its equal division at mitosis. A prerequisite for this achievement is synchronized DNA-replication and centrosome duplication. In this context the expression of cyclins A and E has been shown to play a principal role. RESULTS: Our results demonstrated a correlation between centrosome amplification, cell cycle fidelity and the level of mRNA and protein expression of cyclins A and E during the part of the cell cycle defined as G1-phase by means of DNA content based histogram analysis. It is shown that the normal diploid breast cell line HTB-125, the genomically relatively stable aneuploid breast cancer cell line MCF-7, and the genomically unstable aneuploid breast cancer cell line MDA-231 differ remarkably concerning both mRNA and protein expression of the two cyclins during G1-phase. In MDA-231 cells the expression of e.g. cyclin A mRNA was found to be ten times higher than in MCF-7 cells and about 500 times higher than in HTB-125 cells. Topoisomerase II alpha showed high mRNA expression in MDA compared to MCF-7 cells, but the difference in protein expression was small. Furthermore, we measured centrosome aberrations in 8.4% of the MDA-231 cells, and in only 1.3% of the more stable aneuploid cell line MCF-7. MDA cells showed 27% more incorporation of BrdU than reflected by S-phase determination with flow cytometric DNA content analysis, whereas these values were found to be of the same size in both HTB-125 and MCF-7 cells. CONCLUSIONS: Our data indicate that the breast cancer cell lines MCF-7 and MDA-231, although both DNA-aneuploid, differ significantly regarding the degree of cell cycle disturbance and centrosome aberrations, which partly could explain the different genomic stability of the two cell lines. The results also question the reliability of cytometric DNA content based S-phase determination in genomically unstable tumor cell populations.

Antigens, Neoplasm↗
PubMed2000

Development of an in vivo assay to identify structural determinants in murine leukemia virus reverse transcriptase important for fidelity.

Error-prone DNA synthesis by retroviral reverse transcriptases (RTs) is a major contributor to variation in retroviral populations. Structural features of retroviral RTs that are important for accuracy of DNA synthesis in vivo are not known. To identify structural elements of murine leukemia virus (MLV) RT important for fidelity in vivo, we developed a D17-based encapsidating cell line (ANGIE P) which is designed to express the amphotropic MLV envelope. ANGIE P also contains an MLV-based retroviral vector (GA-1) which encodes a wild-type bacterial beta-galactosidase gene (lacZ) and a neomycin phosphotransferase gene. Transfection of ANGIE P cells with wild-type or mutated MLV gag-pol expression constructs generated GA-1 virus that was able to undergo only one cycle of viral replication upon infection of D17 cells. The infected D17 cell clones were characterized by staining with 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal), and the frequencies of inactivating mutations in lacZ were quantified. Three mutations in the YVDD motif (V223M, V223S, and V223A) and two mutations in the RNase H domain (S526A and R657S) exhibited frequencies of lacZ inactivation 1.2- to 2.3-fold higher than that for the wild-type MLV RT (P < 0.005). Two mutations (V223I and Y598V) did not affect the frequency of lacZ inactivation. These results establish a sensitive in vivo assay for identification of structural determinants important for accuracy of DNA synthesis and indicate that several structural determinants may have an effect on the in vivo fidelity of MLV RT.

Animals↗
PubMed2001

Molecular anatomy and pathophysiologic implications of drug resistance in hepatitis B virus infection.

Synthesis of the hepatitis B virus (HBV) DNA genome occurs within the viral nucleocapsid in a mechanistically ordered fashion. The nucleocapsid contains small pores that permit influx of nucleotide triphosphates and metabolites of nucleoside analogues such as lamivudine for DNA synthesis. Lamivudine is a potent inhibitor of HBV and human immunodeficiency virus (HIV) reverse transcriptases, but substitutions of isoleucine or valine for methionine within the tyrosine-methionine-aspartate-aspartate (YMDD) motif are associated with virologic and clinical resistance to lamivudine therapy. Under lamivudine selection pressure, the high viral production rate and the low fidelity viral polymerase contribute to frequent development of the YMDD mutants. However, the pattern and dynamics of emergence of the mutant viruses over the wild-type virus are determined by multiple factors including replication efficiency, host immune response, and availability of replication space. Structural modeling of HIV reverse transcriptase has permitted key insights into the molecular basis of lamivudine resistance of HBV based on evolutionary relatedness of HIV and HBV. The side groups of isoleucine and valine of the YMDD mutants sterically prevent lamivudine from appropriately configuring into the nucleotide binding site of the reverse transcriptase. Aminotransferase flares are associated with lamivudine therapy and may signify clinical resistance with emergence of YMDD mutants. They may also herald the recovery phase with seroconversion and viral clearance. Reconstitution of the endogenous anti-HBV immune response may be equally important in the control of viral replication by lamivudine and other nucleoside analogues.

Drug Resistance, Microbial↗
PubMed1994

Infectious transcripts from PCR-amplified broad bean mottle bromovirus cDNA clones and variable nature of leader regions in RNA 3 segment.

The genome of broad bean mottle bromovirus (BBMV) contains three positive-sense ssRNA segments, each capped with m7GpppA. Full-length transcribable cDNA clones for four strains of BBMV were constructed by employing reverse transcriptase-PCR (RT-PCR) and a high fidelity Vent DNA polymerase. The transcribed BBMV RNAs contained a 5' non-viral G residue and, although delayed, produced symptoms similar to those observed in plants infected with authentic virion RNAs. The transcripts replicated inefficiently in protoplasts. In contrast, transcript-derived progeny BBMV RNAs had the repaired termini, were as infectious as the authentic BBMV RNAs and replicated to high levels in protoplasts. In vitro translation of synthetic RNAs confirmed the previously proposed gene expression strategy for BBMV. Sequencing of virion RNAs from the Bawden strain revealed two forms of BBMV RNA3 components, the longer form containing 21 5' extra nucleotides derived by the duplication of two short 5' leader regions. The relative concentration of the two RNA 3 forms was found to be host-dependent, with the longer form prevailing in broad bean and Nictiana clevelandii infections and the shorter form in bean infections.

Base Sequence↗
PubMed1995

[Structure of chromatin. 2: levels of organization of DNA in the nucleus. Highly organized structures].

In the interphase nucleus, the 30 nm fiber, whose characteristics were discussed in the first part of this review, is condensed 10-15 fold to form loops or domains of chromatin with a DNA packing ratio of 600. In the metaphase chromosomes, the packing ratio is 12000. The existence of loops in the interphase nucleus has been suggested by experiments from electronic microscopy, sedimentation and nuclease digestion. These loops of 20-200Kb are attached at their bases to a non-histone protein network, that is the nuclear matrix or scaffold whose major component is the topoisomerase II. There is disagreement regarding the arrangement of the loops in metaphase chromosomes and several models have been proposed. Six of these models are presented. A number of data suggest that the sequences of attachment (SARs/MARs) define functional units containing related genes. Thus, the compartmentation of the genome in topographically independent domains might ensure the fidelity of epigenetic transmission of the chromatin structure, and it might help to control gene expression. In the interphase nucleus, the chromosomes coexist with other domains involved in major nuclear functions such as transcription, replication or post-transcriptional modifications and whose compartmentation is not always evident.

Centromere↗
PubMed1991

Dependence of the mutation spectrum in a shuttle plasmid replicated in human lymphoblasts on dose of gamma radiation.

The frequencies and types of mutations induced in the target gene, supF-tRNA, of the shuttle vector pZ189 were analysed following the replication of the gamma-irradiated plasmid in the human lymphoblastoid cell line, GM606. The mutation frequency measured in progeny of unirradiated pZ189 was 1.02 x 10(-4), increasing to 17.5 x 10(-4) at 1000 cGy, and to 63.4 x 10(-4) at 5000 cGy, approximately 17- and 62-fold over background levels, respectively. Simultaneously, the number of plasmids capable of replicating in Escherichia coli decreased with increasing radiation dose to 4% of the control value at 5000 cGy. Electrophoresis of the irradiated DNA showed a correlation between increases in mutation frequency and decreases in plasmid survival, and the formation of open-circular and linear DNA. The majority of the spontaneous (69.8%) and induced mutations (85.7%) at 1000 and 79.4% at 5000 cGy) were base substitutions and were generally of similar types among all groups. However, changes at 2500 (12.7%) and 5000 cGy (13.2%) involving A:T base pairs were greater than those in unirradiated controls (3.4%) or those at 1000 cGy (2.0%). This increase in A:T base pair mutations could be a result of reduced repair fidelity when the DNA is extensively damaged by high doses of ionizing radiation.

Cell Line↗
PubMed1992

Optimization of long-distance PCR using a transposon-based model system.

The ability to amplify routinely long PCR products (5-25 kb) with high specificity and fidelity, regardless of target template sequence or structure, would provide significant benefits to genome mapping and sequencing endeavors. Although occasional reports have described the generation of long PCR products, such results have been difficult to replicate and have frequently utilized probe hybridization to identify the specific product from nonspecific amplified DNA. Production of specific PCR products has generally been limited to target templates of less than 3 kb. To extend the effective range of standard PCR amplification, it may be necessary to utilize alternative reaction conditions and/or components, such as novel thermostable DNA polymerases or accessory proteins. We describe the use of a model system to evaluate systematically methodological changes that might enable efficient long-range PCR. Specifically, the transposon Tn5supF has been used to introduce randomly identical, known primer binding sites within separate isolates of phage clones carrying identical inserts. Transposon-based PCR allows us to study amplification of DNA fragments that vary in size and sequence using only a single set of primers. In the present studies, we describe conditions that enable PCR amplification of specific DNA templates ranging in size up to 9 kb. Some of the key features of our methodology include the use of recombinant Thermus thermophilus (rTth) DNA polymerase, the addition of gelatin to the reaction mixture, the use of wax-mediated "hot starts" and, lastly, the use of auto-segment extension thermocycling. These results also provide insights into additional approaches that might further enhance our ability to perform long-distance PCR.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1992

A fundamental role for cell cycle regulation in the chemosensitivity of cancer cells?

The majority of clinically effective anticancer drugs inhibit some aspect of the machinery responsible for DNA replication and chromosome segregation. Drug action also arrests cells at defined points in the cell cycle called checkpoints. These checkpoints ensure that subsequent cell cycle events are inhibited until the inflicted damage is repaired. The fidelity of checkpoint control and susceptibility of cells to apoptosis while repair is underway may be important factors in the success of chemotherapy. We discuss these concepts and focus particularly on possible applications to improved antitumor therapy with DNA damaging agents.

Antineoplastic Agents↗
PubMed1997

Increased fidelity of drug-selected M184V mutated HIV-1 reverse transcriptase as the basis for the effectiveness of 3TC in HIV clinical trials.

HIV-infected individuals, who received 3TC monotherapy over one year, generally had lower plasma viral burden than at base-line. This was in spite of high-level resistance to this compound and the appearance of the M184V substitution in the HIV reverse transcriptase (RT) gene, responsible for diminished sensitivity to 3TC. This apparent contradiction is explained by an increase in the fidelity of the HIV RT, conferred by the M184V mutation, on the basis of the following observations. First, titers of viral neutralizing antibodies, as measured against sequential autologous HIV isolates, remained stable in this population in contrast to rapid declines in patients treated with other drugs. This suggests that increased fidelity of M184V RT may limit variability in the HIV env gene and result in protracted effectiveness of anti-viral immune responsiveness. Second, recombinant HIV, that contained the M184V substitution in RT, could not replicate in the presence of d4T, AZT, Nevirapine, Delavirdine or Saquinavir, using previously described protocols for the generation of drug resistance in vitro.

Anti-HIV Agents↗
PubMed2005

In vivo analysis of replication and immunogenicity of proviral clones of human T-lymphotropic virus type 1 with selective envelope surface-unit mutations.

Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell lymphoma/leukemia (ATL). The HTLV-1 envelope gene exhibits limited variability when examined from infected individuals, but has not been tested using infectious clones of the virus in animal models. In vitro assays indicate that HTLV-1 envelope (Env) Ser75Ile, Asn95Asp, and Asn195Asp surface unit (SU) mutants are able to replicate in and immortalize lymphocytes. Herein, we examined the effects of these Env mutants in rabbits inoculated with HTLV-1 immortalized ACH.75, ACH.95, or ACH.195 cell lines (expressing full-length molecular clones with the SU mutations) or the ACH.1 cell line (expressing wild-type SU). All rabbits became infected, and the fidelity of the mutations was maintained throughout the 8-week study. However, SU point mutations resulted in decreased antibody responses to viral group-associated antigen (Gag) and Env antigens. ACH.195 rabbits had a selective decreased antibody response to SU, and one ACH.195 rabbit had an antibody response to both HTLV-1 and HTLV-2 SUs. Some mutant inoculation groups had altered proviral loads. However, peripheral-blood mononuclear cell (PBMC) proviral loads did not correlate with antibody responses. Our data are the first to demonstrate that mutations in critical determinants of HTLV-1 Env SU altered antibody responses and proviral loads, but do not prevent viral replication in vivo.

Amino Acid Substitution↗
PubMed1999

New yeast genes important for chromosome integrity and segregation identified by dosage effects on genome stability.

Phenotypes produced by gene overexpression may provide important clues to gene function. Here, we have performed a search for genes that affect chromo-some stability when overexpressed in the budding yeast Saccharomyces cerevisiae. We have obtained clones encompassing 30 different genes. Twenty-four of these genes have been previously characterized. Most of them are involved in chromatin dynamics, cell cycle control, DNA replication or mitotic chromosome segregation. Six novel genes obtained in this screen were named CST (chromosome stability). Based on the pattern of genomic instability, inter-action with checkpoint mutations and sensitivity to chromosome replication or segregation inhibitors, we conclude that overexpression of CST4 specifically interferes with mitotic chromosome segregation, and CST6 affects some aspect of DNA metabolism. The other CST genes had complex pleiotropic phenotypes. We have created deletions of five genes obtained in this screen, CST9, CST13, NAT1, SBA1 and FUN30. None of these genes is essential for viability, and deletions of NAT1 and SBA1 cause chromosome instability, a phenotype not previously associated with these genes. This work shows that analysis of dosage effects is complementary to mutational analysis of chromosome transmission fidelity, as it allows the identification of chromosome stability genes that have not been detected in mutational screens.

Aneuploidy↗
PubMed2001

Structure of the replicating complex of a pol alpha family DNA polymerase.

We describe the 2.6 A resolution crystal structure of RB69 DNA polymerase with primer-template DNA and dTTP, capturing the step just before primer extension. This ternary complex structure in the human DNA polymerase alpha family shows a 60 degrees rotation of the fingers domain relative to the apo-protein structure, similar to the fingers movement in pol I family polymerases. Minor groove interactions near the primer 3' terminus suggest a common fidelity mechanism for pol I and pol alpha family polymerases. The duplex product DNA orientation differs by 40 degrees between the polymerizing mode and editing mode structures. The role of the thumb in this DNA motion provides a model for editing in the pol alpha family.

Binding Sites↗