deoxyribonuclease bamhi

Summary

Summary: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence G/GATCC at the slash. BamHI is from Bacillus amyloliquefaciens N. Numerous isoschizomers have been identified. EC 3.1.21.-.

Top Publications

  1. Engler L, Sapienza P, Dorner L, Kucera R, Schildkraut I, Jen Jacobson L. The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC. J Mol Biol. 2001;307:619-36 pubmed
    ..This electrostatic repulsion destabilizes the enzyme-DNA complex and favors metal ion binding and progression to the transition state for cleavage. ..
  2. Young D, Govan J, Lively M, Deiters A. Photochemical regulation of restriction endonuclease activity. Chembiochem. 2009;10:1612-6 pubmed publisher
    ..Interestingly, these groups do not appear to dramatically affect initial binding of the enzyme to the DNA substrate, but rather prevent recognition of the specific cleavage site. ..
  3. Perez J, O Loughin T, Simeone F, Weissleder R, Josephson L. DNA-based magnetic nanoparticle assembly acts as a magnetic relaxation nanoswitch allowing screening of DNA-cleaving agents. J Am Chem Soc. 2002;124:2856-7 pubmed
    ..These qualities render the developed nanoparticles and their nanoassemblies as magnetic relaxation switches capable of screening for DNA-cleaving compounds by magnetic resonance methods such as MRI and NMR. ..
  4. Fuxreiter M, Osman R. Probing the general base catalysis in the first step of BamHI action by computer simulations. Biochemistry. 2001;40:15017-23 pubmed
    ..On the basis of these findings we propose that the first step of endonuclease catalysis does not require a general base; rather, the essential attacking nucleophile in BamHI catalytic action is stabilized by the metal ions. ..
  5. Korsmeyer S, Hieter P, Ravetch J, Poplack D, Waldmann T, Leder P. Developmental hierarchy of immunoglobulin gene rearrangements in human leukemic pre-B-cells. Proc Natl Acad Sci U S A. 1981;78:7096-100 pubmed
  6. Kinsella J, Ivanisevic A. Enzymatic clipping of DNA wires coated with magnetic nanoparticles. J Am Chem Soc. 2005;127:3276-7 pubmed
    ..We show that, despite the presence of the nanoparticles on the DNA, the enzyme is still able to recognize the cleavage site and effectively digest the assembly. ..
  7. Sun J, Viadiu H, Aggarwal A, Weinstein H. Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex. Biophys J. 2003;84:3317-25 pubmed
    ..We show that a favorable sliding pathway of the protein along DNA is helical. ..
  8. Lynch T, Sligar S. Experimental and theoretical high pressure strategies for investigating protein-nucleic acid assemblies. Biochim Biophys Acta. 2002;1595:277-82 pubmed
    ..The disruption of these contacts can be attributed to an observed pressure-induced increase in hydration at the protein-DNA interface during the elevated pressure simulation. ..
  9. Wagner B, Miller D, Lear T, Antczak D. The complete map of the Ig heavy chain constant gene region reveals evidence for seven IgG isotypes and for IgD in the horse. J Immunol. 2004;173:3230-42 pubmed
    ..Fluorescence in situ hybridization was used to localize the IGHC region to Equus caballus (ECA) 24qter, the horse chromosome corresponding to human chromosome 14, where the human IGH locus is found. ..

More Information

Publications62

  1. Pumphrey C, Gray W. Identification and analysis of the simian varicella virus thymidine kinase gene. Arch Virol. 1996;141:43-55 pubmed
    ..Identification of the SVV TK ORF will facilitate studies that examine the role of viral TKs in pathogenesis and antiviral sensitivity and provides a potential insertion site for the expression of foreign genes...
  2. Figueroa F, Vincek V, Kasahara M, Bell G, Klein J. Mapping of the Sod-2 locus into the t complex on mouse chromosome 17. Immunogenetics. 1988;28:260-4 pubmed
  3. Zheng X, Bevilacqua P. Efficient construction of long DNA duplexes with internal non-Watson-Crick motifs and modifications. Nucleic Acids Res. 2001;29:E6 pubmed
  4. Bujnicki J. Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol. 2000;50:39-44 pubmed
  5. Hwang H, Kim H, Myong S. Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity. Proc Natl Acad Sci U S A. 2011;108:7414-8 pubmed publisher
    ..The high spatio-temporal resolution data and sensitivity to short distances combined with the ability to bypass protein labeling makes this assay an effective alternative or a complement to FRET. ..
  6. Wackym P, Cioffi J, Erbe C, Popper P. G-protein Golfalpha (GNAL) is expressed in the vestibular end organs and primary afferent neurons of Rattus norvegicus. J Vestib Res. 2005;15:11-5 pubmed
    ..Golfalpha was found in both the end organs and the ganglia and could serve unique roles in the physiology of the vestibular neuroepithelium. ..
  7. Kim S, Park E, Lim C. Stress-dependent regulation of the gene encoding gamma-glutamylcysteine synthetase from the fission yeast. Mol Biol Rep. 2004;31:23-30 pubmed
    ..It was also induced by low concentrations of glucose and sucrose. These results suggest that the expression of S. pombe GCS gene is regulated by various stresses and carbon sources. ..
  8. Viktorova T, Korytina G, Makarova O, Ianbaeva D, Iakupova E, Khusnutdinova E. [Analysis of the N-acetyltransferase 2 gene polymorphism in the patients with chronic obstructive pulmonary disease and in populations of the Volga-Ural region]. Genetika. 2003;39:855-7 pubmed
    ..60; p = 0.036). The data obtained suggest a possible association between the drug resistance in the COPD patients with the rapid acetylator phenotype, which can lead to the development of the chronic form of the disease. ..
  9. Rijnsburger M, Delwel S, Boutaga K, van Steenbergen T, Savelkoul P, van Winkelhoff A. Comparison of restriction enzyme analysis and amplified fragment length polymorphism typing of Porphyromonas gingivalis isolated from spouses. Oral Microbiol Immunol. 2007;22:369-73 pubmed
    ..Different types were found in two couples with both the REA and the AFLP method. The AFLP typing technique confirms earlier observations on the transmission of P. gingivalis between spouses. This new technique can replace REA typing. ..
  10. Cooper S, Murphy R, Dolman G, Hussey D, Hope R. A molecular and evolutionary study of the beta-globin gene family of the Australian marsupial Sminthopsis crassicaudata. Mol Biol Evol. 1996;13:1012-22 pubmed
  11. Chen K, Gottesman M. Useful tool to generate unidirectional deletion vectors by utilizing the star activity of BamHI in an NcoI-BamHI-XhoI cassette. Biotechniques. 2005;38:198, 200, 202, 204 pubmed
  12. Alzhanov D, Alzhanova D, Zheleznaya L, Matvienko N. Thermophilic strain Bacillus species AA contains several site-specific endonucleases. Biochemistry (Mosc). 1998;63:537-45 pubmed
    ..BspAAIII recognizes the sequence 5'-GGATCC-3' and is an isomer of BamHI. The optimal temperature and pH values are 42-48 degreesC and 7.0-8.0, respectively. ..
  13. Bernhard F, Demel G, Soltani K, Döhren H, Blinov V. Identification of genes encoding for peptide synthetases in the gram-negative bacterium Lysobacter sp. ATCC 53042 and the fungus Cylindrotrichum oligospermum. DNA Seq. 1996;6:319-30 pubmed
    ..Therefore, the localized modules may activate the amino acids threonine and glycine. ..
  14. Yu S, Geng J, Zhou P, Feng A, Chen X, Hu J. Analysis of plasmid DNA damage induced by melanin with capillary electrophoresis. J Pharm Biomed Anal. 2007;43:816-21 pubmed
  15. Raha M, Sockett H, Macnab R. Characterization of the fliL gene in the flagellar regulon of Escherichia coli and Salmonella typhimurium. J Bacteriol. 1994;176:2308-11 pubmed
    ..Thus, FliL does not appear to have a major role in flagellar structure or function and is therefore unlikely to be a component of the motor or switch; the effect on motility caused by truncation of the gene is probably an indirect one. ..
  16. Blount P, Sukharev S, Moe P, Schroeder M, Guy H, Kung C. Membrane topology and multimeric structure of a mechanosensitive channel protein of Escherichia coli. EMBO J. 1996;15:4798-805 pubmed
    ..Finally, cross-linking studies suggest that the functional MscL complex is a homohexamer. In summary, these data are all consistent with a protein domain assignment and topological model which we propose and discuss. ..
  17. Mok M, Marians K. The Escherichia coli preprimosome and DNA B helicase can form replication forks that move at the same rate. J Biol Chem. 1987;262:16644-54 pubmed
    ..The single-stranded DNA binding protein was not required to maintain this high rate of movement in the case of leading strand DNA synthesis catalyzed by the DNA polymerase III holoenzyme and the DNA B helicase. ..
  18. Ivanova N, Belyavsky A. Identification of differentially expressed genes by restriction endonuclease-based gene expression fingerprinting. Nucleic Acids Res. 1995;23:2954-8 pubmed
    ..One of the genes was found to encode terminal deoxynucleotidyl transferase; others are apparently previously unknown genes. ..
  19. Stephens R, Sanchez Pescador R, Wagar E, Inouye C, Urdea M. Diversity of Chlamydia trachomatis major outer membrane protein genes. J Bacteriol. 1987;169:3879-85 pubmed
    ..The molecular basis of omp1 gene diversity among C. trachomatis serovars was observed to be clustered nucleotide substitutions for closely related serovars and insertions or deletions for distantly related serovars...
  20. Bull T, Sheridan J, Martin H, Sumar N, Tizard M, Hermon Taylor J. Further studies on the GS element. A novel mycobacterial insertion sequence (IS1612), inserted into an acetylase gene (mpa) in Mycobacterium avium subsp. silvaticum but not in Mycobacterium avium subsp. paratuberculosis. Vet Microbiol. 2000;77:453-63 pubmed
    ..Homologues of the GS element in MTB show a marked similarity of organisation, suggesting a parallel role for these genes in both pathogens. ..
  21. Qian J, Feingold J, Stoll C, May E. Transforming growth factor-alpha: characterization of the BamHI, RsaI, and TaqI polymorphic regions. Am J Hum Genet. 1993;53:168-75 pubmed
    ..001) association between the RsaI and the BamHI genotype. The frequency of the rare BamHI allele was significantly higher (P < .001) in transformed cell lines (.30) than in controls (.076). ..
  22. Corvalan A, Ding S, Koriyama C, Carrascal E, Carrasquilla G, Backhouse C, et al. Association of a distinctive strain of Epstein-Barr virus with gastric cancer. Int J Cancer. 2006;118:1736-42 pubmed
    ..This finding is contrary to the proposed hypothesis that EBV strains are geographically but not disease-restricted and identified a healthy population group that share the same strain that predominate in EBVaGC cases. ..
  23. Malygin E, Zinoviev V, Evdokimov A, Lindstrom W, Reich N, Hattman S. DNA (cytosine-N4-)- and -(adenine-N6-)-methyltransferases have different kinetic mechanisms but the same reaction route. A comparison of M.BamHI and T4 Dam. J Biol Chem. 2003;278:15713-9 pubmed
  24. Ishii H, Ogino T, Berger C, Köchli Schmitz N, Nagato T, Takahara M, et al. Clinical usefulness of serum EBV DNA levels of BamHI W and LMP1 for Nasal NK/T-cell lymphoma. J Med Virol. 2007;79:562-72 pubmed
    ..These data suggest that simultaneous measurement of serum levels of both BamHI W and LMP1 DNAs may be useful for diagnosis, disease monitoring, and prediction of prognosis for nasal NK/T-cell lymphoma patients. ..
  25. Mordasini T, Curioni A, Andreoni W. Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations. J Biol Chem. 2003;278:4381-4 pubmed
    ..A new perspective is opened for the understanding of the functional role of metal ions in biological processes. ..
  26. Boguski M, Birkenmeier E, Elshourbagy N, Taylor J, Gordon J. Evolution of the apolipoproteins. Structure of the rat apo-A-IV gene and its relationship to the human genes for apo-A-I, C-III, and E. J Biol Chem. 1986;261:6398-407 pubmed
    ..However, conservation of the fundamental amphipathic pattern allowed members of this protein family to retain their lipid-binding properties. ..
  27. Michelsen B, Lernmark A. Molecular cloning of a polymorphic DNA endonuclease fragment associates insulin-dependent diabetes mellitus with HLA-DQ. J Clin Invest. 1987;79:1144-52 pubmed
    ..Both serologic markers were split and a non-DR3/non-DR4 IDDM patient was 4-kb positive. HLA-DQ seems therefore closer, than HLA-DR, to an IDDM susceptibility gene. ..
  28. Lundwall A, Olsson A. Semenogelin II gene is replaced by a truncated line 1 repeat in the cotton-top tamarin. Biol Reprod. 2001;65:420-5 pubmed
    ..Thus, a mammalian ancestor probably carried a single gene that in the rodent lineage developed into the semenoclotin gene and in the primate lineage into a progenitor of the semenogelin genes. ..
  29. Andreev I, Spiridonova K, Solovyan V, Kunakh V. Variability of ribosomal RNA genes in Rauwolfia species: parallelism between tissue culture-induced rearrangements and interspecies polymorphism. Cell Biol Int. 2005;29:21-7 pubmed
    ..serpentina tissue cultures. The results demonstrate that rDNA variability observed in intact plants as well as in long-term cultures is attributed to differences in the same regions of ribosomal RNA genes. ..
  30. Arciszewska L, Grainge I, Sherratt D. Action of site-specific recombinases XerC and XerD on tethered Holliday junctions. EMBO J. 1997;16:3731-43 pubmed
  31. van Beek J, Brink A, Vervoort M, van Zijp M, Meijer C, van den Brule A, et al. In vivo transcription of the Epstein-Barr virus (EBV) BamHI-A region without associated in vivo BARF0 protein expression in multiple EBV-associated disorders. J Gen Virol. 2003;84:2647-59 pubmed
    ..It is concluded that the BARF0 protein is unlikely to play a role in vivo in EBV-positive malignancies. ..
  32. Walker A, Collins F, Siddique T, Yamaoka L, Herbstreith M, Pericak Vance M, et al. D21S194, a jump clone from D21S16. Nucleic Acids Res. 1990;18:1931 pubmed
  33. Deng G, Lu Y, Chen S, Miao J, Lu G, Li H, et al. Activated c-Ha-ras oncogene with a guanine to thymine transversion at the twelfth codon in a human stomach cancer cell line. Cancer Res. 1987;47:3195-8 pubmed
    ..This results in the substitution of valine for glycine at the 12th amino acid of the Mr 21,000 protein. ..
  34. Novak U, Griffin B. Requirement for the C-terminal region of middle T-antigen in cellular transformation by polyoma virus. Nucleic Acids Res. 1981;9:2055-73 pubmed
    ..Transfection of Rat-1 cells with plasmids that contained viral DNA with deletions which corresponded to the last fourteen or more amino acids of the middle T-antigen never gave rise to cellular transformation. ..
  35. Shepard D, Oberfelder R, Welch M, McHenry C. Determination of the precise location and orientation of the Escherichia coli dnaE gene. J Bacteriol. 1984;158:455-9 pubmed
    ..This approach has permitted the precise determination of both termini of the dnaE gene and the determination of the orientation of the gene within the E. coli chromosome. ..
  36. Sangvik M, Littauer P, Simonsen G, Sundsfjord A, Dahl K. mef(A), mef(E) and a new mef allele in macrolide-resistant Streptococcus spp. isolates from Norway. J Antimicrob Chemother. 2005;56:841-6 pubmed
    ..pneumoniae and pharyngeal carrier strains of various viridans streptococci. However, mef(A) is more prevalent in S. pneumoniae and S. pyogenes due to clonal spread. A new mef allele was found in two different STs of S. pyogenes. ..
  37. Zhang J, Chen H, Weinmaster G, Hayward S. Epstein-Barr virus BamHi-a rightward transcript-encoded RPMS protein interacts with the CBF1-associated corepressor CIR to negatively regulate the activity of EBNA2 and NotchIC. J Virol. 2001;75:2946-56 pubmed
    ..We conclude that RPMS acts as a negative regulator of EBNA2 and Notch activity through its interactions with the CBF1-associated corepressor complex. ..
  38. Selvaraj G, Kirkwood C, Bines J, Buttery J. Molecular epidemiology of adenovirus isolates from patients diagnosed with intussusception in Melbourne, Australia. J Clin Microbiol. 2006;44:3371-3 pubmed
    ..IS-associated isolates are similar to circulating non-IS-associated strains. ..
  39. Huang J, Xie Z. Polymorphisms in the vitamin D receptor gene and multiple sclerosis risk: a meta-analysis of case-control studies. J Neurol Sci. 2012;313:79-85 pubmed publisher
    ..Tt+TT), and 1.04 (95% CI: 0.78-1.38) for the homozygote model (tt vs. TT). ORs for other VDR polymorphisms were similar. The VDR Apa-I, Bsm-I, Fok-I and Taq-I polymorphisms are not associated with MS risk. ..
  40. Chen H, Huang J, Wu F, Liao G, Hutt Fletcher L, Hayward S. Regulation of expression of the Epstein-Barr virus BamHI-A rightward transcripts. J Virol. 2005;79:1724-33 pubmed
    ..More-abundant BART expression in epithelial cells correlated with the relative expression of positive and negative regulators in these cells. ..
  41. Ryan K, DasGupta S, Beverley S. Shuttle cosmid vectors for the trypanosomatid parasite Leishmania. Gene. 1993;131:145-50 pubmed
  42. Lehel C, Los D, Wada H, Györgyei J, Horvath I, Kovacs E, et al. A second groEL-like gene, organized in a groESL operon is present in the genome of Synechocystis sp. PCC 6803. J Biol Chem. 1993;268:1799-804 pubmed
    ..2-kb transcript of groESL operon increased 100-fold within 15 min upon heat stress. A 9-base pair inverted repeat revealed around the groESL promoter might be involved in regulation of the heat shock response. ..
  43. Takahashi T, Kawamura Y, Sakata N, Elmesiry G, Takemon Y, Tanida K, et al. Nucleotide sequence of BamHI family satellite DNA and its unit length polymorphism in bluegill sunfish Lepomis macrochirus. Mol Biol Rep. 2001;28:119-22 pubmed
    ..The results may reflect ongoing homogenization of satellite DNA type over a short evolutionary time scale. ..
  44. Acharya A, Roy K. An alternative approach for screening active bam HI variants: overexpression in T-7 RNA polymerase based system. Indian J Biochem Biophys. 2001;38:303-8 pubmed
    ..coli. This provides an alternate way to screen the active endonuclease and its variants. ..
  45. Tanabe C, Aoyagi K, Sakiyama T, Kohno T, Yanagitani N, Akimoto S, et al. Evaluation of a whole-genome amplification method based on adaptor-ligation PCR of randomly sheared genomic DNA. Genes Chromosomes Cancer. 2003;38:168-76 pubmed
    ..These data show that PRSG can provide a sufficient amount of genomic sequence for a variety of genetic analyses as well as for long-term storage for future work. ..
  46. Szabo P, Panneerselvam C, Clinton M, Frangou Lazaridis M, Weksler D, Whittington E, et al. Prothymosin alpha gene in humans: organization of its promoter region and localization to chromosome 2. Hum Genet. 1993;90:629-34 pubmed
    ..5 kb allowing the identification of numerous, potential cis-acting regulatory sites. This 5'-flanking cloned probe permitted us to localize the prothymosin gene to chromosome 2 in humans. ..
  47. Liguori G, De Gregorio L, Tucci M, Lago C, Barra A, Dragani T, et al. Mapping of the mouse Tdgf1 gene and Tdgf pseudogenes. Mamm Genome. 1997;8:502-5 pubmed
    ..Finally, analysis of the DNA from several Mus musculus strains and from Mus spretus mice revealed a highly variable restriction pattern and the absence of the Tdgf1-ps1 genomic sequence from the Mus spretus genome. ..
  48. Lee W, Hwang Y, Lee S, Subramanian C, Robertson E. An Epstein-Barr virus isolated from a lymphoblastoid cell line has a 16-kilobase-pair deletion which includes gp350 and the Epstein-Barr virus nuclear antigen 3A. J Virol. 2001;75:8556-68 pubmed
  49. Olsson P, Hammarstrom L, Cox D, Smith C. Involvement of both HLA and Ig heavy chain haplotypes in human IgA deficiency. Immunogenetics. 1992;36:389-95 pubmed
    ..These findings suggest that the two loci found to be associated with IgA deficiency may act via a common pathway. ..
  50. Dezelee S, Bras F, Vende P, Simonet B, Nguyen X, Flamand A, et al. The BamHI fragment 9 of pseudorabies virus contains genes homologous to the UL24, UL25, UL26, and UL 26.5 genes of herpes simplex virus type 1. Virus Res. 1996;42:27-39 pubmed
    ..Due to the fact that in PrV the UL26 and UL44 genes are adjacent and their ends are conserved, the right border of the inversion must lie within their intergenic region. ..
  51. Yamamoto T, Shirakawa A, Kawaguchi M, Masuda A, Nishikawa T, Kobayashi M. Lytic infection of Epstein-Barr virus (EBV) in hemophagocytic syndrome associated with EBV-induced lymphoproliferative disorder. Ann Hematol. 2004;83:127-32 pubmed
    ..Interestingly, BHLF-positive cells were predominant in all cases. It is possible that reactivation of EBV infection may be involved in triggering the induction of cytokines and abnormal activation of histiocytes. ..
  52. Osoegawa K, de Jong P, Frengen E, Ioannou P. Construction of bacterial artificial chromosome (BAC/PAC) libraries. Curr Protoc Mol Biol. 2001;Chapter 5:Unit 5.9 pubmed publisher
    ..Finally, the isolation of BAC and PAC plasmid DNA for analyzing clones is also presented. ..
  53. Efstathiou S, Ho Y, Minson A. Cloning and molecular characterization of the murine herpesvirus 68 genome. J Gen Virol. 1990;71 ( Pt 6):1355-64 pubmed
    ..23 kb repeat unit. The organization of the MHV-68 genome is, therefore, most similar to that of the lymphotropic gamma 2 group of herpesviruses which include herpesvirus saimiri and herpesvirus ateles. ..