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Deoxyribonucleases, Type I Site-Specific (0):
Recent article
Deoxyribonucleases, Type I Site-Specific
Abstract
We analyzed both the rate of transcription of apoptosis-related genes and the presence of activated apoptotic factors within kidneys of lupus-prone (NZBxNZW) F1 mice during disease progression. The results of this study demonstrated no activation of apoptotic pathways in kidneys of these lupus-prone...
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PMID: 19528352
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PDF is available here.
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Methods in Molecular Biology (543)543 2009
Abstract
We make use of an extrinsic fluorescence probe, the environmentally sensitive fluorophore 1-anilinonaphthalene-8-sulphonic acid (1,8-ANS). Displacement by DNA of 1,8-ANS molecules from the nucleic-acid-binding site of the Type I modification methylase EcoR124I results in red shifting and an intensit...
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PMID: 19378188
PDF is available here.
PDF is available here.
Abstract
I restriction-modification enzymes. The bacteriophage T7 0.3 (ocr) gene is cloned in pUC18 vector. It was shown that T7 Ocr protein inhibits both restriction and modification activities of the type I restriction-modification enzyme (EcoKI) in Escherichia coli K12 cells. The mutation form of Ocr-Ocr...
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PMID: 19334532
PDF is available here.
PDF is available here.
Abstract
We have developed a model of complex formation between the antirestriction proteins and the restriction-modification enzymes R2M2S. Antirestriction proteins are capable of competing displacement of the DNA strand from two sites which are situated as follows: 1) in S-subunit (enzyme contact with the...
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PMID: 19425495
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)5 2008
Abstract
We examined the DNA translocation properties of EcoR124I complexes in which the HsdR subunits had been mutated in the RecB-like nuclease motif II or III. We found that nuclease mutations can have multiple effects on DNA translocation despite being distinct from the helicase domain. In addition to re...
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PMID: 18952104
PDF is available here.
PDF is available here.
Abstract
We report the crystal structures at 2.0 and 2.1 A resolution of the I-DmoI meganuclease in complex with its substrate DNA before and after cleavage, providing snapshots of the catalytic process. Our study suggests that I-DmoI requires only 2 cations instead of 3 for DNA cleavage. The structure sheds...
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PMID: 18974222
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)13 2008
Abstract
We have previously developed plasmid R-M tests and the computer program RM search. To specifically identify Type-I isoschizomers, we engineered a pUC19 derivative plasmid, pTypeI, which contains all of the 27 Type-I recognition sequences in a 248-bp DNA fragment. Furthermore, a series of 27 plasmids...
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PMID: 18562466
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)12 2008
Abstract
We examined the role of the Q and Y residues in DNA binding, translocation and cleavage. Roles for the QxxxY motif in coordinating the catalytic residues or in stabilizing the nuclease domain on the DNA are discussed....
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PMID: 18511464
PDF is available here.
PDF is available here.
FASEB Journal (22)6 2008
Abstract
We have engineered a novel chimeric vector relying on the controlled assembly of a TAT-tagged multisubunit DNA binding protein (EcoR124I) with expression plasmids containing the EcoR124I recognition site. Molecular interactions of this molecular assembly were studied by electrophoretic mobility shif...
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PMID: 18202142
PDF is available here.
PDF is available here.
Abstract
We describe the history of our understanding of this plasmid and the type I restriction-modification (R-M) system that it encodes, which will allow an opportunity to correct errors, or misunderstandings, that have arisen in the literature. We also describe the characterization of the R-M enzyme EcoR...
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PMID: 18535150
PDF is available here.
PDF is available here.
EMBO Journal (27)9 2008
Abstract
We provide estimates of two physicochemical constants that are fundamental to a full description of motor protein activity-the ATP coupling efficiency (the number of ATP consumed per base pair) and the step size (the number of base pairs transported per motor step). Our data indicate that EcoR124I m...
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PMID: 18388857
PDF is available here.
PDF is available here.
Journal of Molecular Biology (376)2 2008
Abstract
We constructed a model of the HsdR using protein fold-recognition and homology modelling to model individual domains, and small-angle neutron scattering data as restraints to combine them into a single molecule. The model reveals an ellipsoidal shape of the enzymatic core comprising the N-terminal a...
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PMID: 18164032
PDF is available here.
PDF is available here.
BMC Microbiology (8)1 2008
Abstract
We have characterised a restriction-modification system EcoA0ORF42P of the commensal Escherichia coli strain A0 34/86 (O83: K24: H31). This system, designated as EcoAO83I, is a new functional member of the Type IB family, whose specificity differs from those of known Type IB enzymes, as was demonstr...
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PMID: 18588664
PDF is available here.
PDF is available here.
BMC Microbiology (8)1 2008
Abstract
Using bioinformatics, we identified genes in the unfinished enteropathogenic Escherichia coli (EPEC) strain E2348/69 genome whose predicted products bear homology to the HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type I restriction-modification systems....
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PMID: 18681975
PDF is available here.
PDF is available here.
Abstract
I restriction-modification system from Escherichia coli. Although EcoR124I has been extensively characterized biochemically, there is no direct structural information available about particular subunits. HsdR is a motor subunit that is responsible for ATP hydrolysis, DNA translocation and cleavage o...
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PMID: 17620716
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (270)1 2007
Abstract
I restriction-modification (R-M) enzymes EcoKI, EcoAI, and EcoR124I - representatives of IA, IB, and IC families, respectively - was analysed in vivo by immunoblotting of endogenous phosphoproteins isolated from Escherichia coli strains harbouring the corresponding hsd genes, and in vitro by a phosp...
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PMID: 17439637
PDF is available here.
PDF is available here.
Journal of Medical Microbiology (56)Pt 5 2007
Abstract
Multilocus sequence typing (MLST) and multi-strain microarray analysis have shown that most human Staphylococcus aureus strains belong to ten dominant clonal complexes (CCs) or lineages, each with unique surface architecture. Meticillin-resistant S. aureus (MRSA) strains currently belong to six of t...
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PMID: 17446283
PDF is available here.
PDF is available here.
Journal of Molecular Biology (361)4 2006
Abstract
We utilize domain A of the monomeric I-DmoI to demonstrate the feasibility of generating functional homodimeric endonucleases that recognize palindromic DNA sequences derived from the original, non-palindromic target. Wild-type I-DmoI domain A is capable of forming a homodimer (H-DmoA) that binds ti...
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PMID: 16872628
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)15 2006
Abstract
We show that it carries a mutation in the sau1hsdR gene and that complementation restored a nontransformable phenotype. Sau1 was also responsible for reduced conjugative transfer from enterococci, a model of vancomycin resistance transfer. This may explain why only four vancomycin-resistant S. aureu...
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PMID: 16855248
PDF is available here.
PDF is available here.
EMBO Journal (25)10 2006
Abstract
We have examined the DNA translocation activity of a helicase, the Type I restriction modification enzyme EcoR124I. We find that EcoR124I can translocate past covalent interstrand crosslinks, inconsistent with an obligatory unwinding mechanism. Instead, translocation of the intact dsDNA occurs princ...
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PMID: 16642041
PDF is available here.
PDF is available here.
Molecular Microbiology (60)4 2006
Abstract
We have identified two genes in Escherichia coli, rnhA and recG, mutations in which lead to the alleviation of restriction. Induction of RA in response to these mutations is consistent with the production of unmodified target sequences following DNA synthesis associated with both homologous recombin...
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PMID: 16677300
PDF is available here.
PDF is available here.
Research in Microbiology (157)3 2006
Abstract
I system, ordinarily named R-M. This system belongs to the DNA immigration control region (ICR). Each ORF is related to different operon structures, which are homologues among themselves and with subunit Hsd R from the endonuclease coding genes. In addition, these ORFs are highly homologous to genes...
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PMID: 16125907
PDF is available here.
PDF is available here.
Genetika (Moskva) (42)3 2006
Abstract
I restriction-modification enzymes. The ArdA of R64 is highly homologous to ColIb-P9 ArdA, differing only by four amino acid residues of the overall 166. However, unlike ColIb-P9 ArdA, which inhibits both the endonuclease and the methylase activities of EcoKI, the R64 ArdA protein inhibits only the...
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PMID: 16649659
PDF is available here.
PDF is available here.
Biotechnology Letters (28)4 2006
Abstract
I (DNases I) were expressed in COS-7 cells, and purified by a single-step procedure. Since affinities for concanavalin A (Con A) and wheatgerm agglutinin (WGA) were strong in these recombinant DNases I, purification using Con A-WGA mixture-agarose column was performed. By this method, the enzymes in...
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PMID: 16555004
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)16 2006
Abstract
We produced test circuits based on recombination intermediates in which 1D translocation across a Holliday junction (HJ) could be assessed by subsequent triplex displacement signals on each DNA arm. Using the EcoR124I restriction-modification enzyme, a 3'-5' double-strand DNA (dsDNA) translocase, we...
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PMID: 16936313
PDF is available here.
PDF is available here.
EMBO Journal (24)23 2005
Abstract
We fully characterized the (re)initiation of DNA translocation by EcoR124I. We found that the methyltransferase core unit of the enzyme loads the motor subunits onto adjacent DNA by allowing them to bind and initiate translocation. Termination of translocation occurs owing to dissociation of the mot...
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PMID: 16292342
PDF is available here.
PDF is available here.
Journal of Molecular Biology (352)4 2005
Abstract
We demonstrate the displacement of EcoR124I following DNA cleavage by the translocating RecBCD enzyme, resulting in the restoration of catalytic function to EcoR124I....
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PMID: 16126220
PDF is available here.
PDF is available here.
Journal of Molecular Biology (348)4 2005
Abstract
We obtained not only the translocation rate but also information on slow isomerisation step(s) at initiation. Furthermore, we demonstrated that enzymes deficient in DNA cleavage but with maximal ATPase activity showed initiation and translocation rates identical to wild-type, confirming that DNA str...
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PMID: 15843021
PDF is available here.
PDF is available here.
Abstract
The regulatory domain of T-protein was located in the C-terminal 270 amino acids, which was the same location as PDH domain. CONCLUSION: T-protein has no independent regulatory domain....
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PMID: 15812896
PDF is available here.
PDF is available here.
Microbiology (151)Pt 2 2005
Abstract
I restriction-modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helic...
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PMID: 15699185
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)6 2005
Abstract
We show that all three enzymes cut this substrate randomly with no preference for a particular base composition surrounding the cleavage site, producing both 5'- and 3'-overhangs of varying lengths. EcoAI preferentially generated 3'-overhangs of 2-3 nt, whereas EcoKI and EcoR124I displayed some pref...
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PMID: 15788748
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)13 2005
Abstract
I restriction enzymes with new recognition sites and two isoschizomers (EcoBI and Eco377I) were identified in a collection of clinical Escherichia coli isolates. These new enzymes were designated Eco394I, Eco826I, Eco851I and Eco912I. Their recognition sequences were determined to be GAC(5N)RTAAY, G...
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PMID: 16040596
PDF is available here.
PDF is available here.
Abstract
The conjugation of thermoresponsive polymers to multisubunit, multifunctional hybrid type 1 DNA restriction-modification (R-M) enzymes enables temperature-controlled "switching" of DNA methylation by the conjugate. Polymers attached to the enzyme at a subunit distal to the methylation subunit allow...
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PMID: 15479059
PDF is available here.
PDF is available here.
Abstract
I restriction-modification enzymes EcoKI, EcoAI, and EcoR124I-the most frequently studied representatives of IA, IB, and IC families-was analyzed by immunoblotting of subcellular fractions isolated from Escherichia coli strains harboring the corresponding hsd genes. EcoR124I shows characteristics si...
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PMID: 15178416
PDF is available here.
PDF is available here.
Molecular Microbiology (51)1 2004
Abstract
We now provide evidence that restriction alleviation may be a characteristic of Type I restriction-modification systems, and that it can be achieved by different mechanisms. Our experiments support disassembly of active endonuclease complexes as a potential mechanism. We identify amino acid substitu...
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PMID: 14651617
PDF is available here.
PDF is available here.
Abstract
I restriction-modification enzymes. The IncI1 ColIb-P9 and R64 are closely related plasmids, and the latter specifies an ArdA homologue that is predicted to be 97.6% (162 residues from 166) identical at the amino acid sequence level with the ColIb = P9 equivalent. However, the R64 ArdA selectively i...
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PMID: 15554191
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)22 2004
Abstract
I restriction-modification (R-M) enzymes elicits an ATP-dependent switch from methylase to endonuclease activity, which involves DNA translocation by the restriction subunit HsdR. Type I R-M enzymes are composed of three (Hsd) subunits with a stoichiometry of HsdR2:HsdM2:HsdS1 (R2-complex). However,...
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PMID: 15598825
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)19 2004
Abstract
We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands. The type I restriction enzyme is able to destroy...
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PMID: 15520467
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)10 2004
Abstract
We further examine the role of the LAGLIDADG residues involved in the helix-helix interaction. The interchangeability of the LAGLIDADG helix interaction was explored by grafting interfacial residues from the homodimeric I-CreI into the corresponding positions in the monomeric I-DmoI. The resulting L...
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PMID: 15190132
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)18 2004
Abstract
We concluded that the KpnBI system is a typical type I R-M system. The deduced amino acid sequences of the three subunits of the KpnBI system show only limited homologies (25 to 33% identity) at best, to the four previously categorized type I families (IA, IB, IC, and ID). Furthermore, their identit...
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PMID: 15475385
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)10 2004
Abstract
We have determined the DNA sequences recognized by the KpnAI, StySEAI, StySENI and StySGI R-M systems from Klebsiella oxytoca strain M5a1, Salmonella eastbourne, Salmonella enteritidis and Salmonella gelsenkirchen, respectively. These type I restriction-modification systems were originally identifie...
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PMID: 15199175
PDF is available here.
PDF is available here.
Abstract
We have found a type of illegitimate recombination that requires an interaction between long homologous DNA sequences. It was detected when a plasmid that carried 2-kb-long inverted repeats was subjected to type I (EcoKI) restriction in vivo within a special mutant strain of Escherichia coli. In the...
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PMID: 14597009
PDF is available here.
PDF is available here.
Bioinformatics (19)11 2003
Abstract
We have developed a novel automatic method, based on patterns of conservation of 237 physical-chemical properties of amino acids in aligned protein sequences, to find related motifs in proteins with little or no overall sequence similarity. As an application, our web-server MASIA identified 12 prope...
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PMID: 12874050
PDF is available here.
PDF is available here.
Abstract
Nucleic Acids Research (31)11 2003
Abstract
We present two novel, chimeric meganucleases, derived from homing endonucleases. The first one is able to induce recombination in yeast and mammalian cells, whereas the second cleaves a novel (chosen) DNA target site. These results are a first step toward the generation of custom endonucleases for t...
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PMID: 12771221
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.
Folia Microbiologica (48)3 2003
Abstract
We purified and characterized both the methyltransferase and the endonuclease containing the HsdS delta 50 subunit (type I restriction endonucleases are composed of three subunits--HsdR required for restriction, HsdM required for methylation and HsdS responsible for DNA recognition) produced from th...
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PMID: 12879741
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.
Molecular Cell (10)4 2002
Abstract
We have generated an artificial highly specific endonuclease by fusing domains of homing endonucleases I-DmoI and I-CreI and creating a new 1400 A(2) protein interface between these domains. Protein engineering was accomplished by combining computational redesign and an in vivo protein-folding scree...
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PMID: 12419232
PDF is available here.
PDF is available here.
Abstract
I restriction endonucleases is generally activated following the head-on collision of two translocating enzymes. However, the resulting distributions of cleavage loci along the DNA vary with different enzymes; in some cases, cleavage is located in a discrete region midway between a pair of recogniti...
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PMID: 11827554
PDF is available here.
PDF is available here.
Folia Microbiologica (47)6 2002
Abstract
I restriction-modification endonucleases EcoKI and EcoR124I by non-equilibrium pH gradient two-dimensional (2-D) gel electrophoresis is described. Three subunits of the enzyme complex, which widely differ from one another in their isoelectric points and molar mass, were identified in crude cell extr...
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PMID: 12630312
PDF is available here.
PDF is available here.
Journal of Molecular Biology (314)1 2001
Abstract
The type IC DNA methyltransferase M.EcoR124I is a trimeric enzyme of 162 kDa consisting of two modification subunits, HsdM, and a single specificity subunit, HsdS. Studies have been largely restricted to the HsdM subunit or to the intact methyltransferase since the HsdS subunit is insoluble when ove...
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PMID: 11724530
PDF is available here.
PDF is available here.
Nucleic Acids Research (29)20 2001
Abstract
We present complementation tests that confirm the allocation of EcoR9I and KpnAI to the ID family. An alignment of the amino acid sequences of the HsdS subunits of StySBLI and EcoR9I identify two variable regions, each predicted to be a target recognition domain (TRD). Consistent with two TRDs, StyS...
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PMID: 11600708
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.
Molecular Microbiology (41)5 2001
Abstract
The hsd locus (host specificity of DNA) was identified in the Neisseria gonorrhoeae genome. The DNA fragment encoding this locus produced an active restriction and modification (R/M) system when cloned into Escherichia coli. This R/M system was designated NgoAV. The cloned genomic fragment (7800 bp)...
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PMID: 11555298
PDF is available here.
PDF is available here.
Abstract
Biochemical Society Transactions (29)Pt 4 2001
Abstract
Type II restriction endonucleases recognize specific DNA sequences and cleave both strands of the DNA at fixed locations at or near their recognition sites. Many of these enzymes are dimeric proteins that recognize, in symmetrical fashion, palindromic DNA sequences. They generally catalyse independe...
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PMID: 11497991
PDF is available here.
PDF is available here.
Biochemical Pharmacology (61)3 2001
Abstract
We investigated the amplification of bleomycin-induced DNA cleavage by synthetic triamides containing N-methylpyrrole (Py) and/or N-methylimidazole (Im), PyPyPy, PyPyIm, PyImPy, and PyImIm, using 32P-labeled DNA fragments obtained from the human c-Ha-ras-1 and p53 genes. Peplomycin, a bleomycin anal...
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PMID: 11172740
PDF is available here.
PDF is available here.
Nucleic Acids Research (29)2 2001
Abstract
The NagC and Mlc proteins are homologous transcriptional regulators that control the expression of several phosphotransferase system (PTS) genes in Escherichia coli. NagC represses nagE, encoding the N:-acetylglucosamine-specific transporter, while Mlc represses three PTS operons, ptsG, manXYZ and p...
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PMID: 11139621
PDF is available here.
PDF is available here.
Abstract
I endonucleases from related strains were not markedly biased, and with pentanucleotides, palindromic and nonpalindromic sequences had nearly identical distributions. The loss of restriction sites may be explained by the free transfer of plasmids encoding restriction enzymes and episodic selection f...
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PMID: 11454303
PDF is available here.
PDF is available here.