dna restriction enzymes

Summary

Summary: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.

Top Publications

  1. pmc REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
    Richard J Roberts
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 38:D234-6. 2010
  2. pmc Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine
    Hua Wang
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:9294-305. 2011
  3. pmc A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
    Richard J Roberts
    New England Biolabs, Beverly, MA 01915, USA
    Nucleic Acids Res 31:1805-12. 2003
  4. pmc A unique family of Mrr-like modification-dependent restriction endonucleases
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
    Nucleic Acids Res 38:5527-34. 2010
  5. pmc Structure and operation of the DNA-translocating type I DNA restriction enzymes
    Christopher K Kennaway
    Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
    Genes Dev 26:92-104. 2012
  6. pmc The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine
    Rasa Sukackaite
    Department of Protein DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, 02241 Vilnius, Lithuania
    Nucleic Acids Res 40:7552-62. 2012
  7. pmc Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities
    Agnieszka Zylicz-Stachula
    Division of Theoretical Physical Chemistry, Department of Chemistry, University of Gdansk, Poland
    BMC Mol Biol 13:13. 2012
  8. pmc A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300
    Shuang yong Xu
    New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:5597-610. 2011
  9. pmc The MspJI family of modification-dependent restriction endonucleases for epigenetic studies
    Devora Cohen-Karni
    Molecular Biology, Cell Biology, and Biochemistry Program, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 108:11040-5. 2011
  10. ncbi Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy
    Frédéric Pâques
    Cellectis SA, 102, route de Noisy, 93 340 Romainville Cedex France
    Curr Gene Ther 7:49-66. 2007

Detail Information

Publications344 found, 100 shown here

  1. pmc REBASE--a database for DNA restriction and modification: enzymes, genes and genomes
    Richard J Roberts
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 38:D234-6. 2010
    ..The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email...
  2. pmc Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine
    Hua Wang
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:9294-305. 2011
    ..Our study offers unique tools for determining more accurate hydroxymethylomes in mammalian cells...
  3. pmc A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
    Richard J Roberts
    New England Biolabs, Beverly, MA 01915, USA
    Nucleic Acids Res 31:1805-12. 2003
    ..It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes...
  4. pmc A unique family of Mrr-like modification-dependent restriction endonucleases
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
    Nucleic Acids Res 38:5527-34. 2010
    ..The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms...
  5. pmc Structure and operation of the DNA-translocating type I DNA restriction enzymes
    Christopher K Kennaway
    Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
    Genes Dev 26:92-104. 2012
    ..The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes...
  6. pmc The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine
    Rasa Sukackaite
    Department of Protein DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, 02241 Vilnius, Lithuania
    Nucleic Acids Res 40:7552-62. 2012
    ..The mechanism for 5mC recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains, despite the differences in their protein folds...
  7. pmc Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities
    Agnieszka Zylicz-Stachula
    Division of Theoretical Physical Chemistry, Department of Chemistry, University of Gdansk, Poland
    BMC Mol Biol 13:13. 2012
    ..Members include related thermophilic REases with five distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI...
  8. pmc A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300
    Shuang yong Xu
    New England Biolabs, Inc 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:5597-610. 2011
    ..aureus strain SA564, and in restricting phage λ infection when the endonuclease is expressed in E. coli...
  9. pmc The MspJI family of modification-dependent restriction endonucleases for epigenetic studies
    Devora Cohen-Karni
    Molecular Biology, Cell Biology, and Biochemistry Program, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 108:11040-5. 2011
    ..Altogether, the MspJI family of enzymes represent appealing tools of choice for method development in DNA epigenetic studies...
  10. ncbi Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy
    Frédéric Pâques
    Cellectis SA, 102, route de Noisy, 93 340 Romainville Cedex France
    Curr Gene Ther 7:49-66. 2007
    ..Finally, we will discuss the main issues that will need to be addressed in order to bring this promising technology to the patient...
  11. pmc Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5-hydroxymethylcytosine
    Aleksandra Szwagierczak
    Ludwig Maximilians University Munich, Department of Biology and Center for Integrated Protein Science Munich, 82152 Planegg Martinsried, Germany
    Nucleic Acids Res 39:5149-56. 2011
    ..We determined the consensus cleavage site of PvuRts1I as (hm)CN(11-12)/N(9-10)G and show first data on its potential to interrogate (hm)C patterns in mammalian genomes...
  12. pmc The phage-host arms race: shaping the evolution of microbes
    Adi Stern
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Bioessays 33:43-51. 2011
    ..The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits...
  13. pmc Cofactor requirement of HpyAV restriction endonuclease
    Siu Hong Chan
    Research Department, New England Biolabs, Inc, Ipswich, Massachusetts, United States of America
    PLoS ONE 5:e9071. 2010
    ..Helicobacter pylori is the etiologic agent of common gastritis and a risk factor for gastric cancer. It is also one of the richest sources of Type II restriction-modification (R-M) systems in microorganisms...
  14. pmc Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases
    Janine G Borgaro
    New England Biolabs Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 41:4198-206. 2013
    ..Lastly, we envision that the unique properties of select PvuRts1I homologues will permit their use as an additive or alternative tool to map the hydroxymethylome...
  15. pmc Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases
    P Lucas
    Centre de Recherche sur la Fonction, , , , , , Canada
    Nucleic Acids Res 29:960-9. 2001
    ..The high sequence variability we observed in the DNA-binding site of homologous LAGLIDADG endonucleases provides insight into how these proteins evolve new DNA specificity...
  16. pmc Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases
    Eri Fukuda
    Laboratory of Social Genome Sciences, Department of Medical Genome Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Genome Biol 9:R163. 2008
    ..A methyl-specific deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated DNAs. Here we examined whether McrBC competes with genome methylation systems through host killing by chromosome cleavage...
  17. pmc The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases
    Hua Wei
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 36:e50. 2008
    ..The FI provides a practical guideline for the use of restriction endonucleases and defines a fundamental property by which restriction endonucleases can be characterized...
  18. pmc Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins
    Hui Li
    Department of Pathology, University of Washington, Box 357705, Seattle, WA 98195, USA
    Nucleic Acids Res 37:1650-62. 2009
    ....
  19. pmc Escherichia coli K-12 restricts DNA containing 5-methylcytosine
    E A Raleigh
    Proc Natl Acad Sci U S A 83:9070-4. 1986
    ..Mcr restriction may seriously interfere with molecular cloning of 5-methylcytosine-containing foreign DNAs. The Mcr phenotypes of some commonly used strains of E. coli K-12 are reported...
  20. ncbi The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide
    A Piekarowicz
    Institute of Microbiology, University of Warsaw, Nowy Swiat 67, Warsaw, 00 046, Poland
    J Mol Biol 293:1055-65. 1999
    ..The MTase activity modified symmetrically located adenine residues on both strands within the recognition sequence yielding N6-methyl adenine. Furthermore, the MTase was active as a dimer...
  21. pmc Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds
    Sylvestre Grizot
    Cellectis SA, 102 Avenue Gaston Roussel, 93235 Romainville Cedex, France
    Nucleic Acids Res 38:2006-18. 2010
    ..The DmoCre based meganucleases can therefore offer new possibilities for various genome engineering applications...
  22. pmc Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA
    Guang Liu
    Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
    PLoS Genet 6:e1001253. 2010
    ..This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA...
  23. pmc Context-dependent conservation of DNA methyltransferases in bacteria
    Aswin Sai Narain Seshasayee
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India
    Nucleic Acids Res 40:7066-73. 2012
    ..Despite their sporadic occurrence, conserved R-M systems are present in strength in two highly transformable genera, in which they may contribute to selection against integration of foreign DNA...
  24. pmc Exploring the DNA mimicry of the Ocr protein of phage T7
    Gareth A Roberts
    EaStCHEM School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh, EH9 3JZ, UK
    Nucleic Acids Res 40:8129-43. 2012
    ....
  25. pmc The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their recognition sites
    Eva Sisáková
    DNA Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
    Nucleic Acids Res 41:1071-80. 2013
    ..In their favoured in vitro buffer, both LlaGI and LlaBIII produce a normal distribution of random cleavage loci centred midway between the sites. In contrast, LlaGI in K(+) ions produces a far more distributive cleavage profile...
  26. pmc The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops
    Rachel M Smith
    DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
    Nucleic Acids Res 37:7219-30. 2009
    ..LlaGI is therefore an example of a polypeptide that is a completely self-contained, multi-functional molecular machine...
  27. pmc An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI
    Rachel M Smith
    DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
    Nucleic Acids Res 37:7231-8. 2009
    ..Cleavage by LlaGI is not targeted to methylated DNA, suggesting that the conserved motifs in the Mrr domain are a conventional sub-family of the PD-(D/E)XK superfamily of DNA nucleases...
  28. ncbi Generation of highly site-specific DNA double-strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI
    R J Monnat
    Department of Pathology, University of Washington, Seattle, Washington 98195, USA
    Biochem Biophys Res Commun 255:88-93. 1999
    ..I-PpoI and I-CreI should be useful for analyzing DNA double-strand break repair in human cells and rDNA...
  29. pmc Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI
    Shuang yong Xu
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 35:4608-18. 2007
    ..Top-strand specific nicking variants, Nt.BsrDI and Nt.BtsI, were successfully engineered by combining the catalytic-deficient B subunit with wild-type A subunit...
  30. ncbi Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency
    Agnieszka Zylicz-Stachula
    Division of Theoretical Physical Chemistry, Department of Chemistry, University of Gdansk, Poland
    Biotechniques 50:397-406. 2011
    ..8 bp, corresponding to a putative 3-bp long recognition site. Thus, the combination of sinefungin and TspGWI represents a novel frequent cutter, next only to CviJI/CviJI*, that should prove useful in DNA cloning methodologies...
  31. pmc Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003
    Mary O'Connell Motherway
    Alimentary Pharmabiotic Centre, Department of Microbiology and Department of Food and Nutritional Sciences, National University of Ireland, Cork, Western Road, Cork, Ireland
    Microb Biotechnol 2:321-32. 2009
    ..breve UCC2003 we successfully increased the transformation efficiency to a level that allows the reliable generation of mutants by homologous recombination using a non-replicative plasmid...
  32. ncbi Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles
    J M Bujnicki
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Warsaw, Poland
    J Mol Microbiol Biotechnol 3:69-72. 2001
    ..The first superfamily-wide comparative analysis, not limited to nucleases of known structure, will guide cloning and characterization of novel enzymes and planning new experiments to better understand those already studied...
  33. ncbi Upstream of the SOS response: figure out the trigger
    Abram Aertsen
    Laboratory of Food Microbiology, Department of Microbial and Molecular Systems M 2 S, Faculty of Bioscience Engineering, K U Leuven, Kasteelpark Arenberg 22, B 3001 Leuven, Belgium
    Trends Microbiol 14:421-3. 2006
    ..We suggest that these endogenous triggers have been recruited by bacteria to enable adaptation to various types of stresses...
  34. pmc Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI
    Betty W Shen
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N A3 025, Seattle, WA 98109, USA
    Structure 18:734-43. 2010
    ....
  35. pmc Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair
    Paula P Cardenas
    Department of Microbial Biotechnology, Centro Nacional de Biotecnologia, CSIC, C Darwin 3, Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
    Nucleic Acids Res 37:4157-69. 2009
    ..Our data suggest that PNPase is involved in various nucleic acid metabolic pathways, and its limited ssDNA exonuclease activity plays an important role in RecA-dependent and RecA-independent repair pathways...
  36. pmc Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering
    Umut Y Ulge
    Department of Biochemistry, Howard Hughes Medical InstituteUniversity of Washington, Box 357705, Seattle, WA 98195, USA
    Nucleic Acids Res 39:4330-9. 2011
    ..These results demonstrate the feasibility of using structure-based computational design to engineer HE variants with novel target site specificities to facilitate genome engineering...
  37. ncbi The type IIB restriction endonucleases
    Jacqueline J T Marshall
    The DNA Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
    Biochem Soc Trans 38:410-6. 2010
    ..Our current knowledge of the Type IIB systems is reviewed in the present paper...
  38. ncbi Heritable targeted mutagenesis in maize using a designed endonuclease
    Huirong Gao
    Pioneer Hi Bred International, Research Center, 7300 NW 62nd Avenue, Johnston, IA 50131 1004, USA
    Plant J 61:176-87. 2010
    ..Re-designed homing endonucleases are a useful molecular tool for introducing targeted mutations in a living organism, specifically a maize plant...
  39. pmc Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family
    J Z Dalgaard
    NCI Frederick Cancer Research and Development Center, ABL Basic Research Program, PO Box B, Building 549, Room 154, Frederick, MD 21702 1202, USA
    Nucleic Acids Res 25:4626-38. 1997
    ..However, there does appear to have been considerable exchange of endonuclease domains amongst elements of the same type. Such events are suggested to be important for the formation of elements of new specficity...
  40. pmc Methylation and expression of amplified esterase genes in the aphid Myzus persicae (Sulzer)
    L M Field
    IACR Rothamsted, Harpenden, Herts AL5 2JQ, U K
    Biochem J 349:863-8. 2000
    ....
  41. ncbi Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA
    Colm Nestor
    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, Scotland
    Biotechniques 48:317-9. 2010
    ..Potential differential enrichment of 5mC and hmC DNA sequences may be facilitated using a 5mC monoclonal antibody...
  42. pmc Site-specific DNA transesterification catalyzed by a restriction enzyme
    Giedrius Sasnauskas
    Institute of Biotechnology, Graiciuno 8, Vilnius, LT 02241, Lithuania
    Proc Natl Acad Sci U S A 104:2115-20. 2007
    ..We propose that BfiI first makes a covalent enzyme-DNA intermediate, and then it resolves it by a nucleophilic attack of water or an alcohol, to yield hydrolysis or transesterification products, respectively...
  43. pmc Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family
    Agnieszka Zylicz-Stachula
    Division of Environmental Molecular Biotechnology, Department of Chemistry, University of Gdansk, Sobieskiego 18, Gdansk 80 952, Poland
    BMC Mol Biol 10:52. 2009
    ..enzyme family, which belongs to type II restriction endonucleases (REases), however, it features also some characteristics of types I and III. Members include related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II...
  44. ncbi The GTP-dependent restriction enzyme McrBC from Escherichia coli forms high-molecular mass complexes with DNA and produces a cleavage pattern with a characteristic 10-base pair repeat
    Uwe Pieper
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Biochemistry 41:5245-54. 2002
    ....
  45. ncbi Mrr instigates the SOS response after high pressure stress in Escherichia coli
    Abram Aertsen
    Laboratory of Food Microbiology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, B 3001 Heverlee, Leuven, Belgium
    Mol Microbiol 58:1381-91. 2005
    ..These results provide evidence for a specific pathway that transmits the perception of HP stress to induction of the SOS response and support a role for Mrr in bacterial stress physiology...
  46. ncbi Mechanism of activation of a human oncogene
    C J Tabin
    Nature 300:143-9. 1982
    ..Experiments are presented that localize the genetic lesion that led to activation of the oncogene. The lesion has no affect on levels of expression of the oncogene. Instead, it affects the structure of the oncogene-encoded protein...
  47. pmc Cleavage of a model DNA replication fork by a methyl-specific endonuclease
    Ken Ishikawa
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Shirokanedai, Tokyo 108 8639, Japan
    Nucleic Acids Res 39:5489-98. 2011
    ..This process might serve to maintain an epigenetic status along the genome through programmed cell death...
  48. pmc Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes
    F V Fuller-Pace
    Proc Natl Acad Sci U S A 83:9368-72. 1986
    ..Furthermore, the trinucleotide components of the recognition sequences of S. typhimurium and Escherichia coli K-12 are identical, and the 5' segments of their hsdS genes are strikingly homologous rather than variable...
  49. pmc Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target
    Dalin Rifat
    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201 1503, USA
    J Mol Biol 375:720-34. 2008
    ....
  50. pmc Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments
    Mindaugas Laganeckas
    Institute of Biotechnology, Graiciuno 8, LT 02241 Vilnius, Lithuania
    Nucleic Acids Res 39:1187-96. 2011
    ..We also implemented the method as a freely accessible web server at http://www.ibt.lt/bioinformatics/software/pdexk/...
  51. pmc Assessment of the optimization of affinity and specificity at protein-DNA interfaces
    Justin Ashworth
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Nucleic Acids Res 37:e73. 2009
    ..The approach provides a complement to traditional methods of mutational analysis, and should be useful for rapidly formulating hypotheses about the roles of amino acid residues in protein-DNA interfaces...
  52. ncbi Genetic basis of the complementary DpnI and DpnII restriction systems of S. pneumoniae: an intercellular cassette mechanism
    S A Lacks
    Cell 46:993-1000. 1986
    ..Thus, the complementary restriction systems are found on nonhomologous and mutually exclusive cassettes that can be inserted into a particular point in the chromosome of S. pneumoniae on the basis of neighboring homology...
  53. pmc Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins
    Paula P Cardenas
    Centro Nacional de Biotecnologia CSIC, Darwin 3, 28049 Madrid, Spain
    Nucleic Acids Res 39:9250-61. 2011
    ..subtilis PNPase might also contribute to repair via NHEJ...
  54. pmc MSRE-PCR for analysis of gene-specific DNA methylation
    Anatoliy A Melnikov
    Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University Chicago, IL 60611, USA
    Nucleic Acids Res 33:e93. 2005
    ..For selected genes results of MSRE-PCR were confirmed by methylation-specific PCR and bisulfite sequencing. The assay can be configured for any number of desired targets in any user-defined set of genes...
  55. pmc How restriction enzymes became the workhorses of molecular biology
    Richard J Roberts
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Proc Natl Acad Sci U S A 102:5905-8. 2005
    ..This pioneering study set the stage for the modern practice of molecular biology in which restriction enzymes are ubiquitous tools, although they are often taken for granted...
  56. ncbi Restriction and modification systems of Neisseria gonorrhoeae
    D C Stein
    University of Maryland, Department of Microbiology, College Park 20742, USA
    Gene 157:19-22. 1995
    ..One of these is a cytosine MTase (NgoVIIIC) and the other is an adenine MTase (NgoVIIIA). Although most of our clones encodes both the ENase and the MTase, none of the six R-M systems are genetically linked on the chromosome...
  57. ncbi Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases
    Pilar Redondo
    Macromolecular Crystallography Group, Spanish National Cancer Research Centre CNIO, c Melchor Fdez Almagro 3, 28029 Madrid, Spain
    Nature 456:107-11. 2008
    ....
  58. ncbi A nucleotide insertion between two adjacent methyltransferases in Helicobacter pylori results in a bifunctional DNA methyltransferase
    Ritesh Kumar
    Department of Biochemistry, Indian Institute of Science, Bangalore, India
    Biochem J 433:487-95. 2011
    ..pylori to evolve genes with unique functions and thus generate variability. For organisms such as H. pylori, which have a small genome, these adaptations could be important for their survival in the hostile host environment...
  59. pmc Organ-specific shifts in mtDNA heteroplasmy following systemic delivery of a mitochondria-targeted restriction endonuclease
    S R Bacman
    Department of Neurology, University of Miami School of Medicine, Miami, FL 33136, USA
    Gene Ther 17:713-20. 2010
    ..These results show the potential of systemic delivery of viral vectors to specific organs for the therapeutic application of mitochondria-targeted restriction enzymes in mtDNA disorders...
  60. pmc The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs
    Robert K Neely
    School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
    BMC Mol Biol 9:48. 2008
    ..Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC...
  61. ncbi The ability of the plasmid-encoded restriction and modification system LlaBIII to protect Lactococcus lactis against bacteriophages
    J Kong
    State Key Laboratory of Microbial Technology, Shandong University Shanda Southern Road 27, Jinan 250100, P R China
    Lett Appl Microbiol 34:249-53. 2002
    ..To investigate the potential of the plasmid-encoded restriction and modification (R/M) system LlaBIII to protect Lactococcua lactis against bacteriophages during milk fermentations...
  62. ncbi Mechanism of DNA recognition by the restriction enzyme EcoRV
    Mai Zahran
    Computational Molecular Biophysics, IWR, University of Heidelberg, 69120 Heidelberg, Germany
    J Mol Biol 401:415-32. 2010
    ..In the third step, the flexibility of the center base pair is probed, and in the case of the full cognate sequence the DNA bends, the complex strengthens and the protein and DNA interact more closely, allowing cleavage...
  63. pmc Transcription regulation of restriction-modification system Esp1396I
    Ekaterina Bogdanova
    Waksman Institute for Microbiology, Department of Biochemistry and Molecular Biology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
    Nucleic Acids Res 37:3354-66. 2009
    ..Instead, symmetry-related elements outside of these repeats appear to be critical for the interaction and are discussed in terms of the recent crystal structure of C.Esp139I bound to the CR promoter...
  64. pmc Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA
    Penghua Zhang
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Protein Expr Purif 69:226-34. 2010
    ..Restriction mapping and run-off DNA sequencing of digested products from the partially purified enzyme indicated that it is an EarI isoschizomer with 6-bp recognition, which we named CatHI (CTCTTC N1/N4)...
  65. ncbi The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers
    J Vieira
    Gene 19:259-68. 1982
    ..The terminal sequences of any DNA cloned in these plasmids can be characterized using the universal M13 primers...
  66. ncbi Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases
    J M Bujnicki
    Mol Microbiol 37:1280-1. 2000
  67. ncbi Activation of the Salmonella typhimurium Mrr protein
    Abram Aertsen
    Laboratory of Food Microbiology, Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems M 2 S, Faculty of Bioscience Engineering, K U Leuven, Kasteelpark Arenberg 22, B 3001 Leuven, Belgium
    Biochem Biophys Res Commun 367:435-9. 2008
    ..Typhimurium mutant could be isolated that displayed an increased basal SOS induction because of a point mutation in the chromosomal mrr gene. Based on these findings the physiological role of Mrr in the cell is discussed...
  68. pmc Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives
    Marion H Sibley
    New England Biolabs, Beverly, MA 01915, USA
    Nucleic Acids Res 32:522-34. 2004
    ..The patterns observed are consistent with the action of a site-specific recombinase. Since no nearby gene codes for a likely recombinase of known families, such a recombinase must be of a new family or unlinked...
  69. ncbi Proteins encoded by the DpnI restriction gene cassette. Hyperproduction and characterization of the DpnI endonuclease
    A G de la Campa
    Biology Department, Brookhaven National Laboratory, Upton, New York 11973
    J Biol Chem 263:14696-702. 1988
    ..It is suggested that this structure provides the specificity for recognition of the methylated DNA sequence, 5'-GmATC-3', that is cleaved by the DpnI endonuclease...
  70. pmc Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases
    J M Clark
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
    Nucleic Acids Res 16:9677-86. 1988
    ..These results demonstrate that template instruction is not an absolute requirement for the catalysis of nucleotidyl transfer reactions by DNA polymerases...
  71. ncbi Comparison of different decontamination methods for reagents to detect low concentrations of bacterial 16S DNA by real-time-PCR
    Sven Klaschik
    Klinik und Poliklinik fur Anasthesiologie und spezielle Intensivmedizin, Universitat Bonn, Sigmund Freud Strasse 25, D 53105 Bonn, Germany
    Mol Biotechnol 22:231-42. 2002
    ..However, decontamination with DNAse may help, together with the use of highly purified PCR reagents, in detecting small amounts of bacterial DNA in clinical specimens...
  72. ncbi A mutational analysis of the PD...D/EXK motif suggests that McrC harbors the catalytic center for DNA cleavage by the GTP-dependent restriction enzyme McrBC from Escherichia coli
    Uwe Pieper
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Biochemistry 41:5236-44. 2002
    ..Thus, whereas McrC variants defective in DNA cleavage can stimulate the GTPase activity of McrB, the DNase activity of McrC is not supported by McrB variants defective in GTP hydrolysis...
  73. pmc Spontaneous access to DNA target sites in folded chromatin fibers
    Michael G Poirier
    Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208 3500, USA
    J Mol Biol 379:772-86. 2008
    ..Thus, nucleosome positioning dramatically influences the accessibility of target sites located inside nucleosomes, while chromatin folding dramatically regulates access to target sites in linker DNA...
  74. pmc Characterization of the genes coding for the Eco RV restriction and modification system of Escherichia coli
    L Bougueleret
    Nucleic Acids Res 12:3659-76. 1984
    ..Possible mechanisms of regulation of the endonuclease gene expression at the translational level are proposed and discussed...
  75. ncbi Shaping the genome--restriction-modification systems as mobile genetic elements
    I Kobayashi
    Institute of Medical Science, University of Tokyo, Shirokanedai, 108 8639, Japan
    Curr Opin Genet Dev 9:649-56. 1999
    ..A comparison of bacterial genomes supports the hypothesis that restriction-modification gene complexes are mobile elements involved in various genome rearrangements and evolution...
  76. pmc Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease
    Sylvestre Grizot
    Cellectis SA, 102 Avenue Gaston Roussel, 93235 Romainville, France
    Nucleic Acids Res 39:6124-36. 2011
    ..Furthermore, the present work describes a sequential method to engineer tailored HEs, wherein three contiguous regions are individually mutated and assembled to create HEs with engineered specificity...
  77. ncbi Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?
    Svetlana Makovets
    Institute of Cell and Molecular Biology, Darwin Building, University of Edinburgh, King s Buildings, Edinburgh EH9 3JR, UK
    Mol Microbiol 51:135-47. 2004
    ..In the absence of efficient restriction alleviation, a Type I restriction enzyme cleaves host DNA and, under these conditions, homologous recombination maintains the integrity of the bacterial chromosome...
  78. pmc Novel non-specific DNA adenine methyltransferases
    Marek Drozdz
    Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02 096 Warsaw, Poland
    Nucleic Acids Res 40:2119-30. 2012
    ..Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine methylation...
  79. ncbi Restriction endonucleases: classification, properties, and applications
    Raymond J Williams
    Protein Purification Dept, Promega Corp, Madison, WI 53711 5399, USA
    Mol Biotechnol 23:225-43. 2003
    ..An understanding of the enzymes and their properties can improve their productive application by maintaining critical digest parameters and enhancing or avoiding alternative activities...
  80. pmc Evidence for an evolutionary antagonism between Mrr and Type III modification systems
    Mehari Tesfazgi Mebrhatu
    Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre, Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, B 3001 Leuven, Belgium
    Nucleic Acids Res 39:5991-6001. 2011
    ..This apparent evolutionary antagonism is further discussed in the light of a possible role for Mrr as defense mechanism against the establishment of epigenetic regulation by foreign DNA methyltransferases...
  81. pmc Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems
    Ken Ishikawa
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, Japan
    DNA Res 17:325-42. 2010
    ..These restriction systems clearly demonstrate the presence of conflicts between epigenetic systems...
  82. pmc NEBcutter: A program to cleave DNA with restriction enzymes
    Tamas Vincze
    New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
    Nucleic Acids Res 31:3688-91. 2003
    ..Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini...
  83. ncbi Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I
    J M Hadden
    Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
    Nat Struct Biol 8:62-7. 2001
    ..T7 endonuclease I therefore represents the first crystal structure of a junction resolving enzyme that is a member of the nuclease superfamily of enzymes...
  84. ncbi RecN and RecG are required for Escherichia coli survival of Bleomycin-induced damage
    Jessica L Kosa
    Biological Engineering Division, Department of Chemistry, Massachusetts Institute of Technology, Rm 56 689, 77 Massachusetts Avenue, Cambridge 02139, USA
    Mutat Res 554:149-57. 2004
    ..The most straightforward explanation of these results is that DSB repair involves a structure that serves as a good substrate for RecG, and not RuvAB...
  85. pmc Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease
    Sylvestre Grizot
    Cellectis SA, Cellectis Genome Surgery, 93235 Romainville, France
    Nucleic Acids Res 37:5405-19. 2009
    ..These properties rank this new generation of endonucleases among the best molecular scissors available for genome surgery strategies, potentially avoiding the deleterious effects of previous gene therapy approaches...
  86. pmc Early interrogation and recognition of DNA sequence by indirect readout
    Elizabeth J Little
    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
    Structure 16:1828-37. 2008
    ....
  87. ncbi Reassortment of DNA recognition domains and the evolution of new specificities
    A A Gann
    Department of Molecular Biology, University of Edinburgh, UK
    Mol Microbiol 1:13-22. 1987
    ..We discuss the correlation of the variation in polypeptide sequence with recognition specificities...
  88. pmc The genome of the stick insect Medauroidea extradentata is strongly methylated within genes and repetitive DNA
    Veiko Krauss
    Department of Genetics, Institute of Biology II, University of Leipzig, Leipzig, Germany
    PLoS ONE 4:e7223. 2009
    ..However, some data concerning the distribution of methylcytosine in insect species appear to contradict such roles...
  89. ncbi Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI
    Brett Chevalier
    Division of Basic Sciences, Graduate Program in Molecular and Cellular Biology, University of Washington and the Fred Hutchinson Cancer Research Center, Seattle 98109, USA
    J Mol Biol 329:253-69. 2003
    ....
  90. pmc Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I
    Lei Zhao
    Graduate Program in Molecular Biophysics, Structure and Design, University of Washington, Seattle, WA 98195, USA
    J Mol Biol 385:1498-510. 2009
    ....
  91. pmc The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage
    Jesus Prieto
    Spanish National Cancer Center CNIO, Structural Biology and Biocomputing Programme, NMR Group and Macromolecular Crystallography Group, c Melchor Fdez Almagro 3, 28029 Madrid, Spain
    Nucleic Acids Res 35:3262-71. 2007
    ....
  92. ncbi Target recognition by EcoKI: the recognition domain is robust and restriction-deficiency commonly results from the proteolytic control of enzyme activity
    M O'NEILL
    Institute of Cell and Molecular Biology, University of Edinburgh, Darwin Building, Mayfield Road, King s Buildings, Edinburgh, EH9 3JR, UK
    J Mol Biol 307:951-63. 2001
    ..The significance of four of the six residues (G91, G105, F107 and G141) is enhanced by the finding that even conservative substitutions for these residues impair modification, thereby conferring an r(-)m(-) phenotype...
  93. pmc Tracking EcoKI and DNA fifty years on: a golden story full of surprises
    Wil A M Loenen
    Department of Medical Microbiology, University Maastricht, Maastricht, The Netherlands
    Nucleic Acids Res 31:7059-69. 2003
    ....
  94. pmc Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking
    Jiabing Ji
    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
    PLoS ONE 5:e10577. 2010
    ..These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner...
  95. ncbi [Testing and isolation of high-purity restriction endonucleases]
    L I Puchkova
    Vector State Research Center for Virology and Biotechnology, Kol tsovo, Novosibirsk Oblast, 630559 Russia
    Prikl Biokhim Mikrobiol 38:20-4. 2002
    ..It was shown that high-temperature treatment can be applied not only to thermophilic but also to mesophilic strains of microorganisms of different taxa...
  96. pmc The tetracycline resistance determinants of RP1 and Tn1721: nucleotide sequence analysis
    S H Waters
    Nucleic Acids Res 11:6089-105. 1983
    ..We conclude that a single tetA gene mediates resistance in each of these tet determinants...
  97. pmc Methylation-dependent DNA restriction in Bacillus anthracis
    Ramakrishnan Sitaraman
    Laboratory of Bacterial Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Gene 494:44-50. 2012
    ..anthracis remain unidentified, and we suggest that poor transformation by such DNA could in part be a consequence of the inefficient replication of hemimethylated DNA in B. anthracis...
  98. pmc Nucleotide sequence of the gene (ard) encoding the antirestriction protein of plasmid colIb-P9
    E P Delver
    Department of Biotechnology, USSR Cardiology Research Center, Moscow
    J Bacteriol 173:5887-92. 1991
    ..We suggest that the biological role of the ColIb Ard protein is associated with overcoming host-controlled restriction during bacterial conjugation...
  99. ncbi Chemical-reaction-based site-selective DNA cutter for PCR-free gene manipulation
    Yoji Yamamoto
    Research Center for Advanced Science and Technology, University of Tokyo, 4 6 1 Komaba, Meguro ku, Tokyo, 153 8904, Japan
    Chembiochem 7:673-7. 2006
    ..Apparently, the DNA was kept completely intact during the manipulation. The man-made tool ARCUT has promising features for future biotechnology and molecular biology...
  100. pmc The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro
    Dimitra Serfiotis-Mitsa
    EaStCHEM School of Chemistry, University of Edinburgh, The King s Buildings, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 38:1723-37. 2010
    ..We also present the structure determined by NMR spectroscopy of the pBP136 KlcA protein. The structure shows a novel protein fold and it is clearly not a DNA structural mimic...
  101. ncbi Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP
    U Pieper
    Institut für Biochemie FB 15, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, Giessen, D 35392, Germany
    J Mol Biol 272:190-9. 1997
    ..v) Substitution of N339 and N376 with alanine allowed us to identify NTAD (339 to 342) rather than NKKA (376 to 379) as the equivalent of the third consensus sequence motif characteristic for guanine nucleotide binding proteins, NKXD...

Research Grants63

  1. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  2. Nontoxigenic Clostridium difficile as an Oral Vaccine for C. difficile Infection
    DALE NICHOLAS GERDING; Fiscal Year: 2013
    ..abstract_text> ..
  3. DNA-Binding Protein Discovery by the Combinatorial Method REPSA
    Michael van Dyke; Fiscal Year: 2013
    ..We expect our research to ultimately catalyze numerous studies by us and other laboratories leading to a better understanding of E. coli biology at a molecular level and provide a framework for similar studies in other organisms. ..
  4. PHAGE T4 HEAD ASSEMBLY AND INITIATION OF INFECTION
    Lindsay W Black; Fiscal Year: 2013
    ..Finally, understanding viral packaging has an important bearing on the mechanism of closely related enzymes of importance to fundamental DNA processes, e.g. helicases and NTP driven DNA translocating restriction endonucleases. ..
  5. Mitochondrial DNA Damage: Cellular Responses, Aging and Disease
    Christi A Walter; Fiscal Year: 2013
    ..The proposed studies are intended to address the goal of defining effects specifically emanating from mitochondrial DNA damage. ..
  6. DNA targeting by TAL effectors
    Daniel F Voytas; Fiscal Year: 2013
    ..These experiments will be conducted in both Arabidopsis and human cells to determine breadth of applicability and to take advantage of the strengths of each model to assess off-target effects. ..
  7. Mitochondrial Dysfunction in Neurodegeneration and Compensatory Approaches
    CARLOS TORRES MORAES; Fiscal Year: 2013
    ..We are confident that the accomplishment of these two aims will lead to not only a better understanding of the role of mitochondrial defects in age-related neurodegeneration but also to novel approaches to counteract these effects. ..
  8. A Novel Computational Package for DNA Enzyme Design
    Jingdong Tian; Fiscal Year: 2010
    ..The general goal of this research is to develop a computational tool to enable study and reengineering of DNA restriction enzymes. The package will include the following components: 1) nucleic acid recognition site perturbation tools, ..
  9. REBASE-The Restriction Enzyme Database
    Richard J Roberts; Fiscal Year: 2011
    ..It is a unique resource for the practice of biotechnology and its contents are used directly or indirectly by many sections of the research health care community. ..
  10. GENETIC AND ECOLOGIC DIFFERENTIATION OF MALARIA VECTORS
    LEON LOUNIBOS; Fiscal Year: 1991
    ..A histological technique which identifies multiple blood meals in the mosquito midgut will be used to assess the incidence of multiple feeding in nature and evaluate its significance for malaria transmission...
  11. GENETIC STUDY OF PROTEASES IN BACTEROIDES GINGIVALIS
    Jeffrey Felton; Fiscal Year: 1991
    ..g)...
  12. CONTROL OF TRANSCRIPTION OF ISOLATED EUCARYOTIC GENES
    Michael Holland; Fiscal Year: 1980
    ..The long term goal of these studies is the eventual reconstitution of selective transcription of specific eucaryotic genes from purified components...
  13. 800 MHz Spectrometer for Biomolecular NMR in Missouri
    STEVEN VAN DOREN; Fiscal Year: 2006
    ..The CdtB subunit is sufficient to cause DNA damage and to arrest the cell cycle in mammalian cells. [unreadable] [unreadable]..
  14. SKIN-REACTIVE MICROCOCCAL EXOPROTEINS--MOLECULAR BIOLOGY
    KIRK WUEPPER; Fiscal Year: 1990
    ..Utilization of the data may prove worthwhile should vaccine development be considered in this disease, which can have up to 10% mortality...
  15. MOLECULAR MECHANISMS IN SCLERODERMA--SCL-70/TOPO I
    Angeline Douvas; Fiscal Year: 1990
    ..Based on the outcome of these studies it may be possible to design more specific and effective therapies for this disorder...
  16. SUBUNIT INTERACTIONS IN DNA BINDING PROTEINS
    Catherine Royer; Fiscal Year: 1992
    ..This dynamic and thermodynamic data will add to our understanding of the physical mechanisms of the transfer of binding information from one subunit to the others in these biologically important oligomeric proteins...
  17. REPRESSORS OF HUMAN AND GLOBIN GENE EXPRESSION
    Deborah Gumucio; Fiscal Year: 2001
    ..This should provide a valuable tool for the further dissection of the regulators of hemoglobin switching. ..
  18. HOST DEFENSE FACTORS IN ORAL ECOLOGY
    JOEL RUDNEY; Fiscal Year: 1991
    ..Designs devised to address those questions should contribute greatly to understanding of the role of host defense factors as determinants of interperson differences in oral ecology...
  19. HIGH RESOLUTION PHYSICAL MAPS OF 4P AND 5Q
    JOHN WASMUTH; Fiscal Year: 1992
    ..In addition to answering specific questions about these two regions of the human genome, the approaches to be developed and used in this project should aid in mapping other portions of the genome...
  20. MOLECULAR BIOLOGY OF B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA
    Elizabeth Newcomb; Fiscal Year: 1993
    ..This study will identify the transforming activity associated with B-CLL disease. Understanding the genetic mechanism of oncogene activation in B- CLL disease may have potential for improved patient diagnosis and treatment...
  21. NEW APPROACHES TO ANALYSIS OF BIOPOLYMERS
    Alexander Varshavsky; Fiscal Year: 1990
    ..The results of the proposed studies should be of immediate utility for molecular biological studies on cancer as well as for many other fields of biochemical research...
  22. REPLICATION OF CHLOROPLAST DNA
    KRISHNA TEWARI; Fiscal Year: 1992
    ..The replication of D-loop containing plasmids in vitro will be studied using pure DNA polymerase, topoisomerase I priming enzyme, DNA binding proteins, and any as yet unidentified proteins that are needed in the replication of ctDNA...
  23. CHARACTER AND ROLE OF HMG 1,2-DNA INTERACTIONS
    WILLIAM SCOVELL; Fiscal Year: 1991
    ..Different levels of alpha-amanitin will be incorporated in the assay to distinguish whether the HMG proteins exhibit any preferential effect on transcription by RNA polymerase I, II or III...
  24. CAMPYLOBACTER PYLORI IN GASTROINTESTINAL DISEASE
    JOHN PENNER; Fiscal Year: 1990
    ..The longer term objective is to conduct epidemiological studies to trace the sources and routes of transmission of C. pyloridis and obtain convincing evidence to delineate the role of the species in diseases of the stomach and duodenum...
  25. IDENTIFY A MAJOR GENE RESPONSIBLE FOR CLEFTING
    DAVID BIXLER; Fiscal Year: 1992
    ..With the use of the cephalometric technique we can improve this value to nearly 70%. This represents a considerable improvement in identification of gene carriers and hence an increased precision in identifying the cleft genotype...
  26. PHYSICAL MAP FOR HUMAN GENOMIC REGION
    Robert Gemmill; Fiscal Year: 1990
    ..This map should provide a foundation upon which a comprehensive map of the entirety of chromosome 3 can be built...
  27. ENZYMES INVOLVED IN METHYLASE/DPNI CLEAVAGE STRATEGIES
    Michael McClelland; Fiscal Year: 1992
    ..3) Identification of 'linking clones' containing rare cleavage sites for the production of a physical map of these rare sites in the human genome...
  28. DIET CANCER AND ONCOGENE EXPRESSION IN INBRED MICE
    ELSIE WAINFAN; Fiscal Year: 1990
    ....
  29. Regulation of restriction-modification genes expression
    Konstantin Severinov; Fiscal Year: 2007
    ....
  30. Site-Specific Recognition Restriction Enzymes
    WILLIAM MACCONNELL; Fiscal Year: 2006
    ..This method will create a new class of DNA restriction enzymes that can be designed by the researcher to specifically recognize a 20 base pair or longer unique ..
  31. UTEROFERRIN GENE EXPRESSION DURING DEVELOPMENT
    ROSALIA SIMMEN; Fiscal Year: 1990
    ..The proposed work will provide a foundation for further understanding the biological significance of Uf and may clarify the mechanisms underlying maternal-fetal interactions in mammalian systems that are essential for fetal development...
  32. FUNCTION OF CPG-RICH ISLANDS IN HUMAN DNA
    ORLANDO MILLER; Fiscal Year: 1990
    ..We will determine whether these sequences have enhancer or promoter activity, their time of replication, and whether this timing is tissue specific and is related to methylation and/or nuclease sensitivity...
  33. DIFFERENTIATION OF ACTIN MYOGENESIS
    Robert Schwartz; Fiscal Year: 1991
    ..In this way, it might be possible to understand the defects in gene regulation in inherited neuromuscular diseases...
  34. FANCONI ANEMIA--HETEROGENEITY AND CARRIER DETECTION
    ARLEEN AUERBACH; Fiscal Year: 2007
    ..This will be combined with functional complementation[unreadable] in an effort to accelerate the identification of these genes.[unreadable] [unreadable]..
  35. Chromatin remodeling and MHC class II gene transcription
    JOSEPH FONTES; Fiscal Year: 2003
    ..Through these specific aims the importance and mechanistic basis of chromatin remodeling in the transcription of MHC class II genes will be determined. ..
  36. VIRAL REGULATORY MECHANISMS IN INFECTION AND LYSOGENY
    Ethel Jackson; Fiscal Year: 1980
    ..The action of major P22 regulatory genes will be defined in terms of differences in time or amount of transcription of specific groups of genes following infection by a regulatory mutant. ..
  37. BASIS FOR THE IFP PHENOTYPE OF DIABETOGENIC EMC VIRUS
    GEORGE JORDAN; Fiscal Year: 1990
    ..Using data provided by this project, it may be possible to predict the virulence of human viruses from a knowledge of genetic structure...
  38. INTERACTIONS OF ANTITUMOR AGENTS WITH NUCLEIC ACIDS
    David Graves; Fiscal Year: 1990
    ....
  39. MOLECULAR DEFECT IN PROTOPORPHYRIA
    David Brenner; Fiscal Year: 1992
    ..Further experiments will be determined by the above fundamental studies and might include DNA mediated gene transfer and cloning of ferrochelatase cDNAs derived from cultured fibroblasts from patients with protoporphyria...
  40. DIVERSITY IN H-2 HAPLOTYPES
    Larry Pease; Fiscal Year: 1990
    ..Direct DNA sequence analysis of homologous portions of MHC genes will provide estimates of spontaneous mutation and copy mediated mutation rates. Hybrid genes will be constructed and introduced into cells in culture to assess function...
  41. HYBRID ENDONUCLEASES FOR GENOMIC RESEARCH AND ANALYSIS
    Srinivasan Chandrasegaran; Fiscal Year: 2003
    ..Their long term goal is the application of chimeric nucleases to correct a genetic defect in an animal model. ..
  42. NATURAL HOST CONTROL MECHANISMS IN LEUKEMIA
    Theodore Pincus; Fiscal Year: 1980
    ..We plan to learn whether immunological tolerance to virus antigens may influence leukemia development, and whether viral immunologic suppressor or enhancing activity may exist under certain conditions...
  43. BRANCH CAPTURE REACTION IN PHYSICAL MAPPING
    James Wetmur; Fiscal Year: 1993
    ..The BCR method will be available for collaborative studies of other human chromosomes...
  44. RESTRICTION BASED ANALYSIS OF GENE EXPRESSION (RAGE)
    Hsing Jien Kung; Fiscal Year: 2001
    ..These profiles of gene expression could provide valuable diagnostic and prognostic markers for many types of common human cancers as well as useful information for drug development and evaluation. ..
  45. XCEN-XQ21.3 IN OVERLAPPING YEAST ARTIFICIAL CHROMOSOMES
    Kenneth Fischbeck; Fiscal Year: 1993
    ..The strategy of anchoring contigs at exons and HTF islands targets DNA segments that are likely to contain genes and therefore to have biological and medical importance...
  46. MOLECULAR AND BIOLOGIC ANALYSES OF HIV FROM THE BRAIN
    Cecilia Cheng Mayer; Fiscal Year: 1991
    ....
  47. PHYSICAL APPROACH TO GENETICS OF CEREBELLUM DEVELOPMENT
    J Sutcliffe; Fiscal Year: 1993
    ..6. The integrated maps will be studied with reference to the syntenic region of human chromosome 21 to identify candidates for the critical genes whose aneuploidy is responsible for Down's Syndrome...
  48. NON RAS ONCOGENES IN CHEMICALLY INDUCED RAT LIVER TUMORS
    PETER SHANK; Fiscal Year: 1990
    ..Ultimately we hope to define the role of these proto-oncogenes in both normal rat development and the development of hepatic cell carcinoma...
  49. MOLECULAR GENETICS TRAINING IN HUMAN GENETICS AND GENE S
    Dwight Stambolian; Fiscal Year: 1990
    ..Methods for comparison will include restriction fragment mapping and DNA sequencing. Understanding the evolution of the ribosomal gene will give us a panoramic view of evolution that may not be possible with any other gene...
  50. MAREK'S DISEASE VIRUS: ANALYSIS OF LATENT GENES
    Akiko Tanaka; Fiscal Year: 1991
    ..Finally, we will identify the proteins specified by those latent genes by means of generating specific antibodies to these gene products and immunoprecipitation and/or Western blot analysis by these antibodies...
  51. Validating VIL-6 as a target for KSHV-associated disease
    Scott Wong; Fiscal Year: 2005
    ..The results should help elucidate the role of the vlL-6 in virus infection and provide new insights into the future development of diagnostics and therapies for gamma-2 herpesvirus-induced malignancies. ..
  52. DISCOVERING NEW RARE CUTTING RESTRICTION ENZYMES
    Elisabeth Raleigh; Fiscal Year: 1999
    ..The proposed technique should provide an efficient strategy for discovering new restriction specificities, particularly rare-cutters. ..
  53. DNA STRUCTURE AND DYNAMICS IN BAMHI-DNA INTERACTIONS
    MARY HATCHER SKEERS; Fiscal Year: 2000
    ..3) Use high-resolution NMR to provide a structural description of the DNA dodecamer. ..
  54. DNA SYNTHESIS AND GENETIC RECOMBINATION IN BACILLUS
    ADAYAPALAM GANESAN; Fiscal Year: 1991
    ..The recently discovered restriction-modification enzymes in competent cells are to be purified and their role in recombination will be studied by a proposed new in vitro system. ..
  55. METABOLISM OF EXTRACELLULAR MATRIX IN INJURED CORNEAS
    WINSTON KAO; Fiscal Year: 1992
    ..In another series of experiments, we will characterize factors which inhibit the epithelial cell proliferation of injured rabbit corneas...
  56. DNA SEQUENCING--ITERATIVE STEPS BY PRODUCT REGENERATION
    Charles Grose; Fiscal Year: 1999
    ..The sequenced segments will be correct and of sufficient length for extensive bottom up genome sequence reconstruction. ..
  57. SEGMENTAL LABELING FOR PROTEIN STRUCTURE BY NMR
    Tom Muir; Fiscal Year: 2002
    ....
  58. Isothermal cDNA/mRNA Amplification Technology
    ROGER LASKEN; Fiscal Year: 2003
    ..abstract_text> ..
  59. Restriction Endonuclease Structure and Function
    CYNTHIA DUPUREUR; Fiscal Year: 2005
    ....
  60. MOLECULAR VIROLOGICAL STUDIES OF AIDS CNS DISORDERS
    Irvin Chen; Fiscal Year: 1992
    ..In addition, we will extend such analyses to other isolates of AIDS virus made from other individuals...
  61. MESSENGER RNA CONTROL IN DIFFERENTIATING MUSCLE CELLS
    Robert Singer; Fiscal Year: 1980
    ..Concurrently, the actin protein organization and conformation in developing muscle cells is being investigated by electron microscopy and the isoforms of actin are being investigated by two-dimensional electrophoresis. ..
  62. FIV AS A SMALL LABORATORY ANIMAL MODEL OF HIV
    PHILIP ANDERSEN; Fiscal Year: 1991
    ..Utilization of these reagents will allow a better understanding of FIV pathogenesis in SPF cats, as well as cats infected with other feline pathogens...
  63. DEVELOPMENT OF A MONOVALENT PHAGE DISPLAY VECTOR
    Michael Weiner; Fiscal Year: 1993
    ..This system, in which DNA has an attached monovalent protein probe, can be used for construction of peptide libraries and for generation of antibody-gp3 fusions...