genetic templates

Summary

Summary: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.

Top Publications

  1. pmc Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification
    F B Dean
    Molecular Staging, Inc, New Haven, Connecticut 06511, USA
    Genome Res 11:1095-9. 2001
  2. ncbi DNA primases
    D N Frick
    Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
    Annu Rev Biochem 70:39-80. 2001
  3. pmc Overexpression of human DNA polymerase mu (Pol mu) in a Burkitt's lymphoma cell line affects the somatic hypermutation rate
    Jose F Ruiz
    Centro de Biologia Molecular Severo Ochoa CSIC UAM, Universidad Autonoma, Madrid, Spain
    Nucleic Acids Res 32:5861-73. 2004
  4. pmc Lack of sugar discrimination by human Pol mu requires a single glycine residue
    Jose F Ruiz
    Centro de Biologia Molecular Severo Ochoa CSIC UAM, Campus de la Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid, Spain
    Nucleic Acids Res 31:4441-9. 2003
  5. ncbi Label-retaining epithelial cells in mouse mammary gland divide asymmetrically and retain their template DNA strands
    Gilbert H Smith
    Laboratory of Mammary Gland Biology and Tumorigenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Development 132:681-7. 2005
  6. ncbi A mechanism for initiating RNA-dependent RNA polymerization
    S J Butcher
    Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, PO Box 56 (Viikinkaari 5, 00014 University of Helsinki, Finland
    Nature 410:235-40. 2001
  7. ncbi Intestinal stem cells protect their genome by selective segregation of template DNA strands
    Christopher S Potten
    Epithelial Biology Department, Paterson Institute for Cancer Research, Christie Hospital NHS Trust, Wilmslow Road, Manchester M9 4BX, UK
    J Cell Sci 115:2381-8. 2002
  8. ncbi DNA polymerase-mediated DNA synthesis on a TNA template
    John C Chaput
    Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
    J Am Chem Soc 125:856-7. 2003
  9. ncbi Positive correlation between DNA polymerase alpha-primase pausing and mutagenesis within polypyrimidine/polypurine microsatellite sequences
    Suzanne E Hile
    Department of Pathology, Gittlen Cancer Research Institute, The Pennsylvania State University College of Medicine, Hershey Medical Center, 500 University Drive, Hershey, PA 17033, USA
    J Mol Biol 335:745-59. 2004
  10. ncbi Protein structure prediction and structural genomics
    D Baker
    Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    Science 294:93-6. 2001

Research Grants

  1. WHOLE ANIMAL APOPTOSIS ASSAY FOR CANCER DRUG SCREENING
    George Serbedzija; Fiscal Year: 2000
  2. Effects of Formamidopyrimidine Lesions on DNA
    Marc Greenberg; Fiscal Year: 2006
  3. Instrumentation for Peptide Synthesis Facility
    KATHRYN IVANETICH; Fiscal Year: 2003
  4. DNA replication, DNA repair and microsatellite stability
    Kristin Eckert; Fiscal Year: 2009
  5. Quantitative Real Time PCR Instrumentation
    KATHRYN IVANETICH; Fiscal Year: 2002
  6. Mechanisms of Avian Hepadnavirus Replication
    DANIEL LOEB; Fiscal Year: 2008
  7. MUTATIONAL MECHANISMS OF REPETITIVE DNA IN HUMAN CELLS
    Kristin Eckert; Fiscal Year: 2001
  8. NUCLEIC ACID SEQUENCE ANALYSIS
    KATHRYN IVANETICH; Fiscal Year: 2001
  9. Dissecting the mechanism of viral RNA recombination
    Peter Nagy; Fiscal Year: 2004
  10. Histone Deacetylase Inhibitors as Therapeutics for Friedreich's ataxia
    JOEL GOTTESFELD; Fiscal Year: 2007

Detail Information

Publications295 found, 100 shown here

  1. pmc Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification
    F B Dean
    Molecular Staging, Inc, New Haven, Connecticut 06511, USA
    Genome Res 11:1095-9. 2001
    ..Amplified products can also be used for in vitro cloning, library construction, and other molecular biology applications...
  2. ncbi DNA primases
    D N Frick
    Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
    Annu Rev Biochem 70:39-80. 2001
    ..The small eukaryotic primase subunit contains the active site for RNA synthesis, and its activity correlates with DNA replication during the cell cycle...
  3. pmc Overexpression of human DNA polymerase mu (Pol mu) in a Burkitt's lymphoma cell line affects the somatic hypermutation rate
    Jose F Ruiz
    Centro de Biologia Molecular Severo Ochoa CSIC UAM, Universidad Autonoma, Madrid, Spain
    Nucleic Acids Res 32:5861-73. 2004
    ....
  4. pmc Lack of sugar discrimination by human Pol mu requires a single glycine residue
    Jose F Ruiz
    Centro de Biologia Molecular Severo Ochoa CSIC UAM, Campus de la Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid, Spain
    Nucleic Acids Res 31:4441-9. 2003
    ..The unusual capacity to insert both rNTPs and dNTPs will be discussed in the context of the predicted roles of Pol mu in DNA repair...
  5. ncbi Label-retaining epithelial cells in mouse mammary gland divide asymmetrically and retain their template DNA strands
    Gilbert H Smith
    Laboratory of Mammary Gland Biology and Tumorigenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Development 132:681-7. 2005
    ....
  6. ncbi A mechanism for initiating RNA-dependent RNA polymerization
    S J Butcher
    Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, PO Box 56 (Viikinkaari 5, 00014 University of Helsinki, Finland
    Nature 410:235-40. 2001
    ..Our results provide a working model for the initiation of replication and transcription...
  7. ncbi Intestinal stem cells protect their genome by selective segregation of template DNA strands
    Christopher S Potten
    Epithelial Biology Department, Paterson Institute for Cancer Research, Christie Hospital NHS Trust, Wilmslow Road, Manchester M9 4BX, UK
    J Cell Sci 115:2381-8. 2002
    ..The presence of these protective mechanisms ensures that the small intestine rarely develops cancer and that stem cells can sustain the extensive cell proliferation needed during life...
  8. ncbi DNA polymerase-mediated DNA synthesis on a TNA template
    John C Chaput
    Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
    J Am Chem Soc 125:856-7. 2003
    ..We report that despite having a repeating unit that is one atom shorter than that of DNA, several polymerases showed surprisingly good ability to copy limited stretches of TNA...
  9. ncbi Positive correlation between DNA polymerase alpha-primase pausing and mutagenesis within polypyrimidine/polypurine microsatellite sequences
    Suzanne E Hile
    Department of Pathology, Gittlen Cancer Research Institute, The Pennsylvania State University College of Medicine, Hershey Medical Center, 500 University Drive, Hershey, PA 17033, USA
    J Mol Biol 335:745-59. 2004
    ..Thus, a positive correlation exists between polymerase alpha-primase pausing and mutagenesis within microsatellite DNA alleles...
  10. ncbi Protein structure prediction and structural genomics
    D Baker
    Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    Science 294:93-6. 2001
    ..We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics...
  11. pmc The GAA*TTC triplet repeat expanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner
    E Grabczyk
    Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0830, USA
    Nucleic Acids Res 28:2815-22. 2000
    ..The non-template (GAA) strand folds back creating a loop in the template strand, and the polymerase is paused at the distal triplex-duplex junction...
  12. pmc Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
    Sean J Johnson
    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 100:3895-900. 2003
    ....
  13. pmc BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies
    Milan Fedurco
    Manteia Predictive Medicine S A Zone Industrielle Coinsins, CH 1267, Switzerland
    Nucleic Acids Res 34:e22. 2006
    ..DNA colonies generated using the BTA reagent can be used for further sequence analysis in an unprecedented parallel fashion for low-cost genomic studies...
  14. ncbi CPD damage recognition by transcribing RNA polymerase II
    Florian Brueckner
    Munich Center for Integrated Protein Science CiPS, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Science 315:859-62. 2007
    ..This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II...
  15. pmc Template boundary definition in Tetrahymena telomerase
    Cary K Lai
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3204, USA
    Genes Dev 16:415-20. 2002
    ..Our results indicate that sequence-specific interaction of a telomerase RNA element with the TERT RNA binding domain, not the active site motifs, defines the template boundary...
  16. pmc Mutational analysis of the influenza virus cRNA promoter and identification of nucleotides critical for replication
    Mandy Crow
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
    J Virol 78:6263-70. 2004
    ..Overall, our results suggest that the corkscrew secondary-structure model is required for authentic cRNA promoter activity in vivo, although the precise role of the 3' hairpin loop remains unknown...
  17. ncbi The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication
    Ghislaine Henneke
    IFREMER, UMR 6197, Laboratoire de Microbiologie et Environnements Extrêmes, DRV VP LM2E, BP 70, F 29280 Plouzane, France
    J Mol Biol 350:53-64. 2005
    ..Our data imply that PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork...
  18. ncbi Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase
    Y Whitney Yin
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Science 298:1387-95. 2002
    ..Downstream duplex DNA binds to the fingers domain, and its orientation relative to upstream DNA in the initiation complex implies an unwinding that could facilitate formation of the open promoter complex...
  19. ncbi 8-oxodGTP incorporation by DNA polymerase beta is modified by active-site residue Asn279
    H Miller
    Department of Pharmacological Sciences, SUNY Stony Brook, Stony Brook, New York 11794 8651, USA
    Biochemistry 39:1029-33. 2000
    ..This suggests that interactions of 8-oxodGTP with Asn279 in the polymerase active site may alter the conformation of 8-oxodGTP and therefore alter its misincorporation...
  20. ncbi Single-molecule DNA sequencing of a viral genome
    TIMOTHY D HARRIS
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, USA
    Science 320:106-9. 2008
    ..This demonstrates a strategy for high-throughput low-cost resequencing...
  21. pmc Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase
    Kevin A Fiala
    Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 365:590-602. 2007
    ..This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation...
  22. ncbi A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining
    Stephanie A Nick McElhinny
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Mol Cell 19:357-66. 2005
    ..This apparent gradient of template dependence is largely attributable to a small structural element that is present but different in all three polymerases...
  23. ncbi Crucial role of the RNA:DNA hybrid in the processivity of transcription
    I Sidorenkov
    ABL Basic Research Program, National Cancer Institute Frederic Cancer Research and Development Center, Maryland 21702 1201, USA
    Mol Cell 2:55-64. 1998
    ..Our data show that a hybrid at least 9 nt long, formed between the template DNA and 3'-proximal RNA transcript, is necessary for the high processivity of EC during RNA chain elongation...
  24. pmc Estrogen receptor-alpha and progesterone receptor are expressed in label-retaining mammary epithelial cells that divide asymmetrically and retain their template DNA strands
    Brian W Booth
    Mammary Biology and Tumorigenesis Laboratory, National Cancer Institute, National Institute of Health, Bethesda, Maryland, USA
    Breast Cancer Res 8:R49. 2006
    ..Mouse mammary epithelium contains label-retaining epithelial cells that divide asymmetrically and retain their template DNA...
  25. pmc A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis
    Raquel Juarez
    Centro de Biologia Molecular Severo Ochoa CSIC UAM, Campus Universidad Autónoma Canto Blanco, 28049 Madrid, Spain
    Nucleic Acids Res 34:4572-82. 2006
    ..Recent in vivo and in vitro data suggest that such a dual capacity could be advantageous to resolve microhomology-mediated end-joining reactions...
  26. ncbi Error rate and specificity of human and murine DNA polymerase eta
    T Matsuda
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    J Mol Biol 312:335-46. 2001
    ..The nature and location of these errors suggest that some may be initiated by strand slippage, while others result from additional mechanisms...
  27. ncbi Fate of DNA replication fork encountering a single DNA lesion during oriC plasmid DNA replication in vitro
    Kumiko Higuchi
    Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama cho 8916 5, Ikoma, Nara 630 0101, Japan
    Genes Cells 8:437-49. 2003
    ....
  28. pmc Template boundary definition in mammalian telomerase
    Jiunn Liang Chen
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genes Dev 17:2747-52. 2003
    ..The divergent structure of boundary definition elements in mammals, yeast, and ciliates suggests diverse mechanisms for template boundary definition in telomerase...
  29. pmc Interaction of RNA polymerase with forked DNA: evidence for two kinetically significant intermediates on the pathway to the final complex
    Laura Tsujikawa
    Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106 4935, USA
    Proc Natl Acad Sci U S A 99:3493-8. 2002
    ....
  30. ncbi Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation
    J E Foster
    Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
    Cell 106:243-52. 2001
    ....
  31. pmc The DNA primase of Sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3'-terminal nucleotidyl-transferase activity
    Mariarosaria De Falco
    Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P Castellino, 111, 80131 Napoli, Italy
    Nucleic Acids Res 32:5223-30. 2004
    ..Interestingly, the Sso DNA primase complex is endowed with a terminal nucleotidyl-transferase activity, being able to incorporate nucleotides at the 3' end of synthetic oligonucleotides in a non-templated manner...
  32. pmc Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS)
    C R Newton
    ICI Diagnostics, Northwich, Cheshire, UK
    Nucleic Acids Res 17:2503-16. 1989
    ..Our findings are in complete agreement with allele assignments derived by direct sequencing of PCR products...
  33. ncbi Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions
    Massimo Lopes
    Department of Biology, Institute of Cell Biology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Mol Cell 21:15-27. 2006
    ....
  34. ncbi A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders
    Jennifer A Lee
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, 77030, USA
    Cell 131:1235-47. 2007
    ..We propose that complex duplication and deletion rearrangements associated with PMD, and potentially other nonrecurrent rearrangements, may be explained by this replication-based mechanism...
  35. ncbi High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus
    D J Schneider
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309, USA
    Biochemistry 34:9599-610. 1995
    ..These ssDNA molecules may be useful as inhibitors or as models for the design of small molecule inhibitors of HIV-1 RT in vivo...
  36. pmc Human telomerase contains two cooperating telomerase RNA molecules
    C Wenz
    Swiss Institute for Experimental Cancer Research, CH 1066 Epalinges, Switzerland
    EMBO J 20:3526-34. 2001
    ..We conclude that the telomerase RNA templates in the active enzyme are interdependent and functionally cooperate with each other. We discuss models that may explain the biological and enzymatic roles of telomerase dimerization...
  37. 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...
  38. pmc Potent inhibition of human immunodeficiency virus type 1 replication by template analog reverse transcriptase inhibitors derived by SELEX (systematic evolution of ligands by exponential enrichment)
    Pheroze Joshi
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    J Virol 76:6545-57. 2002
    ..As virion-encapsidated TRTIs can predispose virions for inhibition immediately upon entry, they should prove to be efficacious agents in gene therapy approaches for AIDS...
  39. ncbi Stable association of hsp90 and p23, but Not hsp70, with active human telomerase
    H L Forsythe
    Departments of Pathology and Human Genetics, Massey Cancer Center, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298 0662, USA
    J Biol Chem 276:15571-4. 2001
    ....
  40. pmc Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase
    Minna M Poranen
    Institute of Biotechnology and Department of Biological and Environmental Sciences, Viikki Biocenter, P O Box 56 Viikinkaari 5 00014 University of Helsinki, Finland
    Nucleic Acids Res 36:6633-44. 2008
    ..The structural flexibility caused by Mn(2+) is also important for the enzyme dynamics, explaining the requirement for manganese throughout RNA polymerization...
  41. ncbi Effect of 8-oxoguanine on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II
    Silvia Tornaletti
    Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
    DNA Repair (Amst) 3:483-94. 2004
    ..These results are discussed in the context of possible models for TCR...
  42. ncbi Specialized DNA polymerases, cellular survival, and the genesis of mutations
    Errol C Friedberg
    Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Science 296:1627-30. 2002
    ..The low fidelity of some of these specialized polymerases when copying undamaged DNA may be physiologically functional, including generating immunoglobulin diversity...
  43. ncbi Replication fork reactivation downstream of a blocked nascent leading strand
    Ryan C Heller
    Molecular Biology Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, USA
    Nature 439:557-62. 2006
    ....
  44. ncbi Transcription-targeted DNA deamination by the AID antibody diversification enzyme
    Jayanta Chaudhuri
    Howard Hughes Medical Institute, The Children s Hospital, The Center for Blood Research, and Department of Genetics, Harvard University Medical School, Boston, Massachusetts 02115, USA
    Nature 422:726-30. 2003
    ..We conclude that transcription targets the DNA deamination activity of AID to dsDNA by generating secondary structures that provide ssDNA substrates...
  45. pmc Antiretroviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase increase template-switching frequency
    Galina N Nikolenko
    HIV Drug Resistance Program, NCI Frederick, Bldg 535, Rm 334, Frederick, MD 21702, USA
    J Virol 78:8761-70. 2004
    ..These results also indicate that mutations conferring resistance to antiviral drugs can increase the frequency of RT template switching and may influence the rate of retroviral recombination and viral evolution...
  46. ncbi In vitro replication slippage by DNA polymerases from thermophilic organisms
    E Viguera
    Laboratoire de Genetique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert 78350 Jouy en Josas, France
    J Mol Biol 312:323-33. 2001
    ..We show that these hairpin deletions occurring during PCR are due to replication slippage, and not to a previously proposed process involving polymerization across the hairpin base...
  47. pmc Terminal nucleotidyl transferase activity of recombinant Flaviviridae RNA-dependent RNA polymerases: implication for viral RNA synthesis
    C T Ranjith-Kumar
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    J Virol 75:8615-23. 2001
    ....
  48. pmc Reverse transcriptase incorporation of 1,5-anhydrohexitol nucleotides
    K Vastmans
    Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    Nucleic Acids Res 29:3154-63. 2001
    ..These results could be rationalised based on the X-ray structure of HIV-1 reverse transcriptase...
  49. ncbi MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis
    H Maki
    Department of Biochemistry, Faculty of Medicine, Kyushu University, Fukuoka, Japan
    Nature 355:273-5. 1992
    ..This indicates that elimination from the nucleotide pool of the oxidized form of guanine nucleotide is important for the high fidelity of DNA synthesis...
  50. ncbi KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo
    S Sasse-Dwight
    Department of Chemistry and Biochemistry, University of California, Los Angeles 90024
    J Biol Chem 264:8074-81. 1989
    ....
  51. pmc Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases beta and lambda
    Emmanuele Crespan
    Istituto di Genetica Molecolare IGM CNR via Abbiategrasso 207, I 27100 Pavia, Italy
    Nucleic Acids Res 33:4117-27. 2005
    ..These results show for the first time that neither the base nor the sugar moieties of nucleotides are required for incorporation by family X DNA polymerases...
  52. pmc Poliovirus cre(2C)-dependent synthesis of VPgpUpU is required for positive- but not negative-strand RNA synthesis
    B Joan Morasco
    Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville 32610 0245, USA
    J Virol 77:5136-44. 2003
    ..The pool of excess VPgpUpU synthesized on the cre(2C) hairpin should support high levels of positive-strand synthesis and thereby promote the asymmetric replication of poliovirus RNA...
  53. pmc Requirement of RAD5 and MMS2 for postreplication repair of UV-damaged DNA in Saccharomyces cerevisiae
    Carlos A Torres-Ramos
    Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, Texas 77555 1061, USA
    Mol Cell Biol 22:2419-26. 2002
    ..The possible roles of the Rad6-Rad18 and the Mms2-Ubc13 enzyme complexes in Rad5-dependent damage bypass are discussed...
  54. ncbi Synthesis and miscoding specificity of oligodeoxynucleotide containing 8-phenyl-2'-deoxyguanosine
    K Kohda
    Faculty of Pharmaceutical Sciences, Nagoya City University, Japan
    Chem Res Toxicol 10:1351-8. 1997
    ..dG. The duplex containing 8-PhdG.dA was thermodynamically more stable than dG.dA. We conclude that 8-PhdG is a weak miscoding lesion, capable of generating G-->T and G-->C transversions and deletions in cells...
  55. ncbi Characterization of a viroid-derived RNA promoter for the DNA-dependent RNA polymerase from Escherichia coli
    Martin Pelchat
    RNA Group Groupe ARN, Departement de Biochimie, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
    Biochemistry 41:6561-71. 2002
    ..Finally, we present several insights into the mechanism of the RNAP which reveal that it behaves differently with an RNA template as compared to a DNA one...
  56. pmc Initiation of HIV-2 reverse transcription: a secondary structure model of the RNA-tRNA(Lys3) duplex
    F Freund
    UMR-5097, , Case 103, , 33076 Bordeaux Cedex, France. IFR 66 'Pathologies Infectieuses, Bordeaux
    Nucleic Acids Res 29:2757-65. 2001
    ..In view of these experimental data and sequence comparison between different HIV-2 isolates, we propose a model for the secondary structure of the HIV-2 template-primer initiation complex...
  57. ncbi Proliferating cell nuclear antigen promotes misincorporation catalyzed by calf thymus DNA polymerase delta
    D J Mozzherin
    Department of Pharmacological Sciences, University Medical Center, State University of New York, Stony Brook, New York 11794 8651, USA
    J Biol Chem 271:31711-7. 1996
    ..template-primer complex in the presence of PCNA facilitates unfavorable events catalyzed by pol delta. This model suggests an explicit mechanistic requirement for the intrinsic 3'-5'-exonuclease of pol delta...
  58. ncbi Structure of DNA polymerase I Klenow fragment bound to duplex DNA
    L S Beese
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Science 260:352-5. 1993
    ....
  59. ncbi DnaB helicase stimulates primer synthesis activity on short oligonucleotide templates
    S K Johnson
    Department of Chemistry, Center for Biotechnology, University of Nebraska Lincoln, Lincoln, Nebraska 68588 0304, USA
    Biochemistry 39:736-44. 2000
    ..In contrast, when primase acted alone, it stabilized the 3'-end hairpin conformation of the template so that the template's 3'-hydroxyl served as a "DNA primer" from which primase elongated to create the overlong primers...
  60. ncbi Structural and functional characterization of the coxsackievirus B3 CRE(2C): role of CRE(2C) in negative- and positive-strand RNA synthesis
    Mark J M van Ooij
    Radboud University Medical Centre Nijmegen, Nijmegen Centre for Molecular Life Science, Department of Medical Microbiology, The Netherlands
    J Gen Virol 87:103-13. 2006
    ....
  61. ncbi Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu
    Michelle P Roettger
    Department of Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
    Biochemistry 43:13827-38. 2004
    ..In addition to a slow and distributive DNA polymerase activity, Polmu was identified to possess a weak strand-displacement activity. The potential biological roles of Polmu are discussed...
  62. pmc Identification of an RNA hairpin in poliovirus RNA that serves as the primary template in the in vitro uridylylation of VPg
    A V Paul
    Department of Molecular Genetics and Microbiology, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
    J Virol 74:10359-70. 2000
    ..The mechanism by which the VPgpUpU precursor, made specifically on the cre(2C) template, might be transferred to the site where it serves as primer for poliovirus RNA synthesis, remains to be determined...
  63. ncbi Nucleotides at the extremities of the viral RNA of influenza C virus are involved in type-specific interactions with the polymerase complex
    B Crescenzo-Chaigne
    Unite de Genetique Moleculaire des Virus Respiratoires, URA 1966 CNRS, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
    J Gen Virol 82:1075-83. 2001
    ..Thus, it could be suggested that the nature of the nucleotides as well as the stability of the secondary structure at the extremities of the viral RNA are important determinants of type-specificity...
  64. ncbi Semi-conservative DNA replication through telomeres requires Taz1
    Kyle M Miller
    Telomere Biology Laboratory, Cancer Research UK, 44 Lincoln s Inn Fields, London WC2A 3PX, UK
    Nature 440:824-8. 2006
    ..Stalled forks at dysfunctional human telomeres are likely to accelerate the genomic instability that drives tumorigenesis...
  65. ncbi Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases
    Claudio Rivetti
    Department of Biochemistry and Molecular Biology, University of Parma, 43100, Parma, Italy
    J Mol Biol 326:1413-26. 2003
    ..DNA wrapping in the elongation complex suggests a possible mechanism by which the polymerase may overcome the physical barrier to transcription imposed by the nucleosomes...
  66. ncbi A conserved insertion in protein-primed DNA polymerases is involved in primer terminus stabilisation
    Emmanuelle Dufour
    Centro de Biologia Molecular Severo Ochoa CSIC UAM, Instituto de Biología Molecular Eladio Viñuela CSIC, Universidad Autonoma, Cantoblanco, 28049 Madrid, Spain
    J Mol Biol 331:781-94. 2003
    ..The possible role of the TPR-1 insertion in the set of interactions with the nascent chain during the first steps of TP-DNA replication is discussed...
  67. pmc Evidence for activation of the hepatitis B virus polymerase by binding of its RNA template
    J E Tavis
    Department of Molecular Microbiology and Immunology, St Louis University School of Medicine, Missouri 63104, USA
    J Virol 70:5741-50. 1996
    ....
  68. pmc Template-directed synthesis of a genetic polymer in a model protocell
    Sheref S Mansy
    Howard Hughes Medical Institute, Department of Molecular Biology and the Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Nature 454:122-5. 2008
    ....
  69. pmc Substituent effects on the pairing and polymerase recognition of simple unnatural base pairs
    Gil Tae Hwang
    Department of Chemistry, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
    Nucleic Acids Res 34:2037-45. 2006
    ..The results help identify the determinants of base pair stability and efficient replication and should contribute to the effort to develop stable and replicable unnatural base pairs...
  70. ncbi DNA elongation by the human DNA polymerase lambda polymerase and terminal transferase activities are differentially coordinated by proliferating cell nuclear antigen and replication protein A
    Giovanni Maga
    Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, I 27100 Pavia, Italy
    J Biol Chem 280:1971-81. 2005
    ....
  71. ncbi Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase
    H Cai
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 268:23567-72. 1993
    ..A striking result was that while primers were extended past an abasic lesion by HIV-1 RT in both direct and misalignment modes, avian myeloblastosis virus RT failed to catalyze significant extension by either mode...
  72. ncbi Blocking transcription through a nucleosome with synthetic DNA ligands
    Joel M Gottesfeld
    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    J Mol Biol 321:249-63. 2002
    ..These results establish unambiguously the requirement for octamer mobility for transcription of nucleosomal templates by T7 RNA polymerase...
  73. ncbi Varied DNA polymerase-substrate interactions in the nucleotide binding pocket
    Michael Strerath
    Kekule Institut fur Organische Chemie und Biochemie, Universitat Bonn, Gerhard Domagk Strasse 1, 53121 Bonn, Germany
    Chembiochem 3:578-80. 2002
  74. ncbi RNA displacement and resolution of the transcription bubble during transcription by T7 RNA polymerase
    Manli Jiang
    Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
    Mol Cell 15:777-88. 2004
    ..The results indicate that the transition is a multistep process and reveal a critical role for the nontemplate strand of the DNA...
  75. pmc Reconstitution of a minimal mtDNA replisome in vitro
    Jenny A Korhonen
    Department of Medical Nutrition, Karolinska Institute, Novum, Huddinge, Sweden
    EMBO J 23:2423-9. 2004
    ..The functional interactions between TWINKLE and POLgamma thus explain why mutations in these two proteins cause an identical syndrome...
  76. ncbi Efforts to expand the genetic alphabet: identification of a replicable unnatural DNA self-pair
    Allison A Henry
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 126:6923-31. 2004
    ..The most promising unnatural base pair candidate of this series is the 3-fluorobenzene self-pair, which is replicated with reasonable efficiency and selectivity...
  77. ncbi Significance of nucleobase shape complementarity and hydrogen bonding in the formation and stability of the closed polymerase-DNA complex
    L Dzantiev
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 40:3215-21. 2001
    ..Finally, a stable closed complex is not formed in the presence of a ddNTP or rNTP. These results are discussed in relation to the steric exclusion model for the nucleotide insertion...
  78. ncbi DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs
    Natasha Paul
    Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
    Chem Biol 10:815-25. 2003
    ..These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases...
  79. pmc Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns
    J Horlacher
    Bio Organische Chemie, Eidgenössiche Technische Hochschule Zurich, Switzerland
    Proc Natl Acad Sci U S A 92:6329-33. 1995
    ..These results are discussed in light of the crystal structure for pol beta and general considerations of how polymerases must interact with an incoming base pair to faithfully copy genetic information...
  80. pmc Rescue of stalled replication forks by RecG: simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation
    P McGlynn
    Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
    Proc Natl Acad Sci U S A 98:8227-34. 2001
    ....
  81. pmc End-bridging is required for pol mu to efficiently promote repair of noncomplementary ends by nonhomologous end joining
    Bryan J Davis
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA
    Nucleic Acids Res 36:3085-94. 2008
    ..Taken together, pol mu activity during NHEJ of noncomplementary ends can thus be primarily linked to pol mu's ability to work together with core NHEJ factors to bridge DNA ends and perform a template-dependent gap fill-in reaction...
  82. ncbi Secondary structure of vertebrate telomerase RNA
    J L Chen
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Cell 100:503-14. 2000
    ..The proposed vertebrate telomerase RNA structure displays a strikingly similar topology to the previously determined ciliate telomerase RNA structure, implying an evolutionary conservation of the global architecture of telomerase RNA...
  83. pmc Fidelity of DNA ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides
    J N Housby
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nucleic Acids Res 26:4259-66. 1998
    ..We suggest that sequence selection was imposed by the ligase and not just by base pairing interactions. The ligase directs polymerisation in the 3' to 5' direction which we propose is linked to its role in lagging strand DNA replication...
  84. ncbi Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing
    Deepak T Nair
    Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York 10029, USA
    Nature 430:377-80. 2004
    ....
  85. pmc De novo initiation of RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase
    W Zhong
    Department of Antiviral Therapy, Schering Plough Research Institute, Kenilworth, New Jersey 07033 0539, USA
    J Virol 74:2017-22. 2000
    ..Identification and characterization of the de novo priming or initiation activity by HCV NS5B provides an opportunity to screen for inhibitors that specifically target the initiation step...
  86. ncbi Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex
    Katsuhiko S Murakami
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 296:1285-90. 2002
    ..The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes...
  87. ncbi Replication of a cis-syn thymine dimer at atomic resolution
    Hong Ling
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nature 424:1083-7. 2003
    ..A model of the pol eta-CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol eta and the Dpo4-CPD complex suggests unique features that allow pol eta to efficiently bypass CPDs...
  88. ncbi Cooperation between RNA polymerase molecules in transcription elongation
    Vitaly Epshtein
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Science 300:801-5. 2003
    ..Such cooperation between RNAP molecules links the rate of elongation to the rate of initiation and explains why elongation is still fast and processive in vivo even without anti-arrest factors...
  89. pmc Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces?
    Anatoly P Gmyl
    M P Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow 142782, Russia
    RNA 9:1221-31. 2003
    ....
  90. ncbi Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide
    Karl E Zahn
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    Biochemistry 46:10551-61. 2007
    ....
  91. pmc Cross-linking of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase to template-primer
    E N Peletskaya
    ABL-Basic Research Program, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702-1201, USA
    J Virol 75:9435-45. 2001
    ..This experimental approach can be used to measure distances between any site on the surface of the protein and an interacting molecule...
  92. ncbi Human DNA polymerase lambda possesses terminal deoxyribonucleotidyl transferase activity and can elongate RNA primers: implications for novel functions
    Kristijan Ramadan
    Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich Irchel, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    J Mol Biol 328:63-72. 2003
    ..These two novel properties of human DNA polymerase lambda might suggest additional roles for this enzyme in DNA replication and repair processes...
  93. ncbi Substitution of conserved hydrophobic residues in motifs B and C of HIV-1 RT alters the geometry of its catalytic pocket
    Bechan Sharma
    Department of Biochemistry and Molecular Biology, Center for the Study of Emerging and Re Emerging Pathogens, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
    Biochemistry 41:15685-97. 2002
    ....
  94. ncbi Mechanism of loading the Escherichia coli DNA polymerase III beta sliding clamp on DNA. Bona fide primer/templates preferentially trigger the gamma complex to hydrolyze ATP and load the clamp
    Brandon Ason
    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville 32610 0245, USA
    J Biol Chem 278:10033-40. 2003
    ....
  95. ncbi Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms
    David A Bushnell
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305 5126, USA
    Science 303:983-8. 2004
    ..The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process...
  96. ncbi Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting
    Brian A Young
    Departments of Stomatology and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
    Science 303:1382-4. 2004
    ..Our results support the model that capture of nontemplate bases extruded from the DNA helix underlies the melting process...
  97. ncbi ATP interactions of the tau and gamma subunits of DNA polymerase III holoenzyme of Escherichia coli
    Z Tsuchihashi
    Department of Biochemistry, Stanford University School of Medicine, California 94305
    J Biol Chem 264:17790-5. 1989
    ....
  98. ncbi Comparison of HIV-1 and avian myeloblastosis virus reverse transcriptase fidelity on RNA and DNA templates
    H Yu
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 267:10888-96. 1992
    ....
  99. pmc Construction and purification of site-specifically modified DNA templates for transcription assays
    Rebecca A Perlow
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 31:e40. 2003
    ..Data are supplied demonstrating that these templates support transcription, and we emphasize the potential versatility of the protocol and compare it with other published methods...
  100. pmc Human immunodeficiency virus type 1 genetic recombination is more frequent than that of Moloney murine leukemia virus despite similar template switching rates
    Adewunmi Onafuwa
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 0620, USA
    J Virol 77:4577-87. 2003
    ....
  101. pmc Nontemplated terminal nucleotidyltransferase activity of double-stranded RNA bacteriophage phi6 RNA-dependent RNA polymerase
    Minna M Poranen
    Institute of Biotechnology and Department of Biological and Environmental Sciences, P O Box 56 Viikinkaari 5, 00014 University of Helsinki, Finland
    J Virol 82:9254-64. 2008
    ..We propose that the activity is involved in the termination of the template-dependent RNA polymerization reaction on the linear phi6 genome...

Research Grants73

  1. WHOLE ANIMAL APOPTOSIS ASSAY FOR CANCER DRUG SCREENING
    George Serbedzija; Fiscal Year: 2000
    Cellular apoptotic pathways prevent the propagation of inappropriate cell numbers, cell fates or faulty genetic templates which are implicated in cancer, neurodegeneration, autoimmunity, heart and renal disease...
  2. Effects of Formamidopyrimidine Lesions on DNA
    Marc Greenberg; Fiscal Year: 2006
    ..abstract_text> ..
  3. Instrumentation for Peptide Synthesis Facility
    KATHRYN IVANETICH; Fiscal Year: 2003
    ..The requested instrumentation would be a truly shared resource. No single investigator, group of investigators or department would dominate its use. ..
  4. DNA replication, DNA repair and microsatellite stability
    Kristin Eckert; Fiscal Year: 2009
    ..Microsatellite allele lengths can directly affect gene expression. As microsatellites are polymorphic in human populations, this effect on gene regulation may be an important factor contributing to individual cancer risk. ..
  5. Quantitative Real Time PCR Instrumentation
    KATHRYN IVANETICH; Fiscal Year: 2002
    ..The requested instrumentation would be a truly shared resource. No single investigator, group of investigators or department would dominate its use. ..
  6. Mechanisms of Avian Hepadnavirus Replication
    DANIEL LOEB; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  7. MUTATIONAL MECHANISMS OF REPETITIVE DNA IN HUMAN CELLS
    Kristin Eckert; Fiscal Year: 2001
    ..Our long-term research objective is to test the hypothesis that mutations in repetitive DNA provide an important source of genotypic variation that drives neoplastic progression. ..
  8. NUCLEIC ACID SEQUENCE ANALYSIS
    KATHRYN IVANETICH; Fiscal Year: 2001
    ..The PIs represent 19 UCSF departments. The requested instruments would be truly shared resources. No single investigator, group of investigators or department would dominate their use. ..
  9. Dissecting the mechanism of viral RNA recombination
    Peter Nagy; Fiscal Year: 2004
    ..Knowledge of recombination promises untold health benefits by providing means to limit virus infections and safer vaccines. ..
  10. Histone Deacetylase Inhibitors as Therapeutics for Friedreich's ataxia
    JOEL GOTTESFELD; Fiscal Year: 2007
    ..We are developing small molecules to reverse this effect, with the hope that these molecules may be therapeutic for FRDA. [unreadable] [unreadable] [unreadable]..
  11. Defects of Thymic Output in Wiskott-Aldrich Syndrome
    EILEEN REMOLD O DONNELL; Fiscal Year: 2006
    ....
  12. CELL CULTURE-BASED STUDIES OF HCV PATHOGENESIS
    Michael Lai; Fiscal Year: 2007
    ..These include iNOS induction, double-strand DNA breaks, and induction of error-prone DNA polymerases. The possible involvement of extracellular E2 protein in causing these effects will also be examined. ..
  13. MRI contrast agents targeting carbohydrate biomarkers
    Binghe Wang; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  14. Algorithms to Map Disease & Genetic Effects on the Brain
    Paul Thompson; Fiscal Year: 2005
    ..Validated on unique datasets, these tools will greatly empower biomedical studies that bridge imaging and genetics. They will help investigate the genetic transmission, triggers, and dynamics of disease in whole human populations. ..
  15. CREATING MUTANT ENZYMES FOR GENE THERAPY OF CANCER
    LAWRENCE LOEB; Fiscal Year: 2007
    ..abstract_text> ..
  16. Synthetic Antibodies by Monomolecular Imprinting
    Steven Zimmerman; Fiscal Year: 2007
    ..Applications in medical diagnostics are the most likely early pay-off for this technology. ..
  17. Small molecule therapeutics for Friedreich's ataxia
    JOEL GOTTESFELD; Fiscal Year: 2005
    ..The effects of polyamides on cellular frataxin protein will be determined by western blotting, and the genome-wide effects of polyamide treatment will be assessed by DNA microarray analysis. ..
  18. ZFN-driven Gene Disruption of CCR5 as a Potential Treatment of AIDS
    Fyodor Urnov; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  19. NUCLEASES IN DNA REPAIR AND RECOMBINATION
    SUSAN LOVETT; Fiscal Year: 2006
    ..We will extend genetic analysis of radC to determine what role it may play in repair and recombination. ..
  20. Host factors involved in viral RNA recombination
    Peter Nagy; Fiscal Year: 2006
    ..Knowledge of recombination promises untold health benefits by providing means to limit virus infections and to develop safer vaccines. ..
  21. MOLECULAR RECOGNITION OF ANTIPSYCHOTIC DRUGS AND COCAINE
    JONATHAN JAVITCH; Fiscal Year: 2006
    ..abstract_text> ..
  22. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2004
    ....
  23. Mechanism and Inhibition of Herpes Replication
    ROBERT KUCHTA; Fiscal Year: 2002
    ..Additionally, a number of novel nucleotides will be synthesized to provide a thorough understanding of how the enzyme interacts with the incoming NTP. ..
  24. Protein-Protein Interactions
    David Baker; Fiscal Year: 2009
    ....
  25. DNA REPAIR AND CANCER PRONE HEREDITARY HUMAN DISEASE
    Errol Friedberg; Fiscal Year: 2002
    ....
  26. Bacterial cell cycle control
    SUSAN THOMAS LOVETT; Fiscal Year: 2010
    ..LAY DESCRIPTION: We will study a protein present in all bacteria that appears to control their growth. This will provide important missing information about how bacteria divide and may provide a target for antibiotics. ..
  27. HYPOTRICH GENOME IN DEVELOPMENT AND EVOLUTION
    David Prescott; Fiscal Year: 2001
    ..The experiments deal with the general problem of how an organism can manipulate its own DNA. ..
  28. Computational Modeling of High-Field MR Images
    Paul M Thompson; Fiscal Year: 2010
    ..We will share all images, protocols, and algorithms with our network of 100+ collaborating laboratories. ..
  29. DNA-PROTEIN COMPLEX OF BACILLUS SUBTILITS PHAGE 029
    Margarita Salas; Fiscal Year: 2003
    ..subtilis RNA polymerase at promoters A3 and A2c, the switch from early to late transcription in phage GA-1, and the mechanism of p6 repression at promoters C2 and A2c. ..
  30. DNA METHYLOME STUDY IN TYPE 1 DIABETES
    ART PETRONIS; Fiscal Year: 2009
    ..This effort may have a major impact on our understanding of autoimmune mechanisms in T1D and lead to new strategies in diagnostics and treatment of the disease. ..
  31. Gene Expression Analysis of Aplysia Neural Network
    Jingyue Ju; Fiscal Year: 2009
    ..The full-length cDNA libraries and the Aplysia microarray will provide important resources for investigators to study learning and other behavior paradigms in this important model organism. ..
  32. Genomic Approaches to Neuronal Diversity and Plasticity
    Jingyue Ju; Fiscal Year: 2007
    ..RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page .................................................................................................................................................. 1 Description, ..
  33. Catalytic Mechanisms of RNA Ezymes
    Martha J Fedor; Fiscal Year: 2010
    ..The results of these studies also will provide a framework to guide the development of technical and therapeutic applications involving RNAs as targets and reagents. ..
  34. MOUSE MODELS OF DNA REPAIR - DEFECTIVE HUMAN DISEASES
    Errol Friedberg; Fiscal Year: 2011
    ..abstract_text> ..
  35. Novel oncolytic adenovirus for pancreatic therapy
    Baek Kim; Fiscal Year: 2008
    ..This application proposes to develop a novel gene therapy approach employing oncolytic adenovirus replicating specifically in cancer cells. [unreadable] [unreadable] [unreadable]..
  36. A High-Throughput Assay for Influenza Replicase/RNA Polymerase Inhibitors
    ROBERT KUCHTA; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  37. CONFORMATIONAL VARIABILITY OF RNA
    JULI F FEIGON; Fiscal Year: 2010
    ..Our structural studies will provide molecular insight into how non-coding RNAs are regulated for cell function. ..
  38. GnRH signaling in LbetaT2 gonadotrope cells
    Nicholas Webster; Fiscal Year: 2009
    ..These genetic models will include cell-specific transgenic overexpression of selected co-repressors as well as gonadotrope-specific deletion of components of the Gs and Gq/11 pathways using cre-loxP technology. ..
  39. Modulating Nucleotide Size in DNA for Detection by Nanopore
    Jingyue Ju; Fiscal Year: 2007
    ..The molecular tools developed here will facilitate achieving the long-term goal of single molecule sequencing by nanopores at single base resolution. [unreadable] [unreadable]..
  40. DNA Sequencing with Reversible dNTP and Cleavable Fluorescent ddNTPTerminators
    Jingyue Ju; Fiscal Year: 2009
    ..We anticipate that up to 100 bp of continuous sequences will be produced by this approach, which can be used to pursue a variety of biomedical research projects. ..
  41. Fluorescent Aptamers for Glycoprotein Detection
    Binghe Wang; Fiscal Year: 2006
    ..Furthermore, the same technology, once developed, can also be used for the construction of fluorescent sensors for other cancer-related glycoproteins. ..
  42. MicroRNA Profiles of Pathogen Infection
    Andrew Ellington; Fiscal Year: 2005
    ..3. Apply these methods to the detection of changes in microRNA expression during influenza infection. 4. Apply these methods to the detection of changes in microRNA expression with other infectious agents. ..
  43. DENDRIMERS--POLYMERS FOR SELF ASSEMBLY AND DRUG DELIVERY
    Steven Zimmerman; Fiscal Year: 2001
    ..The strategy involves the chemical cross-linking of a dendrimer surface, followed by the chemical cleavage of labile internal bonds to chemically excise the core. ..
  44. Frontiers in NMR: A Celebration of the UCLA MRR
    Juli Feigon; Fiscal Year: 2003
    ..The Seaborg Event attracts a wide audience from southern California, as well as many alumni from out-of-state, and will thus showcase the new facility to an audience that extends beyond the magnetic resonance scientific community. ..
  45. Environmental Mutagen Society, 34th Annual Meeting
    LAWRENCE LOEB; Fiscal Year: 2003
    ..Awards will be made to US speakers whose major area of interest is in carcinogenesis. ..
  46. PEPTIDE NUCLEIC ACIDS (PNA)-MEDIATED GENE EXPRESSION
    Gan Wang; Fiscal Year: 2003
    ..To investigate parameters that affect PNA delivery efficiency and intracellular PNA binding. To explore the possibility of PNA binding-induced endogenous human gene expression. ..
  47. MOLECULAR EFFECTORS OF ENZYMATIC SYNTHESIS OF DNA
    MUKUND MODAK; Fiscal Year: 2003
    ..The molecular mechanism and functional anatomy of DNA polymerase clarified in this manner will lead to a better understanding of DNA replication, DNA repair and mutagenic effects of chemicals and carcinogenesis. ..
  48. MOLECULAR INTERACTION IN T4 DNA REPLICATION COMPLEX
    PETER VON HIPPEL; Fiscal Year: 2003
    ..abstract_text> ..
  49. OXYGEN INDUCED DNA DAMAGE, MUTATIONS AND CANCER
    LAWRENCE LOEB; Fiscal Year: 2003
    ..Even a modest, 2-fold, decrease could increase the latent period before disease is manifested clinically and thus reduce cancer mortality. ..
  50. SOCIAL INFLUENCES ON CENTRAL ARGININE VASOTOCIN ACTIONS
    John Godwin; Fiscal Year: 2003
    ..Direct influences of social environment on the expression and behavioral actions of AVT would have relevance to humans, where sexual and aggressive behaviors are also under environmental influences. ..
  51. REPLICATION OF HEPATITIS C VIRUS RNA
    Michael Lai; Fiscal Year: 2003
    ..We will also characterize cellular proteins interacting with the polymerase. Finally we will study the effects of ns4b and ns5a on RNA synthesis in vivo. ..
  52. Site-specific incorporation of FRET pairs into intracellular proteins
    Andrew Ellington; Fiscal Year: 2009
    ..This will allow us to follow and track proteins in a cell, and to determine where, when, and how proteins reside next to one another, in either normal or malformed complexes. ..
  53. REPLICATION OF DAMAGED DNA IN HUMAN CELLS
    Marila Cordeiro Stone; Fiscal Year: 2004
    ..This project will provide insight on how PRR and the S checkpoint cooperate to protect human cells from cancer. ..
  54. MOLECULAR GENETICS OF TUMOR VIRUSES AND CELLS
    Carol Greider; Fiscal Year: 2005
    ..The majority of our students and postdoctoral trainees go on to careers in basic research relevant to cancer at high quality academic institutions or pharmaceutical/biotechnology organizations. ..
  55. 2004 & 2006 Membrane Transport Proteins Gordon Conference
    JONATHAN JAVITCH; Fiscal Year: 2005
    ..In keeping with the GRC tradition, the interactions that will result, whether from formal or informal discussions, can be expected to be extraordinarily stimulating and productive. ..
  56. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2004
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
  57. PHARMACOGENETICS IN SURGICAL CRITICAL CARE
    Bradley Freeman; Fiscal Year: 2004
    ..The environment for this project is Washington University School of Medicine, an institution with access to a large clinical volume and established expertise in genomic research. ..
  58. Combinatorial Approaches to Activators of the NGF Recep*
    Nicholas Webster; Fiscal Year: 2005
    ..The Specific Aim of this proposal is to screen the combinatorial asterriquinone library against the NGF receptor. ..
  59. LETHAL MUTAGENESIS OF HIV BY DEOXYNUCLEOSIDE ANALOGS
    LAWRENCE LOEB; Fiscal Year: 2002
    ....
  60. STRUCTURE/FUNCTION STUDIES ON HUMAN TELOMERASE
    WILLIAM DROSOPOULOS; Fiscal Year: 2004
    ..abstract_text> ..
  61. High-throughput Sequencing by Pyrosequencing
    Mostafa Ronaghi; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  62. Mechanisms contributing to frataxin deficiency
    EDWARD GRABCZYK; Fiscal Year: 2009
    ..The novel reporter constructs we developed to dissect the underlying causes of frataxin insufficiency will also serve as high throughput cell-based assays for candidate therapies. ..
  63. NON-H-2 HISTOCOMPATIBILITY GENES AND ENCODED ANTIGENS
    Peter Wettstein; Fiscal Year: 2002
    ....
  64. Aberrant DNA Methylation as a Biomarker of HSIL in Liquid-based Pap Tests
    KAREN GUSTAFSON; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  65. Large-scale sequencing and assembly of the rat genome
    Robert Holt; Fiscal Year: 2002
    ....
  66. The Role of Telomeres and Telomerase in Cancer
    Jerry Shay; Fiscal Year: 2005
    ..abstract_text> ..
  67. GROWTH-RELATED CHANGES IN YEAST CTD PHOSPHORYLATION
    JEFFRY CORDEN; Fiscal Year: 2003
    ..Understanding such pathways and how they may modulate CTD phosphorylation in yeast will field further insight into the transition between growth and non- proliferative states of cells in multicellular organisms. ..
  68. Controlling DNA Condensation In Vitro
    Nicholas Hud; Fiscal Year: 2005
    ..Dr. Hud's results will have direct implications on the feasibility of using static DNA structures in the development of nonviral gene delivery systems. ..
  69. Role of AMPK in hypoglycemia-sensing in the ventromedial hypothalamus
    RORY MCCRIMMON; Fiscal Year: 2008
    ..Finally, the proposal aims to obtain data that will support the hypothesis that recurrent hypoglycemia induces mitochondrial biogenesis in the VMH, an effect that may be mediated by AMPK. ..
  70. In Vivo Antiviral Activity of Saponins
    MICHAEL RONER; Fiscal Year: 2007
    ..The extract is well suited to such an application as it is pH stable, is already approved as a food additive, is inexpensive, readily available and is soluble in water. [unreadable] [unreadable] [unreadable]..
  71. Structure and function of SRP RNA
    Christian Zwieb; Fiscal Year: 2006
    ..These studies will focus on the specific features of two critical interactions and define their dynamic relationship to SRP function. [unreadable] [unreadable]..
  72. HUMAN V(D)J RECOMBINASE IN NEOPLASTIC AND PRIMARY CELLS
    Michael Lieber; Fiscal Year: 2004
    ..Corresponding studies of such regions on minichromosomes will permit the testing of the effects of the direction of DNA replication and transcription. ..