Genomes and Genes
Summary: One of the Type II site-specific deoxyribonucleases (EC 188.8.131.52). It recognizes and cleaves the sequence G/AATTC at the slash. EcoRI is from E coliRY13. Several isoschizomers have been identified. EC 3.1.21.-.
- Sidorova N, Rau D. Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: separating their roles in specific and non-specific binding. J Mol Biol. 2001;310:801-16 pubmed..The seeming lack of a dependence on viscosity suggests the rate-limiting step in dissociation of non-specifically bound protein is a discrete conformational change rather than a general diffusion of the protein away from the DNA. ..
- Bujnicki J. Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol. 2000;50:39-44 pubmed
- Cheng S, Kim R, King K, Kim S, Modrich P. Isolation of gram quantities of EcoRI restriction and modification enzymes from an overproducing strain. J Biol Chem. 1984;259:11571-5 pubmed..5 to 0.9 g of each enzyme/kg of cell paste. ..
- Sorel I, Piétrement O, Hamon L, Baconnais S, Cam E, Pastre D. The EcoRI-DNA complex as a model for investigating protein-DNA interactions by atomic force microscopy. Biochemistry. 2006;45:14675-82 pubmed..Finally, a two-step mechanism, which describes the adsorption of the EcoRI-DNA complexes on the surface, is proposed. This model could also be extended to other protein-DNA complexes. ..
- Sapienza P, Rosenberg J, Jen Jacobson L. Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease. Structure. 2007;15:1368-82 pubmed..The interactions of Thr138 with flanking bases may permit A138T, unlike wild-type enzyme, to form complexes with EcoRI(*) sites that structurally resemble the specific wild-type complex with GAATTC. ..
- Antes T, Goodart S, Huynh C, Sullivan M, Young S, Levy Wilson B. Identification and characterization of a 315-base pair enhancer, located more than 55 kilobases 5' of the apolipoprotein B gene, that confers expression in the intestine. J Biol Chem. 2000;275:26637-48 pubmed..In transgenic mouse expression studies, the 315-bp enhancer conferred intestinal expression to human apoB transgenes. ..
- Nagore L, Mitra S, Jiang D, Jiang S, Zhou Y, Loranc M, et al. Cyanogen bromide-activated coupling: DNA catalytic chromatography purification of EcoRI endonuclease. Nat Protoc. 2006;1:2909-15 pubmed..Furthermore, many of the same materials are also used for transcription factor purification. This protocol can be completed within 4-6 d. ..
- Corcoran D, Clancy D, O Mahony M, Grant K, Hyland E, Shanaghy N, et al. Comparison of Listeria monocytogenes strain types in Irish smoked salmon and other foods. Int J Hyg Environ Health. 2006;209:527-34 pubmed..All isolates were grouped into genetic lineages based on their EcoR1 ribotypes. The attendant risk to public health following consumption of these foods is discussed. ..
- Esposito F, Fiore F, Cimino F, Russo T. Isolation and structural characterization of the rat gene encoding the brain specific snRNP-associated polypeptide "N". Biochem Biophys Res Commun. 1993;195:317-26 pubmed..We isolated and characterized two of these regions. They contain sequences very similar to the cDNA, not interrupted by introns and flanked by a polyA tail at their 3'-ends; hence they are considered two different pseudogenes. ..
- Guerra M, Bernardo F, McLauchlin J. Amplified fragment length polymorphism (AFLP) analysis of Listeria monocytogenes. Syst Appl Microbiol. 2002;25:456-61 pubmed..This preliminary evaluation suggests that this AFLP method will be useful for epidemiological typing of L. monocytogenes. ..
- Wang C, Huang J, Wang J, Gu C, Wang J, Zhang B, et al. Fabrication of the nanogapped gold nanoparticles film for direct electrical detection of DNA and EcoRI endonuclease. Colloids Surf B Biointerfaces. 2009;69:99-104 pubmed publisher..The novel and simple method of fabricating the nanogapped AuNPs film by in situ seeding growth could provide a promising bioanalytical platform for studying both DNA-DNA and DNA-protein interactions. ..
- 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. ..
- Suh P, Ryu S, Moon K, Suh H, Rhee S. Inositol phospholipid-specific phospholipase C: complete cDNA and protein sequences and sequence homology to tyrosine kinase-related oncogene products. Proc Natl Acad Sci U S A. 1988;85:5419-23 pubmed..Therefore, this unexpected similarity raises the possibility that the 148-kDa phospholipase C and cytoplasmic tyrosine kinases are modulated by common cellular component(s). ..
- Hoelzle L, Adelt D, Hoelzle K, Heinritzi K, Wittenbrink M. Development of a diagnostic PCR assay based on novel DNA sequences for the detection of Mycoplasma suis (Eperythrozoon suis) in porcine blood. Vet Microbiol. 2003;93:185-96 pubmed
- Hu H, Lan R, Reeves P. Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar typhimurium reveals phage-type- specific markers and potential for microarray typing. J Clin Microbiol. 2002;40:3406-15 pubmed
- LeBlanc D, Lee L, Titmas B, Smith C, Tenover F. Nucleotide sequence analysis of tetracycline resistance gene tetO from Streptococcus mutans DL5. J Bacteriol. 1988;170:3618-26 pubmed..coli and Campylobacter jejuni from human and animal sources, but not to DNA from Tcs isolates of these two species. ..
- Lau E, Choy D, Li M, Woo J, Chung T, Sham A. The relationship between COLI A1 polymorphisms (Sp 1) and COLI A2 polymorphisms (Eco R1 and Puv II) with bone mineral density in Chinese men and women. Calcif Tissue Int. 2004;75:133-7 pubmed..05 by ANOVA). We conclude that the COLI Al Sp1 binding site is absent in Hong Kong Chinese, whereas the COLI A2 Eco R1 and Puv II genetic polymorphisms may be associated with the BMD of elderly Chinese men. ..
- 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. ..
- Huang Y, Zhao S, Liang H, Chen Z, Liu Y. Multiplex detection of endonucleases by using a multicolor gold nanobeacon. Chemistry. 2011;17:7313-9 pubmed publisher..To demonstrate this application, the inhibitory effects of certain anticancer drugs on HaeIII, EcoRI, and EcoRV activities were studied. The present protocol proved to be sensitive, reliable, and easy to carry out. ..
- Binart N, Chambraud B, Dumas B, Rowlands D, Bigogne C, Levin J, et al. The cDNA-derived amino acid sequence of chick heat shock protein Mr 90,000 (HSP 90) reveals a "DNA like" structure: potential site of interaction with steroid receptors. Biochem Biophys Res Commun. 1989;159:140-7 pubmed..We propose that this region can, in absence of hormone, interact with and cap the positively charged DNA-binding domain of steroid receptors. ..
- Crossen P, Morrison M, Colls B. Increased frequency of the S allele of the L-myc oncogene in non-Hodgkin's lymphoma. Br J Cancer. 1994;69:759-61 pubmed..57, P = 0.032). These data confirm an earlier report and suggest that the presence of the S allele is associated with susceptibility to non-Hodgkin's lymphoma. ..
- Vudriko P, Umemiya Shirafuji R, Okwee Acai J, Tayebwa D, Byaruhanga J, Jirapattharasate C, et al. Genetic mutations in sodium channel domain II and carboxylesterase genes associated with phenotypic resistance against synthetic pyrethroids by Rhipicephalus (Boophilus) decoloratus ticks in Uganda. Pestic Biochem Physiol. 2017;143:181-190 pubmed publisher..B.) decoloratus ticks from Uganda. The Eco RII based PCR-RFLP is a useful tool for rapid detection of stable SP resistant R. (B.) decoloratus ticks. ..
- Rangnekar A, Sarma T, Singh A, Deka J, Ramesh A, Chattopadhyay A. Retention of enzymatic activity of alpha-amylase in the reductive synthesis of gold nanoparticles. Langmuir. 2007;23:5700-6 pubmed
- Couble P, Chevillard M, Moine A, Ravel Chapuis P, Prudhomme J. Structural organization of the P25 gene of Bombyx mori and comparative analysis of its 5' flanking DNA with that of the fibroin gene. Nucleic Acids Res. 1985;13:1801-14 pubmed..The functional significance of these homologous regions is discussed with regard to the highly coordinated expression of these two genes. ..
- Udvardy A, Schedl P, Sander M, Hsieh T. Novel partitioning of DNA cleavage sites for Drosophila topoisomerase II. Cell. 1985;40:933-41 pubmed..In addition, most of the major topoisomerase II cleavage sites closely corresponded to naked DNA hypersensitive sites for the prokaryotic enzyme, micrococcal nuclease. ..
- 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. ..
- Otten M, Wolf P, Gaub H. Protein-DNA force assay in a microfluidic format. Lab Chip. 2013;13:4198-204 pubmed publisher..It is suited for integration with DNA micro-spotting and in vitro expression of transcription factors to form a high-throughput chip for detailed DNA-protein interaction studies. ..
- Yamamoto M, Nagao M, Hotta G, Matsumura Y, Matsushima A, Ito Y, et al. Molecular characterization of IMP-type metallo-?-lactamases among multidrug-resistant Achromobacter xylosoxidans. J Antimicrob Chemother. 2012;67:2110-3 pubmed publisher..xylosoxidans isolates. Moreover, the present findings provide evidence that A. xylosoxidans can receive IMP-type MBL genes via plasmid-mediated transfer, which contributes to their carbapenem resistance. ..
- Miao L, Cao J, Liu R, Wang Y, Zeng Y. [Cloning and sequencing of the proBA gene from the selected mutant resistant to proline analogue from Bacillus subtilis]. Yi Chuan Xue Bao. 2002;29:1111-7 pubmed..The deduced amino acid of proA gene shared a high similarity with that of Bacillus subtilis 168 (77%). ..
- Walker G, Linn C. Detection of Mycobacterium tuberculosis DNA with thermophilic strand displacement amplification and fluorescence polarization. Clin Chem. 1996;42:1604-8 pubmed..Fewer than 10 M. tuberculosis genomes can be amplified and detected with an extremely simple protocol that takes only 20 min and uses relatively simple instrumentation and reagents, all of which can be purchased off-the-shelf. ..
- Vlasak R, Unger Ullmann C, Kreil G, Frischauf A. Nucleotide sequence of cloned cDNA coding for honeybee prepromelittin. Eur J Biochem. 1983;135:123-6 pubmed..Southern blot analysis with this cloned cDNA has shown that it hybridizes with a single EcoRI fragment of honeybee DNA which contains about 3000 base pairs. ..
- Ohnishi S, Maeda S, Nishiguchi S, Arao T, Shimada K. Structure of the mouse C-reactive protein gene. Biochem Biophys Res Commun. 1988;156:814-22 pubmed..With this characterization, the isolation and sequence analyses of a set of mouse and human pentraxin genes, i.e. CRP and serum amyloid P component genes is not complete. ..
- Tamura S, Lynch K, Larner J, Fox J, Yasui A, Kikuchi K, et al. Molecular cloning of rat type 2C (IA) protein phosphatase mRNA. Proc Natl Acad Sci U S A. 1989;86:1796-800 pubmed..Rat kidney type 2C protein phosphatase is distantly related to yeast adenylate cyclase but is not related to the catalytic subunits of two other protein phosphatases (types 1 and 2A). ..
- Nahlik M, Fleming T, McIntosh M. Cluster of genes controlling synthesis and activation of 2,3-dihydroxybenzoic acid in production of enterobactin in Escherichia coli. J Bacteriol. 1987;169:4163-70 pubmed..A protein of approximately 15,000 daltons appears to be encoded by the chromosomal region adjacent to the entAC gene, but no known function in enterobactin biosynthesis or transport can yet be ascribed to this polypeptide. ..
- Moraes Junta C, Passos G. Genomic EcoRI polymorphism and cosmid sequencing reveal an insertion/deletion and a new IGLV5 allele in the human immunoglobulin lambda variable locus (22q11.2/IGLV). Immunogenetics. 2003;55:10-5 pubmed..3 revealed a new allelic variant of the IGLV5 subgroup. These data contribute to a better understanding of the contribution of the germline IGLV genes to the human genetic background and polymorphism. ..
- Kosmider B, Wells R. Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli. Nucleic Acids Res. 2006;34:5369-82 pubmed..Non-B DNA structures (slipped structures with loops, cruciforms, triplexes and tetraplexes) as well as microhomologies are postulated to participate in the recombination and/or repair processes. ..
- Clark A, Sharma V, Brenowitz S, Chu C, Sandler S, Satin L, et al. Genetic and molecular analyses of the C-terminal region of the recE gene from the Rac prophage of Escherichia coli K-12 reveal the recT gene. J Bacteriol. 1993;175:7673-82 pubmed..5-kb portion of the b2 region of lambda. This suggests interesting speculations concerning the evolutionary relationship of lambda and Rac prophages. ..
- Ikeda S, Ozaki K. Action of mitochondrial endonuclease G on DNA damaged by L-ascorbic acid, peplomycin, and cis-diamminedichloroplatinum (II). Biochem Biophys Res Commun. 1997;235:291-4 pubmed..These nucleolytic properties of Endo G in vitro suggest its possible involvement in the maintenance of mtDNA by eliminating defective genomes from the multicopy pool. ..
- Knorr C, Cheng H, Dodgson J. DNA cloning and sequence analysis of chicken AFLP. Anim Genet. 2001;32:156-9 pubmed..Flanking regions of selected AFLP fragments were isolated using Vectorette cloning. The results obtained suggest that the these chicken AFLP most commonly arise from sequence polymorphism at or near the TaqI site. ..
- Huang L, Ripps M, Korman S, Deckelbaum R, Breslow J. Hypobetalipoproteinemia due to an apolipoprotein B gene exon 21 deletion derived by Alu-Alu recombination. J Biol Chem. 1989;264:11394-400 pubmed..We postulate that the deletion of exon 21 is the consequence of a crossover event between the Alu sequences in introns 20 and 21 resulting in nonreciprocal exchange between two chromosomes. ..
- Tsitko I, Rahkila R, Priha O, Ali Vehmas T, Terefework Z, Soini H, et al. Isolation and automated ribotyping of Mycobacterium lentiflavum from drinking water distribution system and clinical specimens. FEMS Microbiol Lett. 2006;256:236-43 pubmed..The drinking water distribution system may, thus, be a source of nontuberculous mycobacteria resistant to multiple drugs. ..
- Matsuo Y, Ijiro K, Shimomura M. Stretching of single DNA molecules complexed with restriction endonuclease by Langmuir-Blodgett method. Colloids Surf B Biointerfaces. 2005;40:123-6 pubmed..A specific sequence of DNA recognized by EcoRI was detected as spatial positions of the stretched DNA molecules. ..
- Tsuchiya Y, Hattori M, Hayashida K, Ishibashi H, Okubo H, Sakaki Y. Sequence analysis of the putative regulatory region of rat alpha 2-macroglobulin gene. Gene. 1987;57:73-80 pubmed..Particularly, a sequence (T/A)T(C/G)TGGGA(A/T) was found about at 170 bp upstream from a putative capping site, which was also found in the 5'flanking region of various acute-phase reactant genes. ..
- Willing M, Cohn D, Byers P. Frameshift mutation near the 3' end of the COL1A1 gene of type I collagen predicts an elongated Pro alpha 1(I) chain and results in osteogenesis imperfecta type I. J Clin Invest. 1990;85:282-90 pubmed
- Lee Y, Lee H, Yim J, Hwang D. The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P. Nucleic Acids Res. 1997;25:3486-9 pubmed..Two dimers of IciA protein, rather than one dimer, on the IciA I site appeared to enhance the binding of RNA polymerase to the promoter 1P, resulting in the activation of transcription from the promoter 1P. ..
- Barney M, Volgyi A, Navarro A, Ryder D. Riboprinting and 16S rRNA gene sequencing for identification of brewery Pediococcus isolates. Appl Environ Microbiol. 2001;67:553-60 pubmed..Although 16S rRNA gene sequencing correctly identified the genus and species of the test Pediococcus isolates, riboprinting proved to be a better method for subspecies differentiation. ..
- Schallenberg J, Moes M, Truss M, Reiser W, Thomm M, Stetter K, et al. Cloning and physical mapping of RNA polymerase genes from Methanobacterium thermoautotrophicum and comparison of homologies and gene orders with those of RNA polymerase genes from other methanogenic archaebacteria. J Bacteriol. 1988;170:2247-53 pubmed
- Suwa Y, Mizukami Y, Sogawa K, Fujii Kuriyama Y. Gene structure of a major form of phenobarbital-inducible cytochrome P-450 in rat liver. J Biol Chem. 1985;260:7980-4 pubmed
- Nawrot B, Sobczak M, Wojcik M, Janicka M, Nowak M, Cypryk M, et al. A novel class of DNA analogs bearing 5'-C-phosphonothymidine units: synthesis and physicochemical and biochemical properties. Oligonucleotides. 2006;16:68-82 pubmed..s)t). ..
- Dijkwel P, Mesner L, Levenson V, D ANNA J, Hamlin J. Dispersive initiation of replication in the Chinese hamster rhodopsin locus. Exp Cell Res. 2000;256:150-7 pubmed..Thus, the DHFR and rhodopsin origins belong to a class of complex, polydisperse origins that appears to be unique to higher eukaryotic cells. ..