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Deoxyribonucleases, Type III Site-Specific (0):
Recent article
Deoxyribonucleases, Type III Site-Specific
Abstract
We demonstrate that Type III enzymes can also cleave DNA with sites in tail-to-tail repeat with high efficiency. The ability to distinguish both inverted repeat substrates from direct repeat substrates in a manner independent of DNA topology or accessory proteins can only be reconciled with an alter...
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PMID: 20435912
PDF is available here.
PDF is available here.
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Abstract
We suggest that an ATPase activity may not automatically indicate a DNA translocase, but can alternatively indicate a molecular switch that triggers communication by thermally driven DNA sliding. The generality of this mechanism to other ATP-dependent communication processes such as mismatch repair...
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PMID: 20298192
PDF is available here.
PDF is available here.
EMBO Journal (26)16 2007
Abstract
We use atomic force microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number and size distribution of loops formed, we conclude that the loops observed do not result from translocation, but are instead formed by a contact between site-bound EcoP15I and a nonspecific region of DNA. Thi...
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PMID: 17660745
PDF is available here.
PDF is available here.
Abstract
We have studied the behavior of EcoP15I, using a novel fast-scan atomic force microscope, which uses a miniaturized cantilever and scan stage to reduce the mechanical response time of the cantilever and to prevent the onset of resonant motion at high scan speeds. With this instrument, we were able t...
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PMID: 17646654
PDF is available here.
PDF is available here.
Abstract
A closer inspection of the amino acid sequence of EcoP15I DNA methyltransferase revealed a region of similarity to the PDXn(D/E)XK catalytic site of type II restriction endonucleases, except for methionine in EcoP15I DNA methyltransferase instead of proline. Substitution of methionine at position 35...
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PMID: 17148461
PDF is available here.
PDF is available here.
Journal of Molecular Biology (366)1 2007
Abstract
We took advantage of the EcoP15I-overexpressing vector pQEP15 and affinity chromatography to generate a quantity of EcoP15I high enough for comprehensive proteolytic digestion studies and analyses of the proteolytic fragments by mass spectrometry. We show here that in the presence of specific DNA th...
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PMID: 17156795
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)15 2007
Abstract
We have previously shown that a phase variable methyltransferase (Mod) associated with a type III R-M system in Haemophilus influenzae strain Rd coordinates the random switching of expression of multiple genes, and constitutes a phase variable regulon--'phasevarion'. We have now identified the recog...
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PMID: 17675301
PDF is available here.
PDF is available here.
Abstract
The electrochemistry of the base excision repair enzyme Endonuclease III (Endo III) in the presence and absence of DNA has been examined on highly oriented pyrolytic graphite (HOPG). At the surface modified with pyrenated DNA, a reversible signal is observed at 20 mV versus NHE for the [4Fe-4S]3+/2+...
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PMID: 16967954
PDF is available here.
PDF is available here.
Toxicology In Vitro (20)3 2006
Abstract
We investigated antigenotoxic potentials of low EGCG concentrations in human peripheral leucocytes. Leucocytes isolated from whole blood were (1) stimulated with phytohaemagglutinin, (2) damaged with genotoxic bleomycin, and (3) post-incubated to allow DNA repair. After each phase DNA integrity was...
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PMID: 16188420
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)14 2006
Abstract
We propose that this hypervariable region encodes the target recognition domain (TRD) of the Mod protein and that variability results in alterations to the recognition sequence of this R-M system. We argue that the high allelic diversity and phase variable nature of this R-M system have arisen due t...
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PMID: 16914439
PDF is available here.
PDF is available here.
Journal of Bacteriology (187)21 2005
Abstract
We examined the effect of bacteriophage functions, expressed in bacterial cells, on restriction of an infecting tester phage in a simple plaque formation assay. The efficiency of plaque formation on an Escherichia coli host carrying EcoRI, a type II restriction system, is not increased by the presen...
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PMID: 16237019
PDF is available here.
PDF is available here.
Abstract
We show that in the presence of exogenous AdoMet, the head-to-head oriented recognition sites are cleaved only on a supercoiled DNA. On a linear DNA, exogenous AdoMet strongly drives methylation while inhibiting cleavage reaction. Strikingly, AdoMet analogue sinefungin results in cleavage at all rec...
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PMID: 16026759
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)15 2005
Abstract
We demonstrate that, like other Type III restriction endonuclease, PstII does not turnover such that a DNA substrate is only fully cleaved at a Res2Mod2-to-site ratio of approximately 1:1. However, unlike other Type III enzymes, the cleavage rate profiles varied with protein concentration: using 5 n...
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PMID: 16120968
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)15 2005
Abstract
We also demonstrate that PstII and EcoP15I cannot interact and cleave a DNA substrate suggesting that Type III enzymes must make specific protein-protein contacts to activate endonuclease activity....
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PMID: 16120967
PDF is available here.
PDF is available here.
Journal of Molecular Biology (341)2 2004
Abstract
We used scanning force microscopy to visualise the protein interaction with linear DNA molecules containing two EcoP15I recognition sites in inverse orientation. In the presence of the cofactors ATP and Mg(2+), EcoP15I molecules were shown to bind specifically to the recognition sites and to form DN...
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PMID: 15276827
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)19 2004
Abstract
We demonstrate that the cleavage site of the R.EcoP15I restriction enzyme does not depend on the sequence context of the recognition site. Strikingly, this study demonstrates that the enzyme can cleave linear DNA having either recognition sites in the same orientation or a single recognition site. C...
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PMID: 15501920
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)14 2004
Abstract
We analysed the activity of EcoPI and EcoP15I on DNA catenanes in which the recognition sites were either on the same or separate rings. While substrates with a pair of sites located on the same ring were cleaved efficiently, catenanes with sites on separate rings were not cleaved. These results exc...
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PMID: 15302916
PDF is available here.
PDF is available here.
Journal of Molecular Biology (333)2 2003
Abstract
DNA cleavage by the type III restriction endonuclease EcoP1I was analysed on circular and catenane DNA in a variety of buffers with different salts. In the presence of the cofactor S-adenosyl methionine (AdoMet), and irrespective of buffer, only substrates with two EcoP1I sites in inverted repeat we...
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PMID: 14529619
PDF is available here.
PDF is available here.
Molecular Biotechnology (23)3 2003
Abstract
Restriction endonucleases have become a fundamental tool of molecular biology with many commercial vendors and extensive product lines. While a significant amount has been learned about restriction enzyme diversity, genomic organization, and mechanism, these continue to be active areas of research a...
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PMID: 12665693
PDF is available here.
PDF is available here.
Zhonghua Yixue Zazhi (82)21 2002
Abstract
1) The frequency of "G" allele of site rs228648 was 62.3% and 75.3% in case group 1 and case group 2 respectively, significantly higher than that in the control group (50.4%, P = 0.004 and P < 0.001). 2) The frequency of G/G genotype of rs228648 was 35% and 53% in case group 1 and case group 2 respe...
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PMID: 12509909
PDF is available here.
PDF is available here.
Abstract
We present a detailed description and analysis of the functional mechanism of the three known NTP-dependent restriction systems: type I and type III restriction-modification enzymes, as well as the methylation-dependent McrBC endonuclease....
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PMID: 12595133
PDF is available here.
PDF is available here.
Nucleic Acids Research (30)16 2002
Abstract
We show that the number of CAG repeats in the HD gene can be determined by restriction of the DNA with the endonuclease EcoP15I and subsequent analysis of the restriction fragment pattern by electrophoresis through non-denaturing polyacrylamide gels using the ALFexpress DNA Analysis System. CAG repe...
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PMID: 12177311
PDF is available here.
PDF is available here.
Journal of Molecular Biology (312)4 2001
Abstract
We investigated how the distance between two inversely oriented recognition sites affects DNA cleavage efficiency. We determined that EcoP15I cleaves DNA efficiently even for two adjacent head to head or tail to tail oriented target sites. Hence, DNA translocation appears not to be required for init...
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PMID: 11575924
PDF is available here.
PDF is available here.
Nucleic Acids Research (29)18 2001
Abstract
I and type III restriction and modification systems, the collision of translocating complexes triggers hydrolysis of phosphodiester bonds in unmodified DNA to generate double-strand breaks. Type I endonucleases break the DNA at unspecified sequences remote from the target sequence, type III endonucl...
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PMID: 11557806
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (202)2 2001
Abstract
The nucleotide sequence of an 11-kb chromosomal BglII fragment from Bacillus cereus American Type Culture Collection (ATCC) 10987 strain revealed two closely adjacent open reading frames organized in an operon, of which the deduced amino acids showed identity to the type III restriction and modifica...
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PMID: 11520613
PDF is available here.
PDF is available here.
Journal of Molecular Biology (310)1 2001
Abstract
We show that DNA restriction by EcoPI restriction enzyme does not take place in the absence of exogenously added AdoMet. Interestingly, the closely related EcoP15I enzyme has endogenously bound AdoMet and therefore does not require the addition of the cofactor for DNA cleavage. By employing a variet...
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PMID: 11419939
PDF is available here.
PDF is available here.
Journal of Molecular Biology (306)3 2001
Abstract
We characterized the structure and mode of action of the related EcoP1I and EcoP15I enzymes. Analytical ultracentrifugation and gel quantification revealed a common Res(2)Mod(2) subunit stoichiometry. Single alanine substitutions in the putative nuclease active site of ResP1 and ResP15 abolished DNA...
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PMID: 11178902
PDF is available here.
PDF is available here.
Abstract
Protein-mediated communications on DNA are universally important. The translocation of DNA driven by a high-energy phosphoryl potential allows long stretches of DNA to be traversed without dissociation. Type-I and type-III enzymes both use a common DNA-tracking mechanism to move along DNA, dependent...
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PMID: 12471895
PDF is available here.
PDF is available here.
Nucleic Acids Research (27)6 1999
Abstract
In a previous study, a recombinant plasmid that contains a CACAG pentanucleotide repeat was isolated from a Pasteurella haemolytica A1 library. Southern hybridization analysis using a (CACAG)5probe indicated the presence of two loci that contain the pentanucleotide repeats on the genome of P.haemoly...
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PMID: 10037813
PDF is available here.
PDF is available here.
Abstract
We describe a type III restriction and modification (R/M) system, LlaFI, in Lactococcus lactis. LlaFI is encoded by a 12-kb native plasmid, pND801, harbored in L. lactis LL42-1. Sequencing revealed two adjacent open reading frames (ORFs). One ORF encodes a 680-amino-acid polypeptide, and this ORF is...
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PMID: 9925601
PDF is available here.
PDF is available here.
Nucleic Acids Research (27)1 1999
Abstract
REBASE is a comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Also included is a listing of homing endonucleases. Information from REBASE is distributed via monthly electr...
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PMID: 9847213
PDF is available here.
PDF is available here.
Biological Chemistry (379)4-5 1998
Abstract
We developed an efficient in vivo selection system that enabled us to detect one cell coding for a restriction-modification system with a new DNA sequence specificity in a background of more than 10(6) cells with the original DNA sequence specificity....
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PMID: 9628354
PDF is available here.
PDF is available here.
Biological Chemistry (379)4-5 1998
Abstract
We have altered various residues in two highly conserved sequences, FxGxG (motif I) and DPPY (motif IV) in these proteins by site-directed mutagenesis. Using a mixture of in vivo and in vitro assays, our results on the mutational analysis of these methyltransferases demonstrate the universal role of...
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PMID: 9628345
PDF is available here.
PDF is available here.
Biological Chemistry (379)4-5 1998
Abstract
We conclude that two different type III enzymes can functionally cooperate in the cleavage of DNA....
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PMID: 9628367
PDF is available here.
PDF is available here.
Journal of Molecular Biology (269)3 1997
Abstract
We have made changes in motifs I and II. While mutations in motif I (GTGKT) clearly affected ATP hydrolysis and resulted in loss of DNA cleavage activity, mutation in motif II (DEPH) significantly decreased ATP hydrolysis but had no effect on DNA cleavage. The double mutant R.EcoPIK90R-H229K showed...
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PMID: 9199404
PDF is available here.
PDF is available here.
Mutation Research (383)1 1997
Abstract
We compared the repair of DNA treated by MMS in vivo or in vitro. Replication forms of lacZ mutants of E. coli phage M13mp18 were used to analyse the effect of the adaptive response on the frequency of GC-->AT transitions occurring in control and mismatch repair deficient strains. It was shown that...
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PMID: 9042417
PDF is available here.
PDF is available here.
Mutation Research (383)1 1997
Abstract
We identified an inducible component to nucleotide excision repair (NER), which is absent in a rad16 delta strain [3]. We have examined the repair of UV induced endonuclease III sensitive-sites (EIIISS), and have shown repair of these lesions to proceed by NER but their removal from nontranscribed r...
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PMID: 9042418
PDF is available here.
PDF is available here.
Journal of Molecular Biology (257)4 1996
Abstract
We have shown by Western blot analysis that the expression of the modification polypeptide subunit positively regulates the amount of restriction subunit present in the cell. The finding that ribosomal alterations affected the expression of restriction activity pointed to additional control at the t...
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PMID: 8636982
PDF is available here.
PDF is available here.
FEMS Microbiology Reviews (17)1-2 1995
Abstract
We favor a model of simultaneous binding of two DNA sites to a dimeric enzyme molecule (neighbouring sites of the same, looping, DNA molecule or sites located on different DNA molecules), while the action of EcoP15 seems to conform with a tracking-collision model of two enzyme molecules bound to inv...
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PMID: 7669344
PDF is available here.
PDF is available here.
EMBO Journal (14)12 1995
Abstract
We have shown previously that suicidal restriction by the type III enzyme EcoP15I is prevented if all the unmodified sites are in the same orientation: restriction by EcoP15I requires a pair of unmethylated, inversely oriented recognition sites. We have now addressed the molecular mechanism of site...
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PMID: 7796821
PDF is available here.
PDF is available here.
Abstract
We show by molecular size-exclusion chromatography and dimethyl suberimidate cross-linking that M.EcoP15I is a dimer in solution. While M.EcoP15I binds approx. threefold more tightly to its recognition sequence, 5'-CAGCAG-3', than to non-specific sequences in the presence of AdoMet or its analogs, t...
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PMID: 7607479
PDF is available here.
PDF is available here.
Abstract
Simultaneous interaction with two recognition sites was found to be a precondition for DNA cleavage by certain type-II and type-III restriction endonucleases. Nevertheless, the molecular mechanisms of the protein-DNA interaction are different between members of both classes of enzymes.
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PMID: 7607484
PDF is available here.
PDF is available here.
Journal of Molecular Biology (247)4 1995
Abstract
We show that purified EcoPI restriction enzyme fails to cleave DNA in the presence of non-hydrolyzable ATP analogs. More importantly, this study demonstrates that EcoPI restriction enzyme has an inherent ATPase activity, and ATP hydrolysis is necessary for DNA cleavage. Furthermore, we show that the...
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PMID: 7723013
PDF is available here.
PDF is available here.
Abstract
I restriction site within the viral genome, and DNA fragments containing the 5' and 3' portions of the HIV genome were subcloned into separate plasmid vectors. The 5' 'half-virus' construct was further modified by incorporating a class IIS restriction site, Esp3I, near the 3' end of the protease gen...
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PMID: 7811249
PDF is available here.
PDF is available here.
Journal of Molecular Biology (242)4 1994
Abstract
We have investigated the DNA binding properties of EcoP15I DNA Mtase using gel mobility shift assays. EcoP15I DNA Mtase binds approximately threefold more tightly to DNA containing its recognition sequence, CAGCAG, than to non-specific sequences in the absence or presence of cofactors. Interestingly...
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PMID: 7932697
PDF is available here.
PDF is available here.
Abstract
These results suggest that photolabeling is at the AdoMet-binding site and that the N-terminal half of M.EcoP15 may be involved in substrate binding....
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PMID: 8181759
PDF is available here.
PDF is available here.
Abstract
These results suggest that photolabeling of EcoP1 DNA modification methylase occurs at the AdoMet binding site....
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PMID: 8038713
PDF is available here.
PDF is available here.
Abstract
The StyLT1 restriction-modification (R-M) system of Salmonella typhimurium has recently been suggested to belong to the type-III R-M systems [De Backer and Colson, Gene 97 (1991) 103-107]. The nucleotide sequences of StyLT1 mod and res have been determined. Two closely adjacent open reading frames w...
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PMID: 8387444
PDF is available here.
PDF is available here.
Abstract
Abstract
Abstract
We show that restriction requires two unmodified recognition sites that can be separated by different distances but which must be in inverse orientation. All of the unmodified sites in newly replicated DNA are of course in the same orientation, which explains why they are not restricted. This result...
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PMID: 1734285
PDF is available here.
PDF is available here.
Abstract
We found no evidence to support earlier inferences that intracellular conditions enhance the formation of cytosine photohydrates or other monobasic forms of DNA damage....
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PMID: 1665910
PDF is available here.
PDF is available here.
FEBS Letters (291)2 1991
Abstract
A statistically significant amino acid sequence similarity is demonstrated between the endonuclease (R) subunit of EcoK restriction-modification (R-M) enzyme, and RNA and DNA helicases of the so-called 'DEAD' family. It is further shown that all three known sequences of R subunits of type-I and type...
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PMID: 1657645
PDF is available here.
PDF is available here.
Nucleic Acids Research (19)18 1991
Abstract
Nucleic Acids Research (19)14 1991
Abstract
Abstract
We show that both the res and mod genes are transcribed from separate promoters. A more detailed investigation of the mod promoter region revealed two promoters located some 70 and 140bp upstream from the translational start codon. In addition, another pair of promoters and a further separate promot...
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PMID: 2046552
PDF is available here.
PDF is available here.
Journal of Bacteriology (173)3 1991
Abstract
The genes encoding the restriction-modification system StyLTI of Salmonella typhimurium were inserted in vivo into the conjugative plasmid pULB21. This allowed us to transfer the StyLTI genes at a very high frequency and to monitor the fate of recipient cells after mating. Transfer of the StyLTI res...
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PMID: 1846862
PDF is available here.
PDF is available here.
Journal of Bacteriology (173)3 1991
Abstract
We report here the two-step cloning of the genes controlling the StyLTI system. The StyLTI methylase gene (mod) was cloned first. Then, the companion endonuclease gene (res) was introduced on a compatible vector. A strain of S. typhimurium sensitive to the coliphage lambda was constructed and used t...
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PMID: 1846861
PDF is available here.
PDF is available here.
Abstract
We report here the identification of the nucleotide (nt) sequence methylated by the StyLTI modification methyltransferase (M.StyLTI). This enzyme was partially purified from an Escherichia coli strain expressing the cloned M.StyLTI-encoding gene, but lacking StyLTI restriction activity, and used to...
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PMID: 1995420
PDF is available here.
PDF is available here.
Abstract
I was common to all 20 of the serotype a isolates, restriction pattern II was associated with 58% of the 73 serotype b isolates examined, while restriction pattern III was associated with the remaining serotype b strains and with all 15 of the serotype c strains.(ABSTRACT TRUNCATED AT 250 WORDS)...
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PMID: 2156041
PDF is available here.
PDF is available here.