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Zavil'gelskiĭ GB, Kotova VI. [Antirestriction activity of T7 Ocr protein in monomeric and dimeric forms]. Mol Biol (Mosk) 2014; 48:176-184. [PMID: 25842838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Ocr protein, encoded by 0.3 (ocr) gene of bacteriophage T7, belongs to the family of antirestriction proteins that specifically inhibit the type I restriction-modification systems. Native Ocr forms homodimer (Ocr)2 both in solution and in the crystalline state. The Ocr protein belongs to the family of mimicry proteins. F53D A57E and E53R V77D mutant proteins were obtained, which form monomers. It was shown that the values of the dissociation constants Kd for Ocr, Ocr F53D A57E and Ocr F53RV77D proteins with EcoKI enzyme differ in 1000 times: Kd (Ocr) = 10(-10) M, Kd (Ocr F53D A57E and Ocr F53R V77D) = 10(-7) M. Antimodification activity of the Ocr monomeric forms is significantly reduced. We have shown, that Ocr dimeric form has fundamental importance for high inhibitory activity.
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2
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Dedkov VS. [Definition of the specificity of DNA-methyltransferase M.Bsc4I in cell lysate by blocking of restriction endonucleases and computer modeling]. Mol Gen Mikrobiol Virusol 2009:3-8. [PMID: 19708199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The specificity of DNA-methyltransferase M.Bsc4I was defined in cellular lysate of Bacillus schlegelii 4. For this purpose, we used methylation sensitivity of restriction endonucleases, and also modeling of methylation. The modeling consisted in editing sequences of DNA using replacements of methylated bases and their complementary bases. The substratum DNA processed by M.Bsc4I also were used for studying sensitivity of some restriction endonucleases to methylation. Thus, it was shown that M.Bsc4I methylated 5'-Cm4CNNNNNNNGG-3' and the overlapped dcm-methylation blocked its activity. The offered approach can appear universal enough and simple for definition of specificity of DNA-methyltransferases.
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Fujimoto DF, Pinilla C, Segall AM. New peptide inhibitors of type IB topoisomerases: similarities and differences vis-a-vis inhibitors of tyrosine recombinases. J Mol Biol 2006; 363:891-907. [PMID: 16996084 PMCID: PMC1876744 DOI: 10.1016/j.jmb.2006.08.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2006] [Revised: 08/20/2006] [Accepted: 08/21/2006] [Indexed: 11/20/2022]
Abstract
Topoisomerases relieve topological tension in DNA by breaking and rejoining DNA phosphodiester bonds. Type IB topoisomerases such as vaccinia topoisomerase (vTopo) and human topoisomerase I are structurally and mechanistically similar to the tyrosine recombinase family of enzymes, which includes bacteriophage lambda Integrase (Int). Previously, our laboratory identified peptide inhibitors of Int from a synthetic peptide combinatorial library. The most potent of these peptides also inhibit vTopo. Here, we used the same mixture-based screening procedure to identify peptide inhibitors directly against vTopo using a plasmid relaxation assay. The two most potent new peptides identified, WYCRCK and KCCRCK, inhibit plasmid relaxation, DNA cleavage and Holliday junction (HJ) resolution mediated by vTopo. The peptides tested bind double-stranded DNA at high concentrations but do not appear to displace the enzyme from its DNA substrate. WYCRCK binds specifically to HJ and perturbs the central base-pairing. This peptide also accumulates HJ intermediates when it inhibits Int-mediated recombination, whereas KCCRCK does not. Interestingly, WYCRCK shares four amino acids with a peptide identified against Int, WRWYCR. The octapeptide WRWYCRCK, containing amino acids from both hexapeptides, is more potent than either against vTopo. All peptides are less potent against the type IA Escherichia coli topoisomerase I or against restriction endonucleases. Like the Int-inhibitory peptide WRWYCR, WYCRCK binds to HJs, and both inhibit junction resolution by vTopo. Our results suggest that the newly identified WYCRCK and peptide WRWYCR interact with a distorted DNA intermediate arising during vTopo-mediated catalysis, or interfere with specific interactions between vTopo and DNA.
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Affiliation(s)
- David F Fujimoto
- Department of Biology, Center for Microbial Sciences and Molecular Biology Institute, San Diego State University, San Diego, CA 92182-4614, USA
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4
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Abstract
It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins.
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Affiliation(s)
- D T F Dryden
- School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK.
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5
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Zavil'gel'skiĭ GB, Letuchaia TA, Rastorguev SM. [Antirestriction and antimodification activities of the ArdA protein encoded by the IncI1 transmissive plasmids R-64 and ColIb-P9]. Genetika 2006; 42:331-8. [PMID: 16649659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proteins of the Ard family are specific inhibitors of type 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 endonuclease activity of this enzyme. The mutant forms of R64 ArdA--A29T, S43A, and Y75W, capable of partially reversing the protein to ColIb-P9 ArdA form--were produced by directed mutagenesis. It was demonstrated that only Y75W mutation of these three variants essentially influenced the functional activity of ArdA: the antimodification activity was restored to approximately 90-99%. It is assumed that R64 ArdA inhibits formation of the complex between unmodified DNA and the R subunit of the type I restriction-modification enzyme EcoKI (R2M2S), which translocates and cleaves DNA. ColIb-P9 ArdA protein is capable of forming the DNA complex not only with the R subunit, but also with the S subunit, which contacts sK site (containing modified adenine residues) in DNA. ArdA bound to the specific sK site inhibits concurrently the endonuclease and methylase activities of EcoKI (R2M2S), while ArdA bound to the nonspecific site in the R subunit blocks only its endonuclease activity.
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6
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Zavil'gel'skiĭ GB, Letuchaia TA, Rastorguev SM. [Antirestriction activity of the IncI1 transmissive plasmid R64 ArdA protein]. Mol Biol (Mosk) 2004; 38:901-6. [PMID: 15554191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The transmissive plasmid IncI1 R64 contains the ardA gene encoding the ArdA antirestriction protein. The R64 ardA gene locating in the leading region of plasmid R64 has been cloned and their sequence has been determined. Antirestriction proteins belonging to the Ard family are specific inhibitors of type 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 inhibits the restriction activity of EcoKi enzyme leaving significant levels of modification activity under conditions in which restriction was almost completely prevented. The ColIb-P9 ArdA inhibits restriction endonuclease and methyltransferase activities simultaneously. It is hypothesized that the ArdA protein forms two complexes with the type I restriction-modification enzyme (R2M2S): (1) with a specific region in the S subunit involved in contact with the sK site in DNA; and (2) with nonspecific region in the R subunit involved in DNA translocation and degradation by restriction endonuclease. The association of the ColIb-P9 ArdA with the specific region inhibits restriction endonuclease and methyltransferase activities simultaneously, whereas the association of the R64 ArdA with a nonspecific region inhibits only restriction endonuclease activity of the R2M2S enzyme.
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Thomas AT, Brammar WJ, Wilkins BM. Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI. J Bacteriol 2003; 185:2022-5. [PMID: 12618468 PMCID: PMC150139 DOI: 10.1128/jb.185.6.2022-2025.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ArdA antirestriction protein of the IncB plasmid R16 selectively inhibited the restriction activity of EcoKI, leaving significant levels of modification activity under conditions in which restriction was almost completely prevented. The results are consistent with the hypothesis that ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification.
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Affiliation(s)
- Angela T Thomas
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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8
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Oana H, Tsumoto K, Yoshikawa Y, Yoshikawa K. Folding transition of large DNA completely inhibits the action of a restriction endonuclease as revealed by single-chain observation. FEBS Lett 2002; 530:143-6. [PMID: 12387882 DOI: 10.1016/s0014-5793(02)03448-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The biochemical characteristics of lambda DNA chains in folded/unfolded states upon cleavage by the restriction enzyme ApaLI were investigated in the presence of spermine. These characteristics of DNA chains depending on their higher-order structure were studied at the single-molecule level using fluorescence microscopy. With a low concentration of spermine, lambda DNA takes a random coiled conformation and allows digestion by the enzyme, while under a high concentration of spermine, lambda DNA takes a compact folded structure and inhibits such attack. Together with comparative experiments on short oligomeric DNA, our results suggest that the transition in the higher-order structure causes on/off-type switching of sensitivity to the enzyme.
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Affiliation(s)
- Hidehiro Oana
- Department of Physics, Kyoto University & CREST, Japan.
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Affiliation(s)
- Brian M Wilkins
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.
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Janz C, Süsse S, Wiesmüller L. p53 and recombination intermediates: role of tetramerization at DNA junctions in complex formation and exonucleolytic degradation. Oncogene 2002; 21:2130-40. [PMID: 11948396 DOI: 10.1038/sj.onc.1205292] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2001] [Revised: 01/02/2002] [Accepted: 01/08/2002] [Indexed: 01/01/2023]
Abstract
Heteroduplex joints represent intermediates of Rad51-dependent recombination processes, which are recognized by p53 with extremely high affinities, in a manner independent of the DNA sequence content. To determine the structural elements required for complex formation, we monitored DNA-binding by protection against restriction endonuclease cleavage. We show that wild-type (wt) p53 interacts with heteroduplex joints in the proximity of the flexible junction. Association of p53 within this junction region was also observed with preformed Rad51-heteroduplex complexes, whereas SSB counteracted p53 binding. At a distance of 31 bp from the junction p53 established very few contacts with the heteroduplex, despite the presence of an A-G mismatch. Consistently, p53-dependent exonucleolytic degradation decreased when we raised the distance between the junction and the heteroduplex terminus by 27 bp. Different from the cancer-related mutant p53(273H), which did not recognize the junction, tetramerization defective p53-1262 was protection competent but displayed reduced complex stability in gel shifts. Moreover, p53-1262 performed exonucleolytic activities towards ssDNA like wtp53, but reduced degradation of heteroduplex joints. These results suggest that during recombination wild-type p53, as a tetramer, stably binds to strand transfer regions, enabling the protein to exonucleolytically correct heteroduplex intermediates early after strand invasion.
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Affiliation(s)
- Christine Janz
- Universitätsfrauenklinik und Poliklinik, Prittwitzstrasse 43, D-89075 Ulm, Germany
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Abstract
Applying various restriction enzymes on a specially designed 1.5 kb DNA fragment revealed that the inhibitory effects of psoralens + UVA irradiation (PUVA) treatment on restriction endonuclease activities are caused by recognition inhibition. In this study restriction enzymes that have a 5'-TpA sequence at the cleaving site (KpnI, XbaI, PmeI and DraI), and the noncleaving site (PacI) in recognition sites, or have two 5'-TpA sequences at the recognition site, and a nonspecific sequence between the recognition and the cleaving sites (BciVI), were inhibited by PUVA treatment. Most of the other restriction enzymes used in this study, which do not have a 5'-TpA sequence at their restriction site, were not inhibited by PUVA treatment, although a 5'-TpA sequence is located adjacent (SmaI) or very close (BamHI, SacI and PstI) to the recognition and cleaving sites for these enzymes. Because SphI, which does not have 5'-TpA at its restriction site, was strongly inhibited by PUVA treatment, the 5'-CpA sequence is suggested to be a new binding site of psoralens after UVA irradiation.
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Affiliation(s)
- F Hanawa
- Forestry and Forest Products Research Institute (FFPRI), P.O. Box 16, Tsukuba, Ibaraki 305-8687, Japan.
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Zavil'gel'skiĭ GB. [Antirestriction]. Mol Biol (Mosk) 2000; 34:854-62. [PMID: 11033812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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Abstract
The study of biochemical pathways requires the isolation and characterization of each and every intermediate in the pathway. For the site-specific recombination reactions catalyzed by the bacteriophage lambda tyrosine recombinase integrase (Int), this has been difficult because of the high level of efficiency of the reaction, the highly reversible nature of certain reaction steps, and the lack of requirements for high-energy cofactors or metals. By screening synthetic peptide combinatorial libraries, we have identified two related hexapeptides, KWWCRW and KWWWRW, that block the strand-cleavage activity of Int but not the assembly of higher-order intermediates. Although the peptides bind DNA, their inhibitory activity appears to be more specifically targeted to the Int-substrate complex, insofar as inhibition is resistant to high levels of non-specific competitor DNA and the peptides have higher levels of affinity for the Int-DNA substrate complex than for DNA alone. The peptides inhibit the four pathways of Int-mediated recombination with different potencies, suggesting that the interactions of the Int enzyme with its DNA substrates differs among pathways. The KWWCRW and KWWWRW peptides also inhibit vaccinia virus topoisomerase, a type IB enzyme, which is mechanistically and structurally related to Int. The peptides differentially affect the forward and reverse DNA transesterification steps of the vaccinia topoisomerase. They block formation of the covalent vaccinia topoisomerase-DNA intermediate, but have no apparent effect on DNA religation by preformed covalent complexes. The peptides also inhibit Escherichia coli topoisomerase I, a type IA enzyme. Finally, the peptides inhibit the bacteriophage T4 type II topoisomerase and several restriction enzymes with 2000-fold lower potency than they inhibit integrase in the bent-L pathway.
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Affiliation(s)
- M Klemm
- Department of Biology and Molecular Biology Institute, San Diego State University, San Diego, CA, 92182, USA
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Gallori E, Vettori C, Alessio E, Vilchez FG, Vilaplana R, Orioli P, Casini A, Messori L. DNA as a possible target for antitumor ruthenium(III) complexes. Arch Biochem Biophys 2000; 376:156-62. [PMID: 10729201 DOI: 10.1006/abbi.1999.1654] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interaction of two experimental ruthenium(III)-containing antitumor complexes-Na[trans-RuCl(4)(DMSO)(Im)] (NAMI) and dichloro(1,2-propylendiaminetetraacetate)ruthenium(III) (RAP)-with DNA was investigated through a number of spectroscopic and molecular biology techniques, including spectrophotometry, circular dichroism, gel shift analysis, and restriction enzyme inhibition. It was found that both complexes slightly alter DNA conformation, modify its electrophoretic mobility, and inhibit DNA recognition and cleavage by some restriction enzymes, though they were less effective than cisplatin in producing such effects. Notably, the effects produced by NAMI on DNA were much larger than those induced by RAP. Implications of these results for the mechanism of action of ruthenium(III) antitumor complexes are discussed.
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Affiliation(s)
- E Gallori
- Department of Chemistry, University of Florence, Florence, 50121, Italy
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Rastorguev SM, Letuchaia TA, Kholodiĭ GI, Mindlin SZ, Nikiforov VG, Zavil'gel'skiĭ GB. [Antirestriction activity of metalloregulatory proteins ArsR and MerR]. Mol Biol (Mosk) 1999; 33:203-6. [PMID: 10377563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Kittler L, Bell A, Baguley BC, Löber G. Inhibition of restriction endonucleases by DNA sequence-reading ligands. Biochem Mol Biol Int 1996; 40:263-72. [PMID: 8896748 DOI: 10.1080/15216549600201752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
DNA sequence-reading bisquaternary ammonium heterocycles SN 6570, SN 6999, SN 6053, SN 6132, SN 6131, SN 18071 and the non-specific binders SN 6113, SN 5754, SN 6324, and SN 4094 influence the enzymatic activity of restriction endonucleases in different manners. A prerequisite for sequence-specific ligand interaction is a dAdT run of at least four base pairs. The sequence-specific binders inhibit the cleavage activity of restriction endonucleases EcoRI, SspI, and Dral with four and six dAdT base pairs in their restriction sites, while the activity of SalI and BamHI with less than four dAdT base pairs in their recognition motifs remains unaffected. On the contrary, the non-specific binding DNA ligands are incapable of suppressing the digestion for restriction nucleases under research. These results are in line with our footprint data. The inhibitory effect is independent of the number of cleavage sites in DNA and of whether the macromolecule exists in the ccc or lds conformation. Sequence specific binding of the ligand SN 6053 in close vicinity to the cleavage sites of restriction endonuclease Dral also interferes with enzyme inhibition.
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Affiliation(s)
- L Kittler
- Institut für Molekulare Biotechnologie e.V. Jena, Germany
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Denissenko MF, Venkatachalam S, Ma YH, Wani AA. Site-specific induction and repair of benzo[a]pyrene diol epoxide DNA damage in human H-ras protooncogene as revealed by restriction cleavage inhibition. Mutat Res 1996; 363:27-42. [PMID: 8632776 DOI: 10.1016/0921-8777(95)00059-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Most genotoxic DNA base modifications localized at key genomic sequences constitute the molecular alterations crucial or mutagenesis and tumorigenesis. We have utilized lesion-rendered inhibition of restriction endonuclease cleavage for the analysis of site-specific DNA damage induced by (+/-)-7,8-dihydroxy-anti-9, 10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (benzo[a]pyrene diol epoxide, anti-BPDE) in human genes. The H-ras protooncogene and insulin gene sequences were used as targets for modification in vitro and in vivo. Selective induction of individual facultative bands, resulting from covalent modification of the cognate recognition sites, was observed in modified plasmid DNA for a number of restriction nucleases. The ras gene-specific damage, at the PstI, BstYI, NotI and BstEII recognition sites, was visualized and quantitated in human genomic DNA adducted by anti-BPDE. Repair of lesions at hexanucleotide sequences and/or regions surrounding the restriction site, was assessed as a gradual disappearance of facultative bands in DNA from repair-proficient human fibroblasts exposed to the carcinogen in confluent culture. Efficiency of the PstI site-specific repair was compared at low and high levels of initial damage. Higher genotoxic dose caused a decrease in the extent of adduct removal from the bulk DNA, while the specific site of the ras gene was still subject to fast repair. No measurable PstI site-specific repair was detected in the insulin gene. These results show the region-selective induction of bulky anti-BPDE DNA damage in non-related genomic targets and suggest that repair of these lesions in human cells proceeds with the efficiency tightly controlled at different levels of initial genotoxic load.
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Affiliation(s)
- M F Denissenko
- Department of Radiology, Ohio State University, Columbus 43210, USA
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Belogurov AA, Delver EP. A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions. Nucleic Acids Res 1995; 23:785-7. [PMID: 7708494 PMCID: PMC306760 DOI: 10.1093/nar/23.5.785] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Antirestriction proteins Ard encoded by some self-transmissible plasmids specifically inhibit restriction by members of all three families of type I restriction-modification (R-M) systems in E.coli. Recently, we have identified the amino acid region, 'antirestriction' domain, that is conserved within different plasmid and phage T7-encoded antirestriction proteins and may be involved in interaction with the type I R-M systems. In this paper we demonstrate that this amino acid sequence shares considerable similarity with a well-known conserved sequence (the Argos repeat) found in the DNA sequence specificity (S) polypeptides of type I systems. We suggest that the presence of these similar motifs in restriction and antirestriction proteins may give a structural basis for their interaction and that the antirestriction action of Ard proteins may be a result of the competition between the 'antirestriction' domains of Ard proteins and the similar conserved domains of the S subunits that are believed to play a role in the subunit assembly of type I R-M systems.
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Affiliation(s)
- A A Belogurov
- Department of Genetic Engineering, Cardiology Research Center, Moscow, Russia
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Jeltsch A, Alves J, Urbanke C, Maass G, Eckstein H, Lianshan Z, Bayer E, Pingoud A. A dodecapeptide comprising the extended chain-alpha 4 region of the restriction endonuclease EcoRI specifically binds to the EcoRI recognition site. J Biol Chem 1995; 270:5122-9. [PMID: 7890621 DOI: 10.1074/jbc.270.10.5122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The restriction endonuclease EcoRI binds and cleaves DNA containing GAATTC sequences with high specificity. According to the crystal structure, most of the specific contacts of the enzyme to the DNA are formed by the extended chain region and the first turn of alpha-helix alpha 4 (amino acids 137-145). Here, we demonstrate that a dodecapeptide (WDGMAAGNAIER), which is identical in the underlined parts of its sequence to EcoRI amino acids 137-145, specifically binds to GAATTC sequences. The peptide inhibits DNA cleavage by EcoRI but not by BamHI, BclI, EcoRV, HindIII, PacI, and XbaI. DNA cleavage by XbaI is slowed down at sites that partially overlap with EcoRI sites. The peptide inhibits cleavage of GAATTC sites by ApoI, which recognizes the sequence RAATTY. It interferes with DNA methylation by the EcoRI methyltransferase but not by the BamHI methyltransferase. It competes with EcoRI for DNA binding. Based on these results, the DNA binding constant of the peptide to GAATTC sequences was calculated to be 3 x 10(4) M-1. DNA binding is not temperature-dependent, suggesting that binding of the peptide is entropy-driven. As the peptide does not show any nonspecific binding to DNA, its DNA binding specificity is similar to that of EcoRI, in spite of the fact that the affinity is much smaller. These results suggest that contacts to the phosphate groups in EcoRI mainly provide binding affinity, whereas the specificity of EcoRI is based to a large extent on sequence-specific base contacts.
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Affiliation(s)
- A Jeltsch
- Institut für Biochemie, Justus-Liebig Universität, Giessen, Germany
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Abstract
Supercoiled pUC19 DNA, photoreacted with psoralen derivatives (xanthotoxin (8-methoxypsoralen, 8-MOP), 4,5',8-trimethylpsoralen (TMP) and angelicin), influences the enzymatic activity of restriction enzymes in a different manner, although all the enzymes employed contain, within their recognition sites, suitable nucleic acid bases for photoproduct formation. The activity of the enzymes is strongly influenced by the photomodification of thymine residues within their recognition sites. 5'-TpA sequences favour intercalation as an essential prerequisite of the photoreaction, while 5'ApT sequences do not. This, in turn, influences photoproduct formation and the inhibition of the action of the restriction enzymes KpnI, SspI, DraI and RsaI, but not EcoRI and BamHI. The inhibitory effect is independent of the number of cleavage sites and also of whether monoaddition products or crosslinks are formed. Psoralen intercalation alone does not affect the activity of the restriction enzymes used.
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Affiliation(s)
- L Kittler
- Institut für Molekulare Biotechnologie e.V., Jena, Germany
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Morrison M, Mackie RI, White BA. The restriction endonuclease RflFII, isolated from Ruminococcus flavefaciens FD-1, recognizes the sequence 5'-AGTACT-3', and is inhibited by site-specific adenine methylation. FEMS Microbiol Lett 1994; 122:181-5. [PMID: 7958770 DOI: 10.1111/j.1574-6968.1994.tb07162.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Molecular studies of the rumen bacterium Ruminococcus flavefaciens are constrained by the lack of stable gene transfer systems. We report here on the characterization of RflFII, a restriction endonuclease isolated from R. flavefaciens FD-1. The enzyme is an isoschizomer of ScaI, and cleavage of the DNA is blunt-ended, between the internal TA dinucleotide sequence of 5'-AGTACT-3'. Chromosomal DNA preparations were used to demonstrate that adenine methylation of DNA within the sequence 5'-GTAC-3' inhibits both RflFII and the restriction endonucleases RsaI and ScaI. Chromosomal DNA from R. flavefaciens FD-1 is also host modified to protect against cleavage by ScaI.
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Affiliation(s)
- M Morrison
- Department of Animal Sciences, University of Illinois, Urbana-Champaign 61801
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Abrol S, Chaudhary VK. Excess of PCR primers inhibit DNA cleavage by some restriction endonucleases. Biotechniques 1993; 15:630, 632. [PMID: 8251165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- S Abrol
- University of Delhi South Campus, New Delhi, India
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23
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Belogurov AA, Delver EP, Rodzevich OV. Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences. J Bacteriol 1993; 175:4843-50. [PMID: 8393008 PMCID: PMC204937 DOI: 10.1128/jb.175.15.4843-4850.1993] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The IncN plasmid pKM101 (a derivative of R46) encodes the antirestriction protein ArdB (alleviation of restriction of DNA) in addition to another antirestriction protein, ArdA, described previously. The relevant gene, ardB, was located in the leading region of pKM101, about 7 kb from oriT. The nucleotide sequence of ardB was determined, and an appropriate polypeptide was identified in maxicells of Escherichia coli. Like ArdA, ArdB efficiently inhibits restriction by members of the three known families of type I systems of E. coli and only slightly affects the type II enzyme, EcoRI. However, in contrast to ArdA, ArdB is ineffective against the modification activity of the type I (EcoK) system. Comparison of deduced amino acid sequences of ArdA and ArdB revealed only one small region of similarity (nine residues), suggesting that this region may be somehow involved in the interaction with the type I restriction systems. We also found that the expression of both ardA and ardB genes is controlled jointly by two pKM101-encoded proteins, ArdK and ArdR, with molecular weights of about 15,000 and 20,000, respectively. The finding that the sequences immediately upstream of ardA and ardB share about 94% identity over 218 bp suggests that their expression may be controlled by ArdK and ArdR at the transcriptional level. Deletion studies and promoter probe analysis of these sequences revealed the regions responsible for the action of ArdK and ArdR as regulatory proteins. We propose that both types of antirestriction proteins may play a pivotal role in overcoming the host restriction barrier by self-transmissible broad-host-range plasmids. It seems likely that the ardKR-dependent regulatory system serves in this case as a genetic switch that controls the expression of plasmid-encoded antirestriction functions during mating.
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Affiliation(s)
- A A Belogurov
- Department of Genetic Engineering, National Cardiology Research Center, Moscow, Russia
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24
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Rodriguez RJ. Polyphosphate present in DNA preparations from filamentous fungal species of Colletotrichum inhibits restriction endonucleases and other enzymes. Anal Biochem 1993; 209:291-7. [PMID: 8385889 DOI: 10.1006/abio.1993.1122] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
During the development of a procedure for the isolation of total genomic DNA from filamentous fungi (Rodriguez, R. J., and Yoder, O.C., Exp. Mycol. 15, 232-242, 1991) a cell fraction was isolated which inhibited the digestion of DNA by restriction enzymes. After elimination of DNA, RNA, proteins, and lipids, the active compound was purified by gel filtration to yield a single fraction capable of complete inhibition of restriction enzyme activity. The inhibitor did not absorb uv light above 220 nm, and was resistant to alkali and acid at 25 degrees C and to temperatures as high as 100 degrees C. More extensive analyses demonstrated that the inhibitor was also capable of inhibiting T4 DNA ligase and TaqI DNA polymerase, but not DNase or RNase. Chemical analyses indicated that the inhibitor was devoid of carbohydrates, proteins, lipids, and nucleic acids but rich in phosphorus. A combination of nuclear magnetic resonance, metachromatic shift of toluidine blue, and gel filtration indicated that the inhibitor was a polyphosphate (polyP) containing approximately 60 phosphate molecules. The mechanism of inhibition appeared to involve complexing of polyP to the enzymatic proteins. All species of Colletotrichum analyzed produced polyP equivalent in chain length and concentration. A modification to the original DNA extraction procedure is described which eliminates polyP and reduces the time necessary to obtain DNA of sufficient purity for restriction enzyme digestion and TaqI polymerase amplification.
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Affiliation(s)
- R J Rodriguez
- Department of Plant Pathology, University of California, Riverside 92521
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25
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Abstract
Plasmids containing double-stranded 10-mer PNA (peptide nucleic acid chimera) targets proximally flanked by two restriction enzyme sites were challenged with the complementary PNA or PNAs having one or two mismatches, and the effect on the restriction enzyme cleavage of the flanking sites was assayed. The following PNAs were used: T10-LysNH2, T5CT4-LysNH2 and T2CT2CT4-LysNH2 and the corresponding targets cloned into pUC 19 were flanked by BamH1, Sal1 or Pstl sites, respectively. In all cases it was found that complete inhibition of restriction enzyme cleavage was obtained with the complementary PNA, a significantly reduced effect was seen with a PNA having one mismatch, and no effect was seen with a PNA having two mismatches. These results show that PNA can be used as sequence specific blockers of DNA recognizing proteins.
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Affiliation(s)
- P E Nielsen
- Department of Biochemistry B, Panum Institute, Copenhagen, Denmark
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26
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Abstract
Chemical modification studies were performed to elucidate the role of Cys-residues in the catalysis/binding of restriction endonuclease Cfr9I. Incubation of restriction endonuclease Cfr9I with N-ethylmaleimide (NEM), iodoacetate, 5,5'-dithiobis (2-nitrobenzoic acid) at pH 7.5 led to a complete loss of the catalytic activity. However, no enzyme inactivation was detectable after modification of the enzyme with iodoacetamide and methyl methanethiosulfonate. Complete protection of the enzyme against inactivation by NEM was observed in the presence of substrate implying that Cys-residues may be located at or in the vicinity of the active site of enzyme. Direct substrate-binding studies of native and modified restriction endonuclease Cfr9I using a gel-mobility shift assay indicated that the modification of the enzyme by NEM was hindered by substrate binding. A single Cys-residue was modified during the titration of the enzyme with DTNB with concomitant loss of the catalytic activity. The pH-dependence of inactivation of Cfr9I by NEM revealed the modification of the residue with the pKa value of 8.9 +/- 0.2. The dependence of the reaction rate of substrate hydrolysis by Cfr9I versus pH revealed two essential residues with pKa values of 6.3 +/- 0.15 and 8.7 +/- 0.15, respectively. The evidence presented suggests that the restriction endonuclease Cfr9I contains a reactive sulfhydryl residue which is non-essential for catalysis, but is located at or near the substrate binding site.
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Affiliation(s)
- V Siksnys
- Institute of Biotechnology Fermentas, Vilnius, Lithuania
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27
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Affiliation(s)
- J E Coad
- Department of Laboratory Medicine and Pathology, University of Minnesota Hospitals and Clinics, Minneapolis 55455
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28
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Mallamaci MA, Bascoy ML, Brown J, Combates NJ, Winkle SA. Locating binding sites for the carcinogen N-acetoxy-N-acetyl-2-aminofluorene using restriction enzyme inhibition assays. J Biomol Struct Dyn 1992; 10:83-96. [PMID: 1329843 DOI: 10.1080/07391102.1992.10508632] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Restriction enzyme inhibition studies have been employed to map the locations of high affinity binding sites of the carcinogen N-acetoxy-N-acetyl-2-aminofluorene (acetoxyAAF) on pBR322, phiX174 and SV40 DNAs. Bound carcinogen levels were kept low (less than 20 bound AAF moieties per DNA molecule) in order to observe only the binding to the high affinity sites. Inhibition of certain restriction enzymes was observed in a limited number of locations on these DNAs. Inhibition increased as bound AAF increased and the particular restriction enzymes inhibited varied with location. On all three DNAs, activities of these enzymes was not affected in other locations. Comparison of the sequences at the sites of inhibition on the three DNAs indicates that all sites have common sequence elements: the presence of either the sequence T(C/G)TT(G/C) or the sequence T(G/C)CTT(G/C).
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Affiliation(s)
- M A Mallamaci
- Department of Biochemistry, Rutgers University, New Brunswick, NJ 08903
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29
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Belogurov AA, Delver EP, Rodzevich OV. IncN plasmid pKM101 and IncI1 plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions. J Bacteriol 1992; 174:5079-85. [PMID: 1321121 PMCID: PMC206324 DOI: 10.1128/jb.174.15.5079-5085.1992] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The IncN plasmid pKM101 (a derivative of R46), like the IncI1 plasmid ColIb-P9, carries a gene (ardA, for alleviation of restriction of DNA) encoding an antirestriction function. ardA was located about 4 kb from the origin of transfer, in the region transferred early during bacterial conjugation. The nucleotide sequence of ardA was determined, and an appropriate polypeptide with the predicted molecular weight of about 19,500 was identified in maxicells of Escherichia coli. Comparison of the deduced amino acid sequences of the antirestriction proteins of the unrelated plasmids pKM101 and ColIb (ArdA and Ard, respectively) revealed that these proteins have about 60% identity. Like ColIb Ard, pKM101 ArdA specifically inhibits both the restriction and modification activities of five type I systems of E. coli tested and does not influence type III (EcoP1) restriction or the 5-methylcytosine-specific restriction systems McrA and McrB. However, in contrast to ColIb Ard, pKM101 ArdA is effective against the type II enzyme EcoRI. The Ard proteins are believed to overcome the host restriction barrier during bacterial conjugation. We have also identified two other genes of pKM101, ardR and ardK, which seem to control ardA activity and ardA-mediated lethality, respectively. Our findings suggest that ardR may serve as a genetic switch that determines whether the ardA-encoded antirestriction function is induced during mating.
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Affiliation(s)
- A A Belogurov
- Department of Genetic Engineering, National Cardiology Research Center, Moscow, Russia
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30
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Loseto F, Alessio E, Mestroni G, Lacidogna G, Nassi A, Giordano D, Coluccia M. Interaction of RuCl2 (dimethylsulphoxide)4 isomers with DNA. Anticancer Res 1991; 11:1549-53. [PMID: 1660691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A wide series of restriction enzymes with a range of specificities was used to investigate the interaction with DNA of Ru(II)-DMSO complexes with anticancer activity. While cis-RuCl2 (DMSO)4 was almost completely inactive, treatment of pBR 322 DNA with trans-RuCl2 (DMSO)4 protected G rich sequences from cutting of specific restriction endonucleases, indicating a preferential interaction with adjacent guanines.
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Affiliation(s)
- F Loseto
- Dip. Scienze Biomediche e Oncologia Umana, Policlinico, Bari, Italy
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31
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Affiliation(s)
- S K Grime
- Boehringer Mannheim Corp., Biochemical Products Division, Indianapolis, IN 46250
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32
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Abstract
Plasmid pGC20 containing the (dGC)9 insert in SmaI recognition site has been used to study the inhibition of cleavage by different restriction endonuclease due to Z-DNA formation in (dCG)10 sequence of the negatively supercoiled plasmid. Data obtained indicate the different sensitivity of restriction endonucleases to DNA conformational perturbations resulted from the Z-DNA formation. Therefore, the inhibition of DNA cleavage by a particular restriction endonuclease cannot serve as a criterion for the estimation of the length of B-Z junctions in circular supercoiled DNAs.
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Affiliation(s)
- E A Lesnik
- Engelhardt Institute of Molecular Biology, USSR Academy of Sciences, Moscow
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33
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Abraham ZH, Symonds N. Purification of overexpressed gam gene protein from bacteriophage Mu by denaturation-renaturation techniques and a study of its DNA-binding properties. Biochem J 1990; 269:679-84. [PMID: 2167662 PMCID: PMC1131641 DOI: 10.1042/bj2690679] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recombinant Mu gam gene protein (Mu GAM) synthesized in Escherichia coli accumulates in the form of insoluble inclusion bodies which, after cell lysis and low-speed centrifugation, can be recovered in the pellet fraction. This property was utilized in a purification procedure for Mu GAM based on guanidine hydrochloride denaturation-renaturation followed by a single DEAE-cellulose chromatographic step. The purified Mu GAM was shown by nitrocellulose-filter-binding experiments to bind with high affinity to linear double-stranded DNA and more weakly to supercoiled and single-stranded forms. Mu GAM protects linear DNA from degradation by a variety of exonucleases, but only weakly inhibits endonuclease activity. These results are in accord with a model of Mu GAM conferring protection from exonuclease activity by binding to the ends of DNA.
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Affiliation(s)
- Z H Abraham
- School of Biological Sciences, University of Sussex, Brighton, U.K
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34
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Abstract
This paper reports the study of the photochemical, physical, and biological properties of 3-azidoamsacrine. The binding of 3-azidoamsacrine to DNA was studied with UV spectroscopy. The UV spectral behavior is quite similar to that of the parent amsacrine and argues that 3-azidoamsacrine is a good photoaffinity labeling agent for amsacrine. The biological properties (cytotoxicity and mutagenicity) of 3-azidoamsacrine in the mammalian mutagenesis V79 and L5178Y assay systems were measured. Light-activated 3-azidoamsacrine is toxic, but not mutagenic, to V79 cells. 3-Azidoamsacrine with and without light activation, as well as amsacrine, are toxic and mutagenic to L5178Y cells. To probe the interactions of 3-azidoamsacrine with DNA, studies of the photoreactivity of this compound were conducted. 3-Azidoamsacrine was photolyzed in the presence of the plasmid pBR322, and the effect of the photoadducts on restriction endonuclease cleavage was investigated. Amsacrine and 3-azidoamsacrine, without light activation, did not block any of the restriction endonucleases. Light-activated 3-azidoamsacrine blocked cleavage by the restriction endonucleases AluI, HinfI, NciI, NaeI, DraI, Sau96I, HpaII, and HaeIII. Photolysis experiments with mononucleosides, blocked mononucleosides, dinucleotides, and DNA all indicated that 3-azidoamsacrine formed adducts with G and A. The structures of these adducts are discussed based upon mass spectral data. Thus, it appears that 3-azidoamsacrine covalently attaches to DNA and that this covalent binding results in the production of toxic and, in some cases, mutagenic lesions in mammalian cells and the inhibition of restriction endonuclease cleavage of DNA.
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Affiliation(s)
- T L Shieh
- Department of Medicinal Chemistry and Pharmacognosy, School of Pharmacy and Pharmacal Sciences, Purdue University, West Lafayette, Indiana 47907
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35
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Skov KA, Adomat H, Chaplin DJ, Farrell NP. Toxicity of [PtCl2(NH3)L] in hypoxia; L = misonidazole or metronidazole. Anticancer Drug Des 1990; 5:121-8. [PMID: 2156514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There is increasing interest in compounds which show selective toxicity to the resistant hypoxic portions of tumors. Cisplatin does not generally show preferential toxicity in hypoxic cells, as do nitroimidazoles. It is proposed that attachment of a nitroimidazole could add a degree of hypoxic selectivity to Pt agents. Platinum complexes containing one nitroimidazole ligand bind to DNA and show higher toxicity in hypoxic than aerobic CHO cells. Cis and trans isomers of complexes with misonidazole (a 2-nitroimidazole) and metronidazole (a 5-nitroimidazole) are compared with respect to binding to DNA (approximately the same), reduction potential (trans miso greater than cis miso greater than cis metro greater than trans metro), and toxicity (trans greater than cis miso, cis greater than trans metro, with trans miso approximately cis metro in hypoxia, despite significantly different reduction potentials). The effect of platination on nitroimidazole toxicity is not entirely explained by DNA binding and increased reduction potential. These compounds do not exhibit cross resistance with cisplatin in L1210 resistant cells. This factor, their selectivity for hypoxia, and preliminary results in vivo indicating potentiation of anti-tumor activity by the vasoactive compound, hydralazine, which increases tumor hypoxia, suggest further development of these compounds for use in tumors with resistant hypoxic portions.
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Affiliation(s)
- K A Skov
- Medical Biophysics Unit, BC Cancer Research Centre, Vancouver, Canada
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36
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Parkes JL, Hubbard FC, Penn A. Resistance of tumor-derived DNA to restriction enzyme digestion. Cancer Invest 1990; 8:169-72. [PMID: 2169329 DOI: 10.3109/07357909009017562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The major finding of this work is that there are specific restriction enzyme inhibitors present in "purified" tumor DNA which cause partial digestion patterns when tumor DNA is digested by standard procedures with any of three commonly employed restriction enzymes (HindIII, KpnI, XbaI). These aberrant patterns are not seen when DNA of cell lines derived from these tumors is digested. Thus, when working with tumor DNA these restriction enzymes should be used with caution.
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Affiliation(s)
- J L Parkes
- Institute of Environmental Medicine, New York University Medical Center, New York 10016
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37
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Affiliation(s)
- J R Sayers
- Max Planck Institut für Experimentelle Medizin, Göttingen, FRG
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38
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Coluccia M, Giordano D, Loseto F, Intini FP, Maresca L, Natile G. Different binding to DNA of enantiomeric platinum complexes assessed by inhibition of restriction enzyme activity. Anticancer Res 1989; 9:795-8. [PMID: 2548438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ability of enantiomeric platinum complexes to block the action of selected restriction enzymes has been investigated. The complexes [PtCl2(DAC)], [PtCl2(DAB)] and [PtCl2(DAP)] (DAC = 1,2-diamminocyclohexane; DAB = 2,3-diamminobutane; DAP = 1,2-diamminopropane) exhibit a guanine-cytosine preference in accord with previous results on cis-[PtCl2(NH3)2] (cis-DDP). The extent of inhibition, however, is significantly different for the different isomers; the R,R form is more active than the others at short incubation time, as the time becomes longer, the differences among isomers level off. It also appears that cis-DDP is more active than [PtCl2(DAC)] in blocking the Cfo I enzyme, though it shows a preference for the G-X-G sequences.
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Affiliation(s)
- M Coluccia
- Istituto di Patologia Generale, Bari, Italy
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39
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Affiliation(s)
- K Schnetz
- Institut für Biologie III, Universität Freiburg, FRG
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40
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Abstract
The inhibition of restriction enzyme digestion of lambda phage DNA by anthracyclines (i.e., adriamycin, daunomycin, epirubicin, idarubicin and esorubicin) commonly used in the treatment of human leukemia and cancer has been studied in vitro. The anthracyclines used inhibit DNA digestion by SmaI, AvaII, HaeIII, HhaI and HpaII, which cut DNA at guanine-cytosine (G-C) sequence sites, and by EcoRI, which cut DNA at adenine adenine-thymine thymine (AATT) sequence sites. Adriamycin completely inhibits DNA restriction by the indicated enzymes, daunomycin, epirubicin and idarubicin determine only a partial inhibition, while esorubicin does not inhibit DNA restriction at all. An attempt is made to correlate the extent of the in vitro interaction between anthracyclines and DNA to in vivo cardiotoxicity.
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Affiliation(s)
- G Corneo
- Cattedra di Patologia Medica II, Università degli Studi di Milano
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41
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Torosian MV, Rabinkova EV, Aĭzenberg OA, Naumova LA, Shishkova OV. [Use of the RI plasmid to study radiation damage to the methyl anti-nuclease barrier in the DNA of Escherichia coli]. Radiobiologiia 1988; 28:7-10. [PMID: 2830634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ionizing radiation (gamma-rays, 100 to 750 Gy) does not impair methyl anti-nuclease barrier in DNA of exposed cells. From this it follows that the methyl anti-nuclease barrier is radioresistant. It is assumed that restrictases are involved in degradation of single-strand DNA regions, that is, in degradation of replicative forks.
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42
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Miranda M, Bonfigli A, Zarivi O, Manilla A, Cimini AM, Arcadi A. Restriction patterns of model DNA treated with 5,6-dihydroxyindole, a potent cytotoxic intermediate of melanin synthesis: effect of u.v. irradiation. Mutagenesis 1987; 2:45-50. [PMID: 2842578 DOI: 10.1093/mutage/2.1.45] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The interaction of 5,6-dihydroxyindole, a putative cytotoxic intermediate of melanin synthesis, with model lambda phage DNA has been investigated by using type II restriction endonucleases and CsCl buoyant density centrifugation. As evidenced by agarose gel electrophoresis and density gradient profiles, the 5,6-dihydroxyindole or u.v. treated DNAs, restricted or not, are modified. U.v. irradiation enhances 5,6-dihydroxyindole binding to DNA, but no sequence specific binding was observed. The action of L-3,4-dihydroxyphenylalanine on the restriction patterns of lambda phage DNA was also investigated and the effect appeared smaller, by qualitative evaluation, than that produced by 5,6-dihydroxyindole.
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Affiliation(s)
- M Miranda
- Department of Cell Biology and Physiology, University of L'Aquila-via Assergi, Italy
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43
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Nakamaye KL, Eckstein F. Inhibition of restriction endonuclease Nci I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis. Nucleic Acids Res 1986; 14:9679-98. [PMID: 3027659 PMCID: PMC341328 DOI: 10.1093/nar/14.24.9679] [Citation(s) in RCA: 498] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
M13 RF IV DNA where phosphorothioate groups are incorporated at restriction endonuclease Nci I recognition sites in the (-)strand is efficiently nicked by the action of this enzyme. Incubation of such nicked DNA with exonuclease III produces gapped DNA. The gap can be filled by reaction with deoxynucleoside triphosphates and DNA polymerase I. When this sequence of reactions is performed with DNA containing a mismatch oligonucleotide primer in the (-)-strand mutational frequencies of 70-90% can be obtained upon transformation. The general nature of this methodology has been further shown to be applicable to other restriction enzymes such as Hind II, Pst I and Fsp I. The mutational frequency obtained using these enzymes is between 40-80% mainly because of less efficient nicking and gapping. Studies on inhibition of Nci I cleavage show that in addition to a phosphorothioate group at the position of cleavage an additional group in the 5'-neighbouring position is necessary for complete inhibition.
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44
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Sokolov NN, Fitsner AB, Anikeĭcheva NV, Khoroshutina EB, Samko OT. [Effect of thiol-specific reagents on the activity of PaeI and PaeII restrictases from Pseudomonas aeruginosa]. Biull Eksp Biol Med 1986; 102:695-7. [PMID: 3026511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
5,5'-dithiobis-2-nitrobenzoic acid, N-ethylmaleimide, and parachloromercuribenzoate have been demonstrated to inhibit the activity of restrictases PaeI and PaeII from Ps. aeruginosa bacterial cells. Restrictase PaeII was more sensitive to the action of thiol-specific reagents, as compared to PaeI. The minimal concentration of reagents for SH-groups that completely inhibited the activity of restrictases PaeI and PaeII was determined. The protective effect against the inhibitory action of 5,5'-dithiobis-2-nitrobenzoic acid on the activity of PaeII was observed after preincubation of these enzymes with phage lambda DNA and Mg2+ cations. It is suggested that restrictase PaeI and PaeII molecules contain SH-groups, essential for the enzymatic activity. They are believed responsible for restrictase binding with DNA substrate.
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45
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Stanchev BS, Grokhovskiĭ SL, Khorlin AA, Gottikh BP, Zhuze AL. [Netropsin, distamycin A, bis-netropsins as selective inhibitors of restrictases and DNAse I]. Mol Biol (Mosk) 1986; 20:1614-24. [PMID: 3027536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The simultaneous analysis of DNAase I "footprinting" data and restriction endonucleases inhibition data was performed on the same DNA end-labelled fragment. The inhibition induced by netropsin, a number of bis-netropsins and distamycin A was investigated. These experiments led us to the following conclusions. The restriction endonucleases inhibition by the ligands is caused by the ligand molecules binding in the close vicinity to the restriction endonuclease recognition sequence. The zone of +/- 4 bp from the center of the restriction endonuclease recognition sequence can be defined as the zone of the influence of the bounded ligand on the restriction endonuclease. But in this case the intersection of recognition sequence and the binding site occupied by a single ligand molecule is not sufficient for the inhibition to occur. Restriction endonuclease cutting sites protected by netropsin can be predicted basing upon known nucleotide sequence specificity of netropsin. Netropsin and bis-netropsins show different nucleotide sequence specificity. This fact can be used for selective inhibition of restriction endonucleases.
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46
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Abstract
The effect of the bifunctional crosslinking reagent glutaraldehyde on the activity of the restriction enzymes Bam HI, Hind III, EcoRI, and Tthlll I was investigated. The four enzymes exhibited differential sensitivity to inactivation. Tthlll I was the most sensitive, with activity losses occurring at levels of 0.0025% and above. Hind III was the most stable of the four and remained fully active at concentrations as high as 0.075%. Addition of BSA to incubation mixtures generally had a stabilizing effect. Implications of these results for the design of glutaraldehyde-based methods for the immobilization of restriction endonucleases are discussed.
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47
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48
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Simúth J, Trnovský J, Jeloková J. Inhibition of bacterial DNA-dependent RNA polymerases and restriction endonuclease by UV-absorbing components from propolis. Pharmazie 1986; 41:131-2. [PMID: 3014571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Several UV-absorbing substances inhibiting the DNA-dependent RNA polymerases of Escherichia coli and Streptomyces aureofaciens, as well as the restriction endonuclease Eco RI have been isolated from the water-soluble extract of Propolis by two-dimensional paper chromatography. The inhibition of bacterial RNA-polymerases by the components of Propolis was probably due to the loss of their ability to bind to DNA. The general characteristic of the UV-absorbing component of Propolis with the most pronounced inhibitory effect upon transcription in vitro is described.
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George J, Nardone G, Chirikjian JG. Sequence-specific BamHI endonuclease. The proposed role of arginine residues in substrate binding and recognition. J Biol Chem 1985; 260:14387-92. [PMID: 2997207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Arginyl residues in BamHI endonuclease were examined because of their alleged role in proteins that contain nucleotide- or phosphate-binding sites. Butanedione, an arginine-specific reagent, inhibited the endonuclease in the presence of sodium borate. The inhibition was decreased by preliminary incubation of the enzyme with DNA or competitive inhibitors which were the 5'-phosphoryl deoxydinucleotide subsets of the BamHI recognition sequence. The dinucleotide pdGpdG protected the enzyme most efficiently against the butanedione modification. Dinucleotides that were unrelated to the recognition sequence failed to protect the enzyme from inactivation. These studies indicate that arginine residues may reside in the enzyme's active site and might function in the sequence-specific recognition of the BamHI palindrome.
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Belogurov AA, Yussifov TN, Kotova VU, Zavilgelsky GB. The novel gene(s) ARD of plasmid pKM101: alleviation of EcoK restriction. Mol Gen Genet 1985; 198:509-13. [PMID: 2989658 DOI: 10.1007/bf00332948] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The host-controlled K restriction of unmodified phage lambda was 10-100-fold alleviated in the wild-type strain E. coli K12, carrying plasmid pKM101 of incompability group N. pKM101-mediated release of K restriction was also observed in lexA-, recA-, and recB- strains of E. coli K12. By restriction mapping Tn5 insertions in pKM101, which reduced pKM101-mediated alleviation of restriction, were shown to be located within the BglIIB fragment approximately 11 kb anticlockwise from the RI site of pKM101. We have termed the gene(s) promoting the alleviation of K restriction of phage lambda ard (alleviation of restriction of DNA). It was shown (1) that ard function affected only the EcoK restriction system and not the EcoB, EcoRI, EcoRIII, or EcoPI systems, (2) ard gene(s) did not mediate EcoK type modification of lambda DNA and did not increase the modification activity of the EcoK system in a way similar to that observed with gene ral of bacteriophage lambda.
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