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Scornec H, Tichit M, Bouchier C, Pédron T, Cavin JF, Sansonetti PJ, Licandro-Seraut H. Rapid 96-well plates DNA extraction and sequencing procedures to identify genome-wide transposon insertion sites in a difficult to lyse bacterium: Lactobacillus casei. J Microbiol Methods 2014; 106:78-82. [PMID: 25135488 DOI: 10.1016/j.mimet.2014.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 11/18/2022]
Abstract
Random transposon mutagenesis followed by adequate screening methods is an unavoidable procedure to characterize genetics of bacterial adaptation to environmental changes. We have recently constructed a mutant library of Lactobacillus casei and we aimed to fully annotate it. However, we have observed that, for L. casei which is a difficult to lyse bacterium, methods used to identify the transposon insertion site in a few mutants (transposon rescue by restriction and recircularization or PCR-based methods) were not transposable for a larger number because they are too time-consuming and sometimes not reliable. Here, we describe a method for large-scale and reliable identification of transposon insertion sites in a L. casei mutant library of 9250 mutants. DNA extraction procedure based on silica membranes in 96-column format was optimized to obtain genomic DNA from a large number of mutants. Then reliable direct genomic sequencing was improved to fit the obtained genomic DNA extracts. Using this procedure, readable and identifiable sequences were obtained for 87% of the L. casei mutants. This method extends the applications of a library of this type, reduces the number of insertions needed to be screened, and allows selection of specific mutants from an arrayed and stored mutant library. This method is applicable to any already existing mutant library (obtained by transposon or insertional mutagenesis) and could be useful for other bacterial species, especially for highly lysis-resistant bacteria species such as lactic acid bacteria.
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Affiliation(s)
- Hélène Scornec
- UMR A PAM, AgroSup Dijon/Université de Bourgogne, 1 Esplanade Erasme, 21000, Dijon, France
| | - Magali Tichit
- Plate-forme Génomique, Département Génomes et Génétique, Institut Pasteur, 28 Rue du Docteur Roux, 75724, Paris cedex 15, France
| | - Christiane Bouchier
- Plate-forme Génomique, Département Génomes et Génétique, Institut Pasteur, 28 Rue du Docteur Roux, 75724, Paris cedex 15, France
| | - Thierry Pédron
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Docteur Roux, 75724, Paris cedex 15, France; Unité INSERM 786, Institut Pasteur, Paris, France
| | - Jean-François Cavin
- UMR A PAM, AgroSup Dijon/Université de Bourgogne, 1 Esplanade Erasme, 21000, Dijon, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Docteur Roux, 75724, Paris cedex 15, France; Unité INSERM 786, Institut Pasteur, Paris, France; Chaire de Microbiologie et Maladies Infectieuses, Collège de France, 11 Place Marcelin Berthelot, 75005, Paris, France.
| | - Hélène Licandro-Seraut
- UMR A PAM, AgroSup Dijon/Université de Bourgogne, 1 Esplanade Erasme, 21000, Dijon, France; Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Docteur Roux, 75724, Paris cedex 15, France
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Removing PCR for the elimination of undesired DNA fragments cycle by cycle. Sci Rep 2014; 3:2303. [PMID: 23892515 PMCID: PMC3725479 DOI: 10.1038/srep02303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/11/2013] [Indexed: 01/21/2023] Open
Abstract
A novel removing polymerase chain reaction (R-PCR) technique was developed, which can eliminate undesired genes, cycle by cycle, with efficiencies of 60.9% (cDNAs), 73.6% (genomic DNAs), and ~ 100% (four DNA fragments were tested). Major components of the R-PCR include drivers, a thermostable restriction enzyme - ApeKI, and a poly(dA) adapter with mismatched restriction enzyme recognition sites. Drivers were generated from the undesired genes. In each cycle of R-PCR, drivers anneal to complementary sequences and allow extension by Taq DNA polymerase. Thus, ApeKI restriction sites in the undesired genes are recovered, and adapters of these undesired DNA fragments are removed. Using R-PCR, we isolated maize upregulated defense-responsive genes and Blumeria graminis specialized genes, including key pathogenesis-related effectors. Our results show that after the R-PCR reaction, most undesired genes, including very abundant genes, became undetectable. The R-PCR is an easy and cost-efficient method to eliminate undesired genes and clone desired genes.
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Letsch MR, Lewis LA. Chloroplast gene arrangement variation within a closely related group of green algae (Trebouxiophyceae, Chlorophyta). Mol Phylogenet Evol 2012; 64:524-32. [PMID: 22659018 DOI: 10.1016/j.ympev.2012.05.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 02/04/2012] [Accepted: 05/14/2012] [Indexed: 11/19/2022]
Abstract
The 22 published chloroplast genomes of green algae, representing sparse taxonomic sampling of diverse lineages that span over one billion years of evolution, each possess a unique gene arrangement. In contrast, many of the >190 published embryophyte (land plant) chloroplast genomes have relatively conserved architectures. To determine the phylogenetic depth at which chloroplast gene rearrangements occur in green algae, a 1.5-4 kb segment of the chloroplast genome was compared across nine species in three closely related genera of Trebouxiophyceae (Chlorophyta). In total, four distinct gene arrangements were obtained for the three genera Elliptochloris, Hemichloris, and Coccomyxa. In Elliptochloris, three distinct chloroplast gene arrangements were detected, one of which is shared with members of its sister genus Hemichloris. Both species of Coccomyxa examined share the fourth arrangement of this genome region, one characterized by very long spacers. Next, the order of genes found in this segment of the chloroplast genome was compared across green algae and land plants. As taxonomic ranks are not equivalent among different groups of organisms, the maximum molecular divergence among taxa sharing a common gene arrangement in this genome segment was compared. Well-supported clades possessing a single gene order had similar phylogenetic depth in green algae and embryophytes. When the dominant gene order of this chloroplast segment in embryophytes was assumed to be ancestral for land plants, the maximum molecular divergence was found to be over two times greater in embryophytes than in trebouxiophyte green algae. This study greatly expands information about chloroplast genome variation in green algae, is the first to demonstrate such variation among congeneric green algae, and further illustrates the fluidity of green algal chloroplast genome architecture in comparison to that of many embryophytes.
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Affiliation(s)
- Molly R Letsch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Rd, Storrs, 06269 CT, USA.
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Maglia G, Heron AJ, Stoddart D, Japrung D, Bayley H. Analysis of single nucleic acid molecules with protein nanopores. Methods Enzymol 2010; 475:591-623. [PMID: 20627172 DOI: 10.1016/s0076-6879(10)75022-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We describe the methods used in our laboratory for the analysis of single nucleic acid molecules with protein nanopores. The technical section is preceded by a review of the variety of experiments that can be done with protein nanopores. The end goal of much of this work is single-molecule DNA sequencing, although sequencing is not discussed explicitly here. The technical section covers the equipment required for nucleic acid analysis, the preparation and storage of the necessary materials, and aspects of signal processing and data analysis.
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Affiliation(s)
- Giovanni Maglia
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
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Barnes IH, Bagnall MC, Browning DD, Thompson SA, Manning G, Newell DG. Gamma-glutamyl transpeptidase has a role in the persistent colonization of the avian gut by Campylobacter jejuni. Microb Pathog 2007; 43:198-207. [PMID: 17600669 PMCID: PMC2778803 DOI: 10.1016/j.micpath.2007.05.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2007] [Accepted: 05/15/2007] [Indexed: 01/12/2023]
Abstract
The contribution of gamma-glutamyl transpeptidase (GGT) to Campylobacter jejuni virulence and colonization of the avian gut has been investigated. The presence of the ggt gene in C. jejuni strains directly correlated with the expression of GGT activity as measured by cleavage and transfer of the gamma-glutamyl moiety. Inactivation of the monocistronic ggt gene in C. jejuni strain 81116 resulted in isogenic mutants with undetectable GGT activity; nevertheless, these mutants grew normally in vitro. However, the mutants had increased motility, a 5.4-fold higher invasion efficiency into INT407 cells in vitro and increased resistance to hydrogen peroxide stress. Moreover, the apoptosis-inducing activity of the ggt mutant was significantly lower than that of the parental strain. In vivo studies showed that, although GGT activity was not required for initial colonization of 1-day-old chicks, the enzyme was required for persistent colonization of the avian gut.
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Affiliation(s)
- If H.A. Barnes
- Veterinary Laboratories Agency (Weybridge), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Department of Biochemistry & Molecular Biology, Medical College of Georgia, 1120 15th Street, Augusta, GA 30912-2100, USA
| | - Mary C. Bagnall
- Veterinary Laboratories Agency (Weybridge), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Darren D. Browning
- Department of Biochemistry & Molecular Biology, Medical College of Georgia, 1120 15th Street, Augusta, GA 30912-2100, USA
| | - Stuart A. Thompson
- Department of Biochemistry & Molecular Biology, Medical College of Georgia, 1120 15th Street, Augusta, GA 30912-2100, USA
| | - Georgina Manning
- Veterinary Laboratories Agency (Weybridge), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Diane G. Newell
- Veterinary Laboratories Agency (Weybridge), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Corresponding author. Tel.: +44 1932357547; fax: +44 1932357268. (D.G. Newell)
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Engemann C, Elssner T, Pfeifer S, Krumbholz C, Maier T, Kleber HP. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch Microbiol 2005; 183:176-89. [PMID: 15731894 DOI: 10.1007/s00203-005-0760-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 01/20/2005] [Accepted: 01/24/2005] [Indexed: 10/25/2022]
Abstract
Enzymes involved in carnitine metabolism of Proteus sp. are encoded by the cai genes organised as the caiTABCDEF operon. The complete operon could be sequenced from the genomic DNA of Proteus sp. Amino acid sequence similarities and/or enzymatic analysis confirmed the function assigned to each protein involved in carnitine metabolism. CaiT was suggested to be an integral membrane protein responsible for the transport of betaines. The caiA gene product was shown to be a crotonobetainyl-CoA reductase catalysing the irreversible reduction of crotonobetainyl-CoA to gamma-butyrobetainyl-CoA. CaiB and CaiD were identified to be the two components of the crotonobetaine hydrating system, already described. CaiB and caiD were cloned and expressed in Escherichia coli. After purification of both proteins, their individual enzymatic functions were solved. CaiB acts as betainyl-CoA transferase specific for carnitine, crotonobetaine, gamma-butyrobetaine and its CoA derivatives. Transferase reaction proceeds, following a sequential bisubstrate mechanism. CaiD was identified to be a crotonobetainyl-CoA hydratase belonging to the crotononase superfamily. Because of amino acid sequence similarities, CaiC was suggested to be a betainyl-CoA ligase. Taken together, these results show that the metabolism of carnitine and crotonobetaine in Proteus sp. proceeds at the CoA level.
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Affiliation(s)
- Claudia Engemann
- Pharmazie und Psychologie, Fakultät für Biowissenschaften, Institut für Biochemie, Universität Leipzig, Germany
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Abstract
Trypanosomiasis is a complex zoonotic disease where human-infective and non-human-infective strains of Trypanosoma brucei interact in the same transmission cycles. Differentiating these strains is paramount to understanding disease epidemiology. Restriction fragment length polymorphism analysis of repetitive DNA has provided such a method for distinguishing human and non-human isolates. Unfortunately, this approach requires large amounts of material and a more rapid approach is required. We have developed a novel technique, mobile genetic element-PCR, for assaying for positional variation of the mobile genetic element, RIME. The trypanosome genome contains up to 400 copies of RIME. Using this approach we have observed considerable variation between strains of T. brucei. Such a technique may offer potential as a method for differentiating non-human- and human-infective trypanosomes and shows promise as a rapid sensitive tool for investigating the epidemiology of sleeping sickness.
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Affiliation(s)
- G Hide
- Centre for Molecular Epidemiology and Ecology, Division of Biological Sciences, University of Salford, M5 4WT, Salford, UK.
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Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) gene studies are now one of the most frequent activities in clinical molecular genetics laboratories. The number of requests is growing, owing to the increasingly wide range of recognized CFTR gene diseases (cystic fibrosis, congenital bilateral absence of the vas deferens, disseminated bronchiectasis, allergic bronchopulmonary aspergillosis and chronic pancreatitis), and the availability of efficient molecular tools for detecting mutations. A growing number of tests capable of simultaneously detecting several frequent CF mutations are being developed, and commercial kits are now available. The most recent kits detect nearly 90% of defective alleles in Caucasians, a rate high enough for carrier screening and for the majority of diagnostic requests. However, because of the wide variety of molecular defects documented in the CFTR gene, only a limited number of laboratories have mastered the entire panoply of necessary techniques, while other laboratories have to refer certain cases to specialized centers with complementary and/or scanning tools at their disposal. A good knowledge of CFTR diseases and their molecular mechanisms, together with expertise in the various techniques, is crucial for interpreting the results. Diagnostic strategies must take into account the indication, the patient's ethnic origin, and the time available in the framework of genetic counseling. This review presents the methods most frequently used for detecting CFTR gene mutations, and discusses the strategies most suited to the different clinical settings.
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Affiliation(s)
- E Girodon-Boulandet
- Service de Biochimie et de Génétique, INSERM U468, Hôpital Henri-Mondor, Créteil, France
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Sivagnanasundaram S, Morris AG, Gaitonde EJ, McKenna PJ, Mollon JD, Hunt DM. A cluster of single nucleotide polymorphisms in the 5'-leader of the human dopamine D3 receptor gene (DRD3) and its relationship to schizophrenia. Neurosci Lett 2000; 279:13-6. [PMID: 10670776 DOI: 10.1016/s0304-3940(99)00921-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The association between schizophrenia and the Ser9Gly variant of the dopamine D3 receptor gene (DRD3) has been the subject of numerous studies. Under meta-analysis this site, or one or more in linkage disequilibrium with it, appears to contribute a small increase to the relative risk of schizophrenia. In this study, 768 bp of the 5'-leader region of DRD3 mRNA was screened for polymorphisms to assess their contribution to the association of DRD3 with schizophrenia. A cluster of three single nucleotide polymorphisms (SNPs) was identified in tight linkage disequilibrium with each other and with the Ser9Gly polymorphism. One of the 5'-leader SNPs encodes a Lys9Glu variant within a 36 amino acid residue stretch of an upstream open reading frame (uORF). Two common haplotypes are found in the population examined; one is linked to the Ser9 coding variant and the other to the Gly9 variant. A panel of 73 schizophrenic patients and 56 matched controls recruited from the East Anglia region of the United Kingdom was screened for disease association at these sites. Since the 5'-leader and coding sites are in tight disequilibrium, the combined genotype of all 4 sites was scored for each patient. A significant association was seen between disease and the frequency distribution of these genotypes (chi2 = 13.19, d.f. = 3, P = 0.0042; Cochran method for sparse cells applied). A 20% excess of one of the heterozygous genotypes, in which the sequences differ at three of the four SNPs, including Ser9/Gly9 in the receptor and Lys9/Glu9 in the uORF, was found in the patient group. An absence of association of disease with the Ser9Gly polymorphism had previously been reported for this panel. This suggests that these SNPs and the corresponding coding changes may exert a combined or synergistic effect on susceptibility to schizophrenia.
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Affiliation(s)
- S Sivagnanasundaram
- Department of Molecular Genetics, Institute of Ophthalmology, University College London, London, UK
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Sowa MP, Coulter LJ, Tait A, Hide G. A novel gene encoding a ras-like GTP-binding protein from Trypanosoma brucei: an evolutionary ancestor of the ras and rap genes of higher eukaryotes? Gene 1999; 230:155-61. [PMID: 10216253 DOI: 10.1016/s0378-1119(99)00072-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The ras superfamily of GTP binding proteins encompasses a wide range of family members, related by conserved amino-acid motifs, and act as molecular binary switches that play key roles in cellular processes. Gene duplication and divergence has been postulated as the mechanism by which such family members have evolved their specific functions. We have cloned and sequenced a ras-like gene, tbrlp, from the primitive eukaryote Trypanosoma brucei. The gene encodes a protein of 227 amino acids and contains the six conserved subdomains that designate it as a ras/rap subfamily member. However, the presence of key diagnostic residues characteristic of both the ras and rap families of GTP confuse the familial classification of this gene. Phylogenetic analysis of the GTP binding domain places its origins at the divergence point of the ras/rap families and suggests that tbrlp is an ancestral gene to the ras/rap genes of higher eukaryotes.
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Affiliation(s)
- M P Sowa
- Wellcome Unit of Molecular Parasitology, University of Glasgow, Glasgow, UK
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Yu S, Ding H, Seah J, Wu K, Chang Y, Chang KS, Tam MF, Syu W. Characterization of a phage specific to hemorrhagic Escherichia coli O157:H7 and disclosure of variations in host outer membrane protein ompC. J Biomed Sci 1998; 5:370-82. [PMID: 9758911 DOI: 10.1007/bf02253447] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- S Yu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, ROC
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Garuti R, Lelli N, Barozzini M, Dotti MT, Federico A, Bertolini S, Calandra S. Partial deletion of the gene encoding sterol 27-hydroxylase in a subject with cerebrotendinous xanthomatosis. J Lipid Res 1996. [DOI: 10.1016/s0022-2275(20)37607-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Callan MF, Reyburn HT, Bowness P, Rowland-Jones S, Bell JI, McMichael AJ. Selection of T cell receptor variable gene-encoded amino acids on the third binding site loop: a factor influencing variable chain selection in a T cell response. Eur J Immunol 1995; 25:1529-34. [PMID: 7614978 DOI: 10.1002/eji.1830250609] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The 3' end of the T cell receptor V beta 7.1 gene contains the five nucleotides CAAGA between the broadly conserved consensus sequence of nucleotides TGC/T GCC AGC AGC (which encode cysteine, alanine, serine and serine at positions 92-95 of the beta chain) and the heptamer that signals rearrangement. These nucleotides are frequently preserved during gene rearrangement, resulting in the common presence of glutamine at position 96 and of aspartate or glutamate at position 97 of the V beta 7.1 chain CDR3 loop in peripheral blood lymphocytes. There is selection of V beta 7.1 and of the V beta 7.1 gene-encoded glutamate at position 97 of the beta chain CDR3 loop in the cytotoxic T lymphocyte response to the HLA B2705-restricted influenza A nucleoprotein epitope SRYWAIRTR. Our results indicate that selection of V beta 7.1 gene-encoded amino acid residues on CDR3 loops may be one factor driving selection of V beta 7.1 in this response.
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Affiliation(s)
- M F Callan
- Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, GB
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Hommes NG, Arp DJ, Sayavedra-Soto LA. Generation of polymerase chain reaction-specific probes for library screening using single degenerate primers. GENETIC ANALYSIS : BIOMOLECULAR ENGINEERING 1995; 12:53-6. [PMID: 7648471 DOI: 10.1016/1050-3862(95)00101-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Degenerate oligonucleotide primers were made to peptide sequences from hydroxylamine oxidoreductase (HAO) from Nitrosomonas europaea. The primers were used singly in PCR reactions to amplify portions of the gene for HAO from genomic DNA. Southern hybridizations using fragments amplified with each primer showed that they labeled the same genomic DNA fragments. The PCR-amplified fragments were successfully used to screen a gene library for clones containing the HAO gene. The method of isolating genes by PCR with single primers has general utility.
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Affiliation(s)
- N G Hommes
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis 97331-2902, USA
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