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Ling F, Hori A, Yoshitani A, Niu R, Yoshida M, Shibata T. Din7 and Mhr1 expression levels regulate double-strand-break-induced replication and recombination of mtDNA at ori5 in yeast. Nucleic Acids Res 2013; 41:5799-816. [PMID: 23598996 PMCID: PMC3675488 DOI: 10.1093/nar/gkt273] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Ntg1 and Mhr1 proteins initiate rolling-circle mitochondrial (mt) DNA replication to achieve homoplasmy, and they also induce homologous recombination to maintain mitochondrial genome integrity. Although replication and recombination profoundly influence mitochondrial inheritance, the regulatory mechanisms that determine the choice between these pathways remain unknown. In Saccharomyces cerevisiae, double-strand breaks (DSBs) introduced by Ntg1 at the mitochondrial replication origin ori5 induce homologous DNA pairing by Mhr1, and reactive oxygen species (ROS) enhance production of DSBs. Here, we show that a mitochondrial nuclease encoded by the nuclear gene DIN7 (DNA damage inducible gene) has 5′-exodeoxyribonuclease activity. Using a small ρ− mtDNA bearing ori5 (hypersuppressive; HS) as a model mtDNA, we revealed that DIN7 is required for ROS-enhanced mtDNA replication and recombination that are both induced at ori5. Din7 overproduction enhanced Mhr1-dependent mtDNA replication and increased the number of residual DSBs at ori5 in HS-ρ− cells and increased deletion mutagenesis at the ori5 region in ρ+ cells. However, simultaneous overproduction of Mhr1 suppressed all of these phenotypes and enhanced homologous recombination. Our results suggest that after homologous pairing, the relative activity levels of Din7 and Mhr1 modulate the preference for replication versus homologous recombination to repair DSBs at ori5.
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Affiliation(s)
- Feng Ling
- Chemical Genetics Laboratory, RIKEN, Hirosawa 2-1, Wako-shi, Saitama 351-0198, Japan.
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Tullman J, Guntas G, Dumont M, Ostermeier M. Protein switches identified from diverse insertion libraries created using S1 nuclease digestion of supercoiled-form plasmid DNA. Biotechnol Bioeng 2011; 108:2535-43. [PMID: 21618478 DOI: 10.1002/bit.23224] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/26/2011] [Accepted: 05/09/2011] [Indexed: 11/07/2022]
Abstract
We demonstrate that S1 nuclease converts supercoiled plasmid DNA to unit-length, linear dsDNA through the creation of a single, double-stranded break in a plasmid molecule. These double-stranded breaks occur not only in the origin of replication near inverted repeats but also at a wide variety of locations throughout the plasmid. S1 nuclease exhibits this activity under conditions typically employed for the nuclease's single-stranded nuclease activity. Thus, S1 nuclease digestion of plasmid DNA, unlike analogous digestion with DNaseI, effectively halts after the first double-stranded break. This property makes easier the construction of large domain insertion libraries in which the goal is to insert linear DNA at a variety of locations throughout a plasmid. We used this property to create a library in which a circularly permuted TEM1 β-lactamase gene was inserted throughout a plasmid containing the gene encoding Escherichia coli ribose binding protein. Gene fusions that encode allosteric switch proteins in which ribose modulates β-lactamase catalytic activity were isolated from this library using a combination of a genetic selection and a screen.
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Affiliation(s)
- Jennifer Tullman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400N. Charles St., Baltimore, Maryland 21218, USA
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Rittié L, Perbal B. Enzymes used in molecular biology: a useful guide. J Cell Commun Signal 2008; 2:25-45. [PMID: 18766469 DOI: 10.1007/s12079-008-0026-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 08/13/2008] [Indexed: 12/31/2022] Open
Abstract
Since molecular cloning has become routine laboratory technique, manufacturers offer countless sources of enzymes to generate and manipulate nucleic acids. Thus, selecting the appropriate enzyme for a specific task may seem difficult to the novice. This review aims at providing the readers with some cues for understanding the function and specificities of the different sources of polymerases, ligases, nucleases, phosphatases, methylases, and topoisomerases used for molecular cloning. We provide a description of the most commonly used enzymes of each group, and explain their properties and mechanism of action. By pointing out key requirements for each enzymatic activity and clarifying their limitations, we aim at guiding the reader in selecting appropriate enzymatic source and optimal experimental conditions for molecular cloning experiments.
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Affiliation(s)
- Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA,
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Cross MJ, Waters DLE, Lee LS, Henry RJ. Endonucleolytic mutation analysis by internal labeling (EMAIL). Electrophoresis 2008; 29:1291-301. [PMID: 18288672 DOI: 10.1002/elps.200700452] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mismatch-specific endonucleases are efficient tools for the targeted scanning of populations for subtle DNA variations. Conventional protocols involve 5'-labeled amplicon substrates and the detection of digestion products by LIF electrophoresis. A shortcoming of such protocols, however, is the limited 5'-signal strength. Normally the sensitivity of fluorescent DNA analyzers is superior to that of intercalating dye/agarose systems, however, pooling capacities of the former and latter approaches to mismatch scanning are somewhat similar. Detection is further limited by significant background. We investigated the activity of CEL nucleases using amplicon substrates labeled both internally and at each 5'-terminus. The amplicons were generated from exon 8 of the rice starch synthase IIa encoding gene. Signal of both 5'-labels was significantly reduced by enzyme activity, while that of the internal label was largely unaffected. In addition, background resulting from internal labeling was a significant improvement on that associated with 5'-labeling. Sizing of the multilabeled substrates suggests that 5'-modification enhances exonucleolytic activity, resulting in the removal of the dye-labeled terminal nucleotides. We have developed an alternative approach to mismatch detection, in which amplicon labeling is achieved via the incorporation of fluorescently labeled deoxynucleotides, which we have named Endonucleolytic Mutation Analysis by Internal Labeling (EMAIL). The strength of the EMAIL assay was demonstrated by the reclassification of a rice line as being heterozygous for the starch gene. This cultivar was assigned as being homozygous by a previous resequencing study. EMAIL shows potential for the clear identification of multiple mutations amongst allelic pools.
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Affiliation(s)
- Michael J Cross
- Grain Foods CRC, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, NSW, Australia.
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Poon K, Macgregor RB. Probing the structure of multi-stranded guanine-rich DNA complexes by Raman spectroscopy and enzymatic degradation. Biophys Chem 1999; 79:11-23. [PMID: 10371018 DOI: 10.1016/s0301-4622(99)00034-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The multi-stranded DNA complexes formed by the oligonucleotides d(T15G4T2G4), Tel, and d(T15G15), TG, were examined by nuclease digestion and Raman spectroscopy. Both Tel and TG can aggregate to form structures consisting of multiple, parallel-oriented DNA strands with two independent structural domains. Overall, the structures of the TG and Tel aggregates appear similar. According to the Raman data, the majority of bases are in C2'-endo/anti conformation. The interaction of guanines at the 3'-ends in both complexes stabilizes the complexes and protects them from degradation by exonuclease III. The 5'-extensions remain single-stranded and the thymines are accessible to single-strand-specific nuclease digestion. The extent of enzymatic cleavage at the junction at the 5' end of the 15 thymines implies a conformational change between this part of the molecule and the guanine-rich region. The differential enzymatic sensitivity of the complexes suggests there are variations in backbone conformations between TG and Tel aggregates. TG aggregates were more resistant to digestion by DNase I, Mung Bean nuclease, and S1 nuclease than Tel complexes. It is proposed that the lower DNase I sensitivity may be partly due to the more stable backbone exhibited by TG than Tel complexes. Structural uniformity along the guanine core of TG is suggested, as there is no indication of structural discontinuities or protected sites in the guanine-rich regions of TG aggregates. The lower extent of digestion by Mung Bean nuclease at the 3' end implies that these bases are inaccessible to the enzyme. This suggests that there is minimal fraying at the ends, which is consistent with the extreme thermal stability of the TG aggregates.
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Affiliation(s)
- K Poon
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Ontario, Canada
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6
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Abstract
Single-strand-specific nucleases, which act on single-stranded nucleic acids and single-stranded regions in double-stranded nucleic acids, are multifunctional enzymes and are ubiquitous in distribution. They find wide application as analytical tools in molecular biology research, although enzymes such as P1 nuclease are also used for production of flavor enhancers such as 5' IMP and 5' GMP. Because these enzymes are mainly used as analytical tools, very little attention was paid to aspects relating to their structure-function relationships. However, during the last few years considerable developments have taken place in this area. Single-strand-specific nucleases, their purification, characteristics, biological role, and applications have been reviewed.
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Affiliation(s)
- S U Gite
- Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
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Fisher R, Krizsanovich-Williams K, Feiss M. Construction and characterization of a cohesive end site mutant of bacteriophage lambda. Virology 1980; 107:144-59. [PMID: 6449778 DOI: 10.1016/0042-6822(80)90280-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Abanobi SE, Columbano A, Mulivor RA, Rajalakshmi S, Sarma DS. In vivo replication of hepatic deoxyribonucleic acid of rats treated with dimethylnitrosamine: presence of dimethylnitrosamine-induced O6-methylguanine, N7-methylguanine, and N3-methyladenine in the replicated hybrid deoxyribonucleic acid. Biochemistry 1980; 19:1382-7. [PMID: 7387997 DOI: 10.1021/bi00548a018] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Experiments were designed to determine whether some chemical lesions such as O6-methylguanine, N7-methylguanine, and N3-methyladenine induced in rat liver DNA by the hepatocarcinogen dimethylnitrosamine permit replication in vivo. For this purpose, [14C]dimethylnitrosamine was administered to methylate the parental strand of liver DNA. Four hours later, a time period when the carcinogen cannot be detected in either the liver or the blood, rats were subjected to partial hepatectomy in order to induce DNA replication. During the S phase, 5-bromo-2-deoxyuridine was administered to render the newly made strands heavy. The rebanded, hybrid, hepatic DNA of density 1.714 g/cm3 and greater was pooled from the neutral cesium chloride gradient, dialyzed, and lyophilized. The hybrid DNA was then treated with S1 nuclease to digest any single-stranded regions. The results obtained indicated the presence of O6-methylguanine, N7-methylguanine, and N3-methyladenine in S1 nuclease resistant, hybrid DNA. The results are interpreted to indicate that these chemical lesions permitted in vivo DNA replication.
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12
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Wani AA, Hadi SM. Partial purification and properties of an endonuclease from germinating pea seeds specific for single-stranded DNA. Arch Biochem Biophys 1979; 196:138-46. [PMID: 41480 DOI: 10.1016/0003-9861(79)90560-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Glover SW. Aspects of genetic engineering in micro-organisms. Adv Microb Physiol 1979; 18:235-71. [PMID: 288307 DOI: 10.1016/s0065-2911(08)60418-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Bahl CP, Wu R, Brousseau R, Sood AK, Hsiung HM, Narang SA. Chemical synthesis of versatile adaptors for molecular cloning. Biochem Biophys Res Commun 1978; 81:695-703. [PMID: 96825 DOI: 10.1016/0006-291x(78)91408-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Dean RG, Cutler RG. Absence of significant age-dependent increase of single-stranded DNA extracted from mouse liver nuclei. Exp Gerontol 1978; 13:287-92. [PMID: 738375 DOI: 10.1016/0531-5565(78)90036-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Wu R, Bahl CP. Synthetic oligodeoxynucleotides for analyses of DNA structure and function. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1978; 21:101-41. [PMID: 358276 DOI: 10.1016/s0079-6603(08)60268-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Scheller RH, Dickerson RE, Boyer HW, Riggs AD, Itakura K. Chemical synthesis of restriction enzyme recognition sites useful for cloning. Science 1977; 196:177-80. [PMID: 847463 DOI: 10.1126/science.847463] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
By a triester chemical synthesis method, three decameric DNA's have been made; these act as substrates for several restriction endonucleases, including Eco RI, Bam I, and Hind III. These homogenous decamers form duplexes that can be efficiently blunt-end ligated to themselves or to other DNA molecules by the action of T4 DNA ligase and thus are useful tools for molecular cloning experiments.
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Schmidt F, Besemer J, Starlinger P. The isolation of IS1 and IS2 DNA. MOLECULAR & GENERAL GENETICS : MGG 1976; 145:145-54. [PMID: 934052 DOI: 10.1007/bf00269586] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA of the IS-elements IS1 and IS2 was prepared by digestion of appropriate heteroduplex molecules with endonuclease S1, followed by sucrose gradient centrifugation or gel electrophoresis. The material obtained is homogeneous with regard to size. The length of IS1 DNA is 820 +/- 65 nucleotides, the length of IS2 DNA is 1,350 +/- 70 nucleotides. IS1 DNA is not cleaved by the restriction endonucleases Eco R1, Hind II or Hind III. IS2 DNA is cleaved once by each of the two latter enzymes. The buoyand density determined by equilibrium centrifugation of Hg-complexes in Cs2so4 corresponds to a GC content of approximately 50%. Labelling with polynucleotide kinase indicates that both IS DNA's have a guanosyl residue at both of their 5'-termini.
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Abstract
A general method has been developed to introduce any double-stranded DNA molecule into cloning vehicles at different restriction endonuclease sites. In this method a chemically synthesized decadeoxyribonucleotide duplex, containing a specific restriction endonuclease sequence, is joinlex DNA is cut by the same restriction endonuclease to generate the cohesive ends. It is then inserted into the restriction endonuclease cleavage site of the cloning vehicle. To demonstrate the feasibility of this new method, we have inserted separately the synthetic lac operator DNA at the Bam I and HindIII cleavage sites of the plasmid pMB9 DNA.
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