circular dna

Summary

Summary: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)

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 Mutation detection and single-molecule counting using isothermal rolling-circle amplification
    P M Lizardi
    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Nat Genet 19:225-32. 1998
  3. pmc Telomeric DNA in ALT cells is characterized by free telomeric circles and heterogeneous t-loops
    Anthony J Cesare
    Lineberger Comprehensive Cancer Center, Rm 11 119, CB 7295, Mason Farm Rd, University of North Carolina, Chapel Hill, NC 27599 7295, USA
    Mol Cell Biol 24:9948-57. 2004
  4. pmc A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification
    Annabel Rector
    Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, BE 3000 Leuven, Belgium
    J Virol 78:4993-8. 2004
  5. ncbi One-year entecavir or lamivudine therapy results in reduction of hepatitis B virus intrahepatic covalently closed circular DNA levels
    Danny Ka Ho Wong
    Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
    Antivir Ther 11:909-16. 2006
  6. ncbi Kinetic proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases
    J Yan
    Department of Physics, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 63:031909. 2001
  7. ncbi Extrachromosomal rDNA circles--a cause of aging in yeast
    D A Sinclair
    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
    Cell 91:1033-42. 1997
  8. pmc Intrinsic stability of episomal circles formed during human immunodeficiency virus type 1 replication
    Theodore C Pierson
    Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins University School of Public Health, Baltimore, Maryland 21205, USA
    J Virol 76:4138-44. 2002
  9. ncbi Homologous recombination generates T-loop-sized deletions at human telomeres
    Richard C Wang
    Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Cell 119:355-68. 2004
  10. pmc Novel circular DNA viruses in stool samples of wild-living chimpanzees
    Olga Blinkova
    Blood Systems Research Institute, San Francisco and the Department of Laboratory Medicine, University of California, San Francisco, CA, USA
    J Gen Virol 91:74-86. 2010

Research Grants

  1. REPLICATION OF DAMAGED DNA IN HUMAN CELLS
    Marila Cordeiro Stone; Fiscal Year: 2004
  2. Mechanisms of transcription initiation in mitochondria
    Dmitry Temiakov; Fiscal Year: 2013
  3. Intervention of HBV DNA synthesis and transcription
    Aleem Siddiqui; Fiscal Year: 2013
  4. Integrase-defective lentiviral based influenza vaccines
    Mirella Salvatore; Fiscal Year: 2010
  5. Designer Nucleases to Cure Chronic Hepatitis B
    Christoph Seeger; Fiscal Year: 2013
  6. Nuclear Import Pathways for HPV Macromolecules
    JUNONA F MOROIANU; Fiscal Year: 2010
  7. KSHV RTA: more than viral replication
    Jae U Jung; Fiscal Year: 2013
  8. PAIRING OF HOMOLOGOUS SEQUENCES IN DROSOPHILA
    KENT GOLIC; Fiscal Year: 2002
  9. Discovery of Anti-HBV cccDNA Compounds from a Unique Natural Products Collection
    Andrea Cuconati; Fiscal Year: 2013
  10. KSHV Epigenetic Regulation
    Jae U Jung; Fiscal Year: 2013

Detail Information

Publications231 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
    ..Using random primers and phi29 DNA polymerase, circular DNA templates can be amplified 10,000-fold in a few hours...
  2. ncbi Mutation detection and single-molecule counting using isothermal rolling-circle amplification
    P M Lizardi
    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Nat Genet 19:225-32. 1998
    ..RCA also shows promise for the detection of padlock probes bound to single-copy genes in cytological preparations...
  3. pmc Telomeric DNA in ALT cells is characterized by free telomeric circles and heterogeneous t-loops
    Anthony J Cesare
    Lineberger Comprehensive Cancer Center, Rm 11 119, CB 7295, Mason Farm Rd, University of North Carolina, Chapel Hill, NC 27599 7295, USA
    Mol Cell Biol 24:9948-57. 2004
    ..Results presented here also indicate that expression of telomerase in GM847 cells does not affect t-loop or extrachromosomal circle formation...
  4. pmc A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification
    Annabel Rector
    Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, BE 3000 Leuven, Belgium
    J Virol 78:4993-8. 2004
    ..The multiply primed RCA method allows the discovery of previously unknown papillomaviruses, and possibly also other circular DNA viruses, without a priori sequence information.
  5. ncbi One-year entecavir or lamivudine therapy results in reduction of hepatitis B virus intrahepatic covalently closed circular DNA levels
    Danny Ka Ho Wong
    Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
    Antivir Ther 11:909-16. 2006
    ..However, the effects of these two antiviral agents on intrahepatic total HBV DNA and covalently closed circular DNA (cccDNA) are not known...
  6. ncbi Kinetic proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases
    J Yan
    Department of Physics, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 63:031909. 2001
    ..Here we show how the same model quantitatively explains the reduced variance of the double-helix linking number (supercoiling) distribution observed experimentally...
  7. ncbi Extrachromosomal rDNA circles--a cause of aging in yeast
    D A Sinclair
    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
    Cell 91:1033-42. 1997
    ..We speculate on the generality of this molecular cause of aging in higher species, including mammals...
  8. pmc Intrinsic stability of episomal circles formed during human immunodeficiency virus type 1 replication
    Theodore C Pierson
    Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins University School of Public Health, Baltimore, Maryland 21205, USA
    J Virol 76:4138-44. 2002
    ..We conclude that these DNA circles are not intrinsically unstable in all cell types and suggest that the utility of 2-LTR circle assays in measuring recent HIV-1 infection of susceptible cells in vivo needs to be reevaluated...
  9. ncbi Homologous recombination generates T-loop-sized deletions at human telomeres
    Richard C Wang
    Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Cell 119:355-68. 2004
    ..These findings show that t-loop deletion by HR influences the integrity and dynamics of mammalian telomeres...
  10. pmc Novel circular DNA viruses in stool samples of wild-living chimpanzees
    Olga Blinkova
    Blood Systems Research Institute, San Francisco and the Department of Laboratory Medicine, University of California, San Francisco, CA, USA
    J Gen Virol 91:74-86. 2010
    ..Sequences encoding proteins distantly related to the replicase protein of single-stranded circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small circular DNA viral genomes...
  11. ncbi Extrachromosomal circular DNA in eukaryotes: possible involvement in the plasticity of tandem repeats
    S Cohen
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
    Cytogenet Genome Res 124:327-38. 2009
    Extrachromosomal circular DNA (eccDNA) is ubiquitous in eukaryotic organisms, and has been noted for more than 3 decades...
  12. ncbi The plastid DNA of the malaria parasite Plasmodium falciparum is replicated by two mechanisms
    D H Williamson
    National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
    Mol Microbiol 45:533-42. 2002
    ....
  13. pmc Zinc finger proteins designed to specifically target duck hepatitis B virus covalently closed circular DNA inhibit viral transcription in tissue culture
    Kimberley A Zimmerman
    Deaprtment of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
    J Virol 82:8013-21. 2008
    ..In summary, designed ZFPs are able to bind to the DHBV enhancer and interfere with viral transcription, resulting in decreased production of viral products and progeny virus genomes...
  14. ncbi Digital quantification using amplified single-molecule detection
    Jonas Jarvius
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
    Nat Methods 3:725-7. 2006
    ..We apply the method for sensitive detection and quantification of the bacterial pathogen Vibrio cholerae...
  15. pmc Rolling circle amplification, a powerful tool for genetic and functional studies of complete hepatitis B virus genomes from low-level infections and for directly probing covalently closed circular DNA
    Séverine Margeridon
    INSERM, U871, Lyon, France
    Antimicrob Agents Chemother 52:3068-73. 2008
    ..Covalently closed circular DNA (cccDNA) from liver biopsies could be amplified directly from as few as 13 copies, using RCA, followed by a ..
  16. pmc Hepatitis B virus (HBV) virion and covalently closed circular DNA formation in primary tupaia hepatocytes and human hepatoma cell lines upon HBV genome transduction with replication-defective adenovirus vectors
    S Ren
    Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, D-79106 Freiburg, Germany
    J Virol 75:1104-16. 2001
    ..These data provide a rational basis for in vivo experiments aimed at developing tupaias into a useful experimental animal system for HBV infection...
  17. ncbi On mechanism of intermediate-sized circular DNA compaction mediated by spermine: contribution of fluorescence lifetime correlation spectroscopy
    Jana Humpolickova
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 3, Prague 8, Czech Republic
    J Fluoresc 18:679-84. 2008
    ..Furthermore, we show that it allows for observation of the equilibrium state transition dynamics...
  18. ncbi Substitutional editing of transcripts from genes of cyanobacterial origin in the dinoflagellate Ceratium horridum
    Stefan Zauner
    Cell Biology, Philipps University Marburg, Karl von Frisch Strasse, D 35032 Marburg, Germany
    FEBS Lett 577:535-8. 2004
    ....
  19. ncbi Rolling-circle amplification of viral DNA genomes using phi29 polymerase
    Reimar Johne
    Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany
    Trends Microbiol 17:205-11. 2009
    ..Recently, the bacteriophage phi29 DNA polymerase has been used for the efficient amplification of circular DNA viral genomes without the need of specific primers by a rolling-circle amplification (RCA) mechanism...
  20. ncbi Evidence that methylation of hepatitis B virus covalently closed circular DNA in liver tissues of patients with chronic hepatitis B modulates HBV replication
    Yanhai Guo
    State Key Laboratory of Cancer Biology, Department of Pharmacogenomics, School of Pharmacy, The Fourth Military Medical University, Xi an, China
    J Med Virol 81:1177-83. 2009
    ..The aim of this study was to compare the methylation status of the intrahepatic covalently closed circular DNA (cccDNA) CpG island 2 and HBV replication capability...
  21. ncbi Complete nucleotide sequence of the circular megaplasmid pHCG3 of Oligotropha carboxidovorans: function in the chemolithoautotrophic utilization of CO, H(2) and CO(2)
    Sven Fuhrmann
    Department of Microbiology and Bayreuth Center of Molecular Biosciences, University of Bayreuth, D 95440 Bayreuth, Germany
    Gene 322:67-75. 2003
    ..carboxidovorans. An oriV encodes the replication proteins RepABC. Sequence comparisons of pHCG3-encoded genes suggest that major genetic exchange between O. carboxidovorans and the proteobacteria has occurred...
  22. pmc CSA: an efficient algorithm to improve circular DNA multiple alignment
    Francisco Fernandes
    Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento INESC ID, Lisboa, Portugal
    BMC Bioinformatics 10:230. 2009
    ..alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an ..
  23. ncbi HIV-1 extrachromosomal 2-LTR circular DNA is long-lived in human macrophages
    Laura Gillim-Ross
    Mount Sinai School of Medicine, Division of Infectious Diseases, New York, NY 10029, USA
    Viral Immunol 18:190-6. 2005
    ..Furthermore, exrachromosomal circular DNA in this cell population could be a source of persisent viral protein expression.
  24. pmc Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
    Davide Demurtas
    Faculty of Biology and Medicine, Center for Integrative Genomics, University of Lausanne, School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
    Nucleic Acids Res 37:2882-93. 2009
    ..We corroborate the results of cryo-EM studies by using Bal31 nuclease to probe for the existence of kinks in 94-bp-long minicircles...
  25. pmc Production and function of the cytoplasmic deproteinized relaxed circular DNA of hepadnaviruses
    Haitao Guo
    Department of Microbiology and Immunology, Drexel University College of Medicine, Doylestown, PA 18902, USA
    J Virol 84:387-96. 2010
    ..viral DNA polymerase ought to be an essential step in the formation of hepadnavirus covalently closed circular DNA (cccDNA)...
  26. pmc Padlock oligonucleotides for duplex DNA based on sequence-specific triple helix formation
    C Escudé
    Laboratoire de Biophysique, Museum national d histoire naturelle, Institut National de la Santé et de la Recherche Médicale Unité 201, Centre National de la Recherche Scientifique, 43, rue Cuvier, 75231 Paris, France
    Proc Natl Acad Sci U S A 96:10603-7. 1999
    ..ends of the triplex-forming oligonucleotide were joined through the action of T4 DNA ligase, thus creating a circular DNA molecule catenated to the plasmid containing the target sequence...
  27. ncbi Protein association with circular DNA: rate enhancement by nonspecific binding
    Ramzi Alsallaq
    Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA
    J Chem Phys 128:115108. 2008
    ..nonspecific-binding-facilitated diffusion-controlled rate of association of a protein with a specific site on a circular DNA is derived. Nonspecific binding is modeled by a short-range attractive surface potential...
  28. ncbi Genomic characterization of a novel virus found in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus) in Western Australia
    Mark D Bennett
    School of Veterinary and Biomedical Sciences, Murdoch University, Perth, Western Australia, 6150, Australia
    Virology 376:173-82. 2008
    ..The discovery of BPCV2 provides evidence of virus-host co-speciation between BPCVs and marsupial bandicoots and has important implications for the phylogeny and taxonomy of circular double-stranded DNA viruses infecting vertebrates...
  29. ncbi Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro
    P Baumann
    Imperial Cancer Research Fund, South Mimms, Herts, United Kingdom
    Cell 87:757-66. 1996
    ..It is proposed that hRad51 mediates homology recognition and initiates strand exchange, but that extensive heteroduplex formation in higher organisms requires the actions of additional proteins...
  30. ncbi Total and covalently closed circular DNA detection in liver tissue of long-term survivors transplanted for HBV-related cirrhosis
    Ilaria Lenci
    Hepatology Unit, Department of Internal Medicine, Tor Vergata University, Via Montpellier 1 00133 Rome, Italy
    Dig Liver Dis 42:578-84. 2010
    ..The risk of HBV reactivation is due to persistence of covalently closed circular (ccc) DNA in hepatocytes. Whether cccDNA persists in livers of long-term transplant survivors who received conventional prophylaxis is unknown...
  31. ncbi Clinical significance of intrahepatic hepatitis B virus covalently closed circular DNA in chronic hepatitis B patients who received cytotoxic chemotherapy
    Chee Kin Hui
    Blood 105:2616-7. 2005
  32. ncbi Intrahepatic hepatitis B virus covalently closed circular DNA can be a predictor of sustained response to therapy
    Joseph J Y Sung
    Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
    Gastroenterology 128:1890-7. 2005
    ..This study aimed to determine whether intrahepatic hepatitis B virus (HBV) covalently closed circular (ccc) DNA and total HBV DNA levels at the end of therapy would predict sustained response to therapy...
  33. ncbi Biochemical analysis of the yeast condensin Smc2/4 complex: an ATPase that promotes knotting of circular DNA
    James E Stray
    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132 3201, USA
    J Biol Chem 278:26238-48. 2003
    ..High mole ratios of Smc2/4 to plasmid promote a geometric change in circular DNA that can be trapped as knots by type II topoisomerases but not as supercoils by a type I topoisomerase...
  34. ncbi Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells
    D J Hazuda
    Department of Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA
    Science 287:646-50. 2000
    ..The antiviral activity of these compounds is due exclusively to inhibition of one of the two catalytic functions of integrase, strand transfer...
  35. ncbi Catalysis of ATP-dependent homologous DNA pairing and strand exchange by yeast RAD51 protein
    P Sung
    Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston 77555 1061
    Science 265:1241-3. 1994
    ..Thus, RAD51 is a eukaryotic recombination protein that can catalyze the strand exchange reaction...
  36. pmc An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12
    D A Maslov
    Department of Biology, University of California, Los Angeles 90024
    Mol Cell Biol 12:56-67. 1992
    ..A minicircle-encoded gRNA overlaps 12 editing sites in G6 mRNA, and chimeric gRNA/mRNA molecules were shown to exist, in agreement with the transesterification model for editing...
  37. ncbi Detection of hepatitis B virus covalently closed circular DNA in paraffin-embedded and cryo-preserved liver biopsies of chronic hepatitis B patients
    R Bart Takkenberg
    Department of Gastroenterology and Hepatology, AMC Liver Center, Center for Infectious Disease and Immunology CINIMA, University of Amsterdam and Royal Tropical Institute, KIT Biomedical Research, Amsterdam, The Netherlands
    Eur J Gastroenterol Hepatol 22:952-60. 2010
    Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) may become an important predictor for treatment outcome or long-term follow-up.
  38. pmc Covalently closed circular DNA is the predominant form of duck hepatitis B virus DNA that persists following transient infection
    Marc F Le Mire
    School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia 5000, Australia
    J Virol 79:12242-52. 2005
    ..These findings further characterize a second form of hepadnavirus persistence in a suppressed or inactive state, quite distinct from the classical chronic carrier state...
  39. ncbi Initial amplification of duck hepatitis B virus covalently closed circular DNA after in vitro infection of embryonic duck hepatocytes is increased by cell cycle progression
    C Borel
    , Lyon, France
    Hepatology 34:168-79. 2001
    ..Taken together, these results show that hepatocyte proliferation may positively regulate the initial amplification of CCC DNA of avian hepadnaviruses, and may explain why mitosis is not necessarily associated with loss of CCC DNA...
  40. pmc Characterization of cp18, a naturally truncated member of the cp32 family of Borrelia burgdorferi plasmids
    B Stevenson
    Laboratory of Microbial Structure and Function, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana 59840, USA
    J Bacteriol 179:4285-91. 1997
    ..These findings suggest that a relatively small recombinant plasmid capable of being stably maintained in B. burgdorferi could be constructed from a cp32 plasmid...
  41. ncbi Complete circular DNA genome of a TT virus variant (isolate name SANBAN) and 44 partial ORF2 sequences implicating a great degree of diversity beyond genotypes
    M Hijikata
    Department of Medical Sciences, Toshiba General Hospital, 6 3 22 Higashi Oh i, Shinagawa ku, Tokyo, 140 8522, Japan
    Virology 260:17-22. 1999
    ..In partial ORF2 sequences determined on 44 isolates taken together, TTV has a broad range of genetic diversity and the SANBAN isolate may represent a new TTV-like viral species or genus and not merely a genotype of TTV...
  42. ncbi Developmentally regulated extrachromosomal circular DNA formation in the mesozoan Dicyema japonicum
    Tomoko Noto
    Department of Biology, Faculty of Science, Kanazawa University, Kanazawa 920 1192, Japan
    Chromosoma 111:359-68. 2003
    ..In situ hybridization revealed that the circular DNA elements were restricted to the early embryonic larvae and gradually faded out as larvae approached maturity...
  43. ncbi Construction, stability, and activity of multivalent circular anticoagulant aptamers
    Daniel A Di Giusto
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney NSW 2052, Australia
    J Biol Chem 279:46483-9. 2004
    Here we describe the design and construction of multivalent circular DNA aptamers...
  44. pmc Extragenomic double-stranded DNA circles in yeast with linear mitochondrial genomes: potential involvement in telomere maintenance
    L Tomaska
    Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 27514, USA
    Nucleic Acids Res 28:4479-87. 2000
    ..75 kb (n = 1-7). Similar results were obtained with two other yeast species (P.philodendra and C. salmanticensis) which possess analogous telomeric structure...
  45. pmc The RdgC protein employs a novel mechanism involving a finger domain to bind to circular DNA
    Geoffrey S Briggs
    Institute of Genetics, University of Nottingham, Queen s Medical Centre, Nottingham NG7 2UH, UK
    Nucleic Acids Res 38:6433-46. 2010
    ..that destabilizing either interface has a serious effect on in vivo function, even though a stable complex with circular DNA was still observed. We conclude that tight binding is required for inhibition of RecA activity...
  46. ncbi Isothermal amplification and multimerization of DNA by Bst DNA polymerase
    G J Hafner
    Queensland University of Technology, Brisbane, Australia
    Biotechniques 30:852-6, 858, 860 passim. 2001
    ..A successful strategy for reducing LIMA-dependent background DNA synthesis in rolling-circle amplification embodiments was devised. This entailed the affinity purification of circular DNA templates before amplification.
  47. pmc The post-incision steps of the DNA base excision repair pathway in Escherichia coli: studies with a closed circular DNA substrate containing a single U:G base pair
    M Sandigursky
    Department of Radiology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Nucleic Acids Res 26:1282-7. 1998
    ..These results suggest that repair patch length may be substrate dependent and a re-evaluation of the post-incision steps of base excision repair is suggested...
  48. ncbi Small polydispersed circular DNA contains strains of mobile genetic elements and occurs more frequently in permanent cell lines of malignant tumors than in normal lymphocytes
    Hannelore Schmidt
    Institute of Pathology, University of Halle Wittenberg, D 06097 Halle Saale, Germany
    Oncol Rep 22:393-400. 2009
    Small polydispersed circular DNA (spcDNA) belongs to the extrachromosomal pool of DNA and is composed of heterogeneous DNA circles...
  49. ncbi Correlation between serum hepatitis B virus core-related antigen and intrahepatic covalently closed circular DNA in chronic hepatitis B patients
    Fumitaka Suzuki
    Department of Hepatology, Toranomon Hospital, Tokyo, Japan
    J Med Virol 81:27-33. 2009
    ..and viral status by the analysis of serum HBeAg, HBsAg, peripheral HBV DNA, and intrahepatic covalently closed circular DNA (cccDNA) in 57 chronic hepatitis B patients...
  50. ncbi Quantification of HBV covalently closed circular DNA from liver tissue by real-time PCR
    Scott Bowden
    Victorian Infectious Diseases Reference Laboratory, North Melbourne, Australia
    Methods Mol Med 95:41-50. 2004
  51. pmc Azido-containing diketo acid derivatives inhibit human immunodeficiency virus type 1 integrase in vivo and influence the frequency of deletions at two-long-terminal-repeat-circle junctions
    Evguenia S Svarovskaia
    HIV Drug Resistance Program Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    J Virol 78:3210-22. 2004
    ..Thus, sequencing analysis of 2-LTR-circle junctions can elucidate the intracellular mechanisms of action of HIV-1 IN inhibitors...
  52. pmc Replication independent formation of extrachromosomal circular DNA in mammalian cell-free system
    Zoya Cohen
    Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 4:e6126. 2009
    Extrachromosomal circular DNA (eccDNA) is a pool of circular double stranded DNA molecules found in all eukaryotic cells and composed of repeated chromosomal sequences...
  53. ncbi Relationship between serum hepatitis B virus DNA and surface antigen with covalently closed circular DNA in HBeAg-negative patients
    L Y Lin
    Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
    J Med Virol 82:1494-500. 2010
    Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is responsible for viral persistence...
  54. pmc Protein-induced bending and DNA cyclization
    J D Kahn
    Department of Chemistry, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 89:6343-7. 1992
    ..The results unambiguously distinguish DNA bends from isotropically flexible sites and can explain cooperative binding by proteins that need not contact each other...
  55. ncbi DNA ligase: structure, mechanism, and function
    I R Lehman
    Science 186:790-7. 1974
    ..coli chromosome. DNA ligase is therefore an essential enzyme required for normal DNA replication and repair in E. coli. Purified DNA ligases have proved to be useful reagents in the construction in vitro of recombinant DNA molecules...
  56. ncbi Simplification of DNA topology below equilibrium values by type II topoisomerases
    V V Rybenkov
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Science 277:690-3. 1997
    ..The results imply that type II topoisomerases use the energy of adenosine triphosphate hydrolysis to preferentially remove the topological links that provide barriers to DNA segregation...
  57. pmc Circle-to-circle amplification for precise and sensitive DNA analysis
    Fredrik Dahl
    The Beijer Laboratory, Department of Genetics and Pathology, Rudbeck Laboratory, SE 75185 Uppsala, Sweden
    Proc Natl Acad Sci U S A 101:4548-53. 2004
    ..We demonstrate the utility of the method for multiplexed genotyping of polymorphic loci and for quantitative DNA analysis...
  58. pmc Characterization of the intracellular deproteinized relaxed circular DNA of hepatitis B virus: an intermediate of covalently closed circular DNA formation
    Haitao Guo
    Drexel Institute for Biotechnology and Virology Research, Department of Microbiology and Immunology, Drexel University College of Medicine, Doylestown, PA 18902, USA
    J Virol 81:12472-84. 2007
    Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is formed by conversion of capsid-associated relaxed circular DNA (rcDNA) via unknown mechanisms and exists in the nucleus of the infected hepatocyte as a minichromosome ..
  59. pmc Genome analysis of a Glossina pallidipes salivary gland hypertrophy virus reveals a novel, large, double-stranded circular DNA virus
    Adly M M Abd-Alla
    Entomology Unit, FAO IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories, A 2444 Seibersdorf, Austria
    J Virol 82:4595-611. 2008
    ..The GpSGHV genome is a double-stranded circular DNA molecule of 190,032 bp containing 160 nonoverlapping open reading frames (ORFs), which are distributed equally ..
  60. pmc Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles
    Scott L Butler
    Infectious Disease Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    J Virol 76:3739-47. 2002
    ..We also used the quantitative PCR methods to analyze the effects of MG132, a proteasome inhibitor, which revealed that viral complexes containing mostly completed cDNAs are the primary substrates for proteasome-mediated degradation...
  61. ncbi DNA disentangling by type-2 topoisomerases
    Gregory R Buck
    Department of Mathematics, Saint Anselm College, Manchester, NH 03102, USA
    J Mol Biol 340:933-9. 2004
    ..Our model accounts for the observed preference for unlinking and unknotting of short DNA plasmids by type-2 topoisomerases and well explains experimental observations...
  62. ncbi The plastid-encoded psbA gene in the dinoflagellate Gonyaulax is not encoded on a minicircle
    Yunling Wang
    Departement de sciences biologiques, Universite de Montreal, 4101 Sherbrooke est, Montreal, Quebec, Canada H1X 2B2
    Gene 371:206-10. 2006
    ..In particular, the psbA gene is associated with DNA of roughly 50-150 kb and appears to have an unusually high complexity...
  63. pmc A novel cell-free system reveals a mechanism of circular DNA formation from tandem repeats
    S Cohen
    Institute of Human Genetics, CNRS, Genome Dynamics and Development, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
    Nucleic Acids Res 29:2542-8. 2001
    One characteristic of genomic plasticity is the presence of extrachromosomal circular DNA (eccDNA). High levels of eccDNA are associated with genomic instability, exposure to carcinogens and aging...
  64. pmc Rolling-circle replication of bacterial plasmids
    S A Khan
    Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pennsylvania 15261, USA
    Microbiol Mol Biol Rev 61:442-55. 1997
    ..A number of in vitro replication systems have been developed for RC plasmids and have provided insight into the mechanism of plasmid RC replication...
  65. pmc DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic virus
    H Jeske
    Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D 70550 Stuttgart, Germany
    EMBO J 20:6158-67. 2001
    ..The consequences of an inherent geminiviral recombination activity for the use of pathogen-derived resistance traits are discussed...
  66. ncbi Roles of host cell factors in circularization of retroviral dna
    Jennifer M Kilzer
    Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Virology 314:460-7. 2003
    ..Prominent circular DNA forms include 2-long-terminal repeat (LTR) circles, made by DNA end joining, and 1-LTR circles, produced in ..
  67. pmc Pankinetoplast DNA structure in a primitive bodonid flagellate, Cryptobia helicis
    J Lukescaron
    Institute of Parasitology, Czech Academy of Sciences, Czech Republic
    EMBO J 17:838-46. 1998
    ..Based on the similarity of the C.helicis minicircles to plasmids, we present a theory on the formation of the kDNA network...
  68. ncbi Amplification of target-specific, ligation-dependent circular probe
    D Y Zhang
    The Lillian, Henry M Stratton Hans Popper Department of Pathology, Department of Otolaryngology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Gene 211:277-85. 1998
    ..Finally, we described a novel isothermal amplification method, ramification extension amplification, utilizing circular nature of C-probe and displacement activity of DNA polymerase...
  69. pmc Simulations of knotting in confined circular DNA
    C Micheletti
    International School for Advanced Studies, Consiglio Nazionale delle Ricerche e Istituto Nazionale di Fisica della Materia Democritos unit, Italian Institute of Technology, Trieste, Italy
    Biophys J 95:3591-9. 2008
    ..the discrepancy due to the insufficient confinement of the equilibrium simulation or does it indicate that out-of-equilibrium mechanisms (such as rotation by packaging motors) affect the genome organization, hence its knot spectrum in P4?..
  70. ncbi The copy number of chloroplast gene minicircles changes dramatically with growth phase in the dinoflagellate Amphidinium operculatum
    V L Koumandou
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
    Protist 158:89-103. 2007
    The chloroplast genome of algae and plants typically comprises a circular DNA molecule of 100-200kb, which harbours approximately 120 genes, and is present in 50-100 copies per chloroplast...
  71. pmc Multiplexed protein profiling on microarrays by rolling-circle amplification
    Barry Schweitzer
    Molecular Staging, Inc, Suite 701, 300 George Street, New Haven, CT 06511, USA
    Nat Biotechnol 20:359-65. 2002
    ..Because microarrays can accommodate approximately 1,000 sandwich immunoassays of this type, a relatively small number of RCA microarrays seem to offer a tractable approach for proteomic surveys...
  72. ncbi Homogeneous detection of single rolling circle replication products
    Gerhard A Blab
    Department of Biophysics, Huygens Laboratory, Leiden University, Leiden, The Netherlands
    Anal Chem 76:495-8. 2004
    ..This high signal-to-background noise ratio leaves room for analysis in a simple detection device at higher speeds or at lower labeling ratios...
  73. pmc An intragenic guide RNA location suggests a complex mechanism for mitochondrial gene expression in Trypanosoma brucei
    Sandra L Clement
    2209 Biomedical Physical Sciences Building, Michigan State University, East Lansing, MI 48824, USA
    Eukaryot Cell 3:862-9. 2004
    ..Together, these data indicate that gRNA genes represent individual transcription units, regardless of their genomic context, and suggest a complex mechanism for mitochondrial gene expression in T. brucei...
  74. pmc An SOS inhibitor that binds to free RecA protein: the PsiB protein
    Vessela Petrova
    Program in Cellular and Molecular Biology, University of Wisconsin, Madison, Madison, WI 53706, USA
    Mol Cell 36:121-30. 2009
    ..However, PsiB binds to RecA protein that is free in solution. The RecA-PsiB complex impedes formation of RecA nucleoprotein filaments on DNA...
  75. pmc Circular DNA and DNA/RNA hybrid molecules as scaffolds for ricin inhibitor design
    Matthew B Sturm
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    J Am Chem Soc 129:5544-50. 2007
    ..Truncated stem-loop versions of the 28S rRNA are RTA substrates. Here, we investigate circular DNA and DNA/RNA hybrid GAGA sequence oligonucleotides as minimal substrates and inhibitor scaffolds for RTA ..
  76. pmc Proximity extension of circular DNA aptamers with real-time protein detection
    Daniel A Di Giusto
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    Nucleic Acids Res 33:e64. 2005
    ..Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the 'proximity ..
  77. pmc cis-Acting sequences that contribute to the synthesis of relaxed-circular DNA of human hepatitis B virus
    Ning Liu
    McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
    J Virol 78:642-9. 2004
    ..This study represents a comprehensive and quantitative analysis of cis-acting sequences that contribute to the synthesis of HBV RC DNA...
  78. ncbi Evolution of dinoflagellate unigenic minicircles and the partially concerted divergence of their putative replicon origins
    Zhaoduo Zhang
    Department of Botany, University of British Columbia, 3529 6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
    Mol Biol Evol 19:489-500. 2002
    ..The other postulates active transposition of putative replicon origins and formation of minicircles by homologous recombination between them...
  79. pmc RecA protein promotes the regression of stalled replication forks in vitro
    M E Robu
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706 1544, USA
    Proc Natl Acad Sci U S A 98:8211-8. 2001
    ..The reaction is not affected by the inclusion of the RecO and R proteins. We present this reaction as one of several potential RecA protein roles in the repair of stalled and/or collapsed replication forks in bacteria...
  80. pmc Circular chloroplast chromosomes: the grand illusion
    Arnold J Bendich
    Department of Biology, University of Washington, Seattle 98195 5325, USA
    Plant Cell 16:1661-6. 2004
  81. ncbi Ku suppresses formation of telomeric circles and alternative telomere lengthening in Arabidopsis
    Barbara Zellinger
    Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
    Mol Cell 27:163-9. 2007
    ..However, telomeres in ku mutants are fully functional, indicating that telomerase efficiently heals ongoing terminal deletions arising from excision of the t circles...
  82. pmc Evidence for gene expression by unintegrated human immunodeficiency virus type 1 DNA species
    Audrey Brussel
    Departement des Maladies Infectieuses, Institut Cochin, INSERM U567, CNRS UMR 8104, Universite Rene Descartes, 22 rue Mechain, 75014 Paris, France
    J Virol 78:11263-71. 2004
    ..Our results support the notion that these circular species of HIV-1 DNA are naturally transcribed during HIV-1 infection, thereby participating in virus replication...
  83. pmc Formation of hepatitis B virus covalently closed circular DNA: removal of genome-linked protein
    Weifan Gao
    Department of Microbiology and Immunology H107, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
    J Virol 81:6164-74. 2007
    ..Interestingly, PF-RC DNA, in contrast to RT-linked RC DNA, contained, almost exclusively, mature plus-strand DNA, suggesting that the RT protein was removed preferentially from mature RC DNA...
  84. pmc Factors influencing the recombinational expansion and spread of telomeric tandem arrays in Kluyveromyces lactis
    Shobhana Natarajan
    Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
    Eukaryot Cell 2:1115-27. 2003
    ..Consistent with this, we demonstrate that 100-nucleotide single-stranded telomeric circles of either strand can promote recombinational telomere elongation...
  85. pmc 3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy
    Arnaud Amzallag
    Laboratory for Computation and Visualization in Mathematics and Mechanics, EPFL FSB IMB, Ecole Polytechnique Federale de Lausanne, CH 1015 Lausanne, Switzerland
    Nucleic Acids Res 34:e125. 2006
    ..We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes...
  86. pmc Single-cell analysis of covalently closed circular DNA copy numbers in a hepadnavirus-infected liver
    Yong Yuan Zhang
    Department of Molecular Genetics and Microbiology, University of New Mexico, 915 Camino de Salud Northeast, Albuquerque, NM 87131, USA
    Proc Natl Acad Sci U S A 100:12372-7. 2003
    ..are maintained by the presence of a small and regulated number of episomal viral genomes [covalently closed circular DNA (cccDNA)] in the nuclei of infected cells...
  87. pmc A new enzymatic route for production of long 5'-phosphorylated oligonucleotides using suicide cassettes and rolling circle DNA synthesis
    Jakob S Lohmann
    Institute of Pathology, Aarhus University, 8000 Aarhus C, Denmark
    BMC Biotechnol 7:49. 2007
    ..Additionally, ligation of chemically synthesized oligonucleotides is less efficient than the ligation of enzymatically produced DNA molecules...
  88. ncbi Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy
    Jozef Nosek
    Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynska dolina CH 1, 842 15, Bratislava, Slovakia
    Curr Genet 44:73-84. 2003
    ..This scenario implies that insertion or deletion of such resolution elements may represent relatively simple routes for interconversion between different forms of the mitochondrial genome...
  89. ncbi Sorting by weighted reversals, transpositions, and inverted transpositions
    Martin Bader
    Faculty of Engineering and Computer Sciences, University of Ulm, Ulm, Germany
    J Comput Biol 14:615-36. 2007
    ..In this paper, we provide a 1.5-approximation algorithm for sorting by weighted reversals, transpositions and inverted transpositions for biologically realistic weights...
  90. pmc PieceMaker: selection of DNA fragments for selector-guided multiplex amplification
    Johan Stenberg
    Department of Genetics and Pathology, Rudbeck Laboratory Se 751 85, Uppsala, Sweden
    Nucleic Acids Res 33:e72. 2005
    ..The PieceMaker program alleviates this problem by selecting restriction enzymes to generate suitable fragments for selection, and generating the output data required to design the selector probes...
  91. ncbi Quantification of hepatitis B virus covalently closed circular DNA in patients with hepatocellular carcinoma
    Danny Ka Ho Wong
    Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
    J Hepatol 45:553-9. 2006
    This study aimed to measure the intrahepatic total hepatitis B virus (HBV) DNA and covalently closed circular DNA (cccDNA) levels in tumor and non-tumor tissues in hepatocellular carcinoma (HCC) patients.
  92. pmc Age-related differences in amplification of covalently closed circular DNA at early times after duck hepatitis B virus infection of ducks
    Yong Yuan Zhang
    Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, 87131, USA
    J Virol 79:9896-903. 2005
    ..We suggest that lower virus replication is due to a less rapid covalently closed circular DNA amplification, leading to lower viremias and a slower spread of infection in the liver, and that the slower ..
  93. pmc Recombination at long mutant telomeres produces tiny single- and double-stranded telomeric circles
    Cindy Groff-Vindman
    University of Georgia at Athens, Department of Genetics, Room C318, Life Sciences Building, Athens, GA 30602, USA
    Mol Cell Biol 25:4406-12. 2005
    ..The very small circles seen here are both predicted products of telomere rapid deletion, a process observed in both human and yeast cells, and predicted templates for roll-and-spread RTE...
  94. pmc Survey of extrachromosomal circular DNA derived from plant satellite repeats
    Alice Navrátilová
    Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ 37005, Czech Republic
    BMC Plant Biol 8:90. 2008
    ..been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays...
  95. pmc DNA supercoiling inhibits DNA knotting
    Yannis Burnier
    Center for Integrative Genomics, University of Lausanne, CH 1015 Lausanne, Switzerland
    Nucleic Acids Res 36:4956-63. 2008
    ..DNA supercoiling, such as found in bacterial cells, creates a situation where intramolecular passages leading to knotting are opposed by the free-energy change connected to transitions from unknotted to knotted circular DNA molecules.
  96. ncbi Complete circular DNA in the mitochondria-like organelles of Blastocystis hominis
    Ivan Wawrzyniak
    Laboratoire Microorganismes, Génome et Environnement, UMR CNRS 6023, Universite Blaise Pascal, 63177 Aubiere Cedex, France
    Int J Parasitol 38:1377-82. 2008
    ..Using genome sequencing project data, we describe here the complete sequence of a 29,270-bp circular DNA molecule that presents mitochondrial features (such as oxidative phosphorylation complex I subunits) but lacks ..
  97. pmc The dynamic processivity of the T4 DNA polymerase during replication
    Jingsong Yang
    Department of Chemistry, 414 Wartik Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 101:8289-94. 2004
    ....
  98. ncbi Persistence of the hepatitis B virus covalently closed circular DNA in HepaRG human hepatocyte-like cells
    O Hantz
    INSERM, U871, 69003 Lyon, France
    J Gen Virol 90:127-35. 2009
    ..Analysis of viral DNA showed slow and inefficient conversion of the input relaxed circular DNA into covalently closed circular (CCC) DNA, but no further amplification...
  99. ncbi Plastid-derived single gene minicircles of the dinoflagellate Ceratium horridum are localized in the nucleus
    T Laatsch
    Institute of Botany, Heinrich Heine University Dusseldorf, Dusseldorf, Germany
    Mol Biol Evol 21:1318-22. 2004
    ....
  100. ncbi A family of selfish minicircular chromosomes with jumbled chloroplast gene fragments from a dinoflagellate
    Z Zhang
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 18:1558-65. 2001
    ..The conserved organization of the 9G-9A-9G cores alone favors the idea that they are replicon origins and suggests that they may enable the aberrant minicircles to parasitize the chloroplast's replication machinery as selfish circles...
  101. pmc Construction and characterization of mismatch-containing circular DNA molecules competent for assessment of nick-directed human mismatch repair in vitro
    Erik D Larson
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Nucleic Acids Res 30:E14. 2002
    ..All repair events were inhibited by a peptide that interacts with proliferating cell nuclear antigen and inhibits both mismatch repair and long-patch replication...

Research Grants62

  1. REPLICATION OF DAMAGED DNA IN HUMAN CELLS
    Marila Cordeiro Stone; Fiscal Year: 2004
    ..Duplex circular DNA molecules containing an undamaged di-thymine, a single (cis,syn)TT or a (6-4)TT, within the same sequence and ..
  2. Mechanisms of transcription initiation in mitochondria
    Dmitry Temiakov; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Human mitochondria maintain a small circular DNA that encodes several subunits of the proteins involved in oxidative phosphorylation as well as ribosomal and transport RNA...
  3. Intervention of HBV DNA synthesis and transcription
    Aleem Siddiqui; Fiscal Year: 2013
    ..The final product of this reaction is a partially double stranded DNA, which is converted to covalently closed circular DNA (cccDNA) in the nucleus cccDNA serves as a template for viral mRNA synthesis and proteins...
  4. Integrase-defective lentiviral based influenza vaccines
    Mirella Salvatore; Fiscal Year: 2010
    ..in the integrase gene, do not integrate into the genome, nor do they replicate, but are maintained as episomal circular DNA in the nucleus (E-DNA) in the absence of integration...
  5. Designer Nucleases to Cure Chronic Hepatitis B
    Christoph Seeger; Fiscal Year: 2013
    ..be blocked by therapy with nucleoside analogs, infected hepatocytes are not cured, because covalently closed circular DNA (CCC DNA), the template for transcription of viral RNAs persists in infected cells...
  6. Nuclear Import Pathways for HPV Macromolecules
    JUNONA F MOROIANU; Fiscal Year: 2010
    ..HPV virions consist of a molecule of double-stranded circular DNA contained within an icosahedral capsid composed of L1 major capsid protein and L2 minor capsid protein...
  7. KSHV RTA: more than viral replication
    Jae U Jung; Fiscal Year: 2013
    ..During latency, the KSHV genome persists as a multicopy circular DNA assembled into nucleosomal structures...
  8. PAIRING OF HOMOLOGOUS SEQUENCES IN DROSOPHILA
    KENT GOLIC; Fiscal Year: 2002
    ..two different FRT sites that cannot recombine with each other, so that integration of a sequences from a circular DNA molecule can occur only when two recombination events take place between FRT1 and FRT2 elements on both the ..
  9. Discovery of Anti-HBV cccDNA Compounds from a Unique Natural Products Collection
    Andrea Cuconati; Fiscal Year: 2013
    ..a novel high throughput assay system to detect inhibitors of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) formation and/or maintenance...
  10. KSHV Epigenetic Regulation
    Jae U Jung; Fiscal Year: 2013
    ..During latency, the KSHV genome persists as a multicopy circular DNA assembled into nucleosomal structures...
  11. Screen for an unexploited step in the HBV life cycle
    Andrea Cuconati; Fiscal Year: 2009
    ..to develop a high throughput assay system to detect inhibitors of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) formation and/or maintenance...
  12. Development and Commercial Optimization of Circular DNA Conversion for Opti-pore
    Philip R Buzby; Fiscal Year: 2011
    ..Critical for the Opti-pore process is the proprietary biochemical DNA conversion approach, Circular DNA Conversion (CDC)...
  13. X-LINKED OCULAR ALBINISM & RETINITIS PIGMENTOSA
    Anand Swaroop; Fiscal Year: 1993
    ..Housekeeping genes for essential metabolic functions will be removed by hybridizing single stranded circular DNA from eye/retina cDNA libraries with biotinylated complementary RNA from human B-lymphocytes, and by ..
  14. Single Molecule Sequencing by Nanopore induced Photon Emission (SM-SNIPE)
    Zhiping Weng; Fiscal Year: 2013
    ..Our second Aim is to develop and optimize our proprietary DNA conversion approach, Circular DNA conversion (CDC)...
  15. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2009
    ..product (GenomiPhi from GE Healthcare) the pWGA platform is particularly efficient in amplifying (by 108 fold) circular DNA from low copy numbers (100 copies) of input...
  16. Cloning and Engineering of Nicking enzymes
    Shuang yong Xu; Fiscal Year: 2004
    ..and isolate variants that nick DNA: genetic selection by transformation of I exonuclease treated Sapl nicked-circular DNA to enrich plasmids encoding Sapl nicking activity, molecular break lights generated by Sapl nicking enzyme ..
  17. REGULATION OF HEPADNAVIRUS REPLICATION
    Christoph Seeger; Fiscal Year: 2005
    ..for the assembly and disintegration of capsids and the process governing the synthesis of covalently closed circular DNA, which depends on unidentified cellular factors...
  18. MECHANISM OF BASE EXCISION REPAIR IN HIGHER EUKARYOTES
    Yoshihiro Matsumoto; Fiscal Year: 2003
    ..Since previous studies suggest the importance of the structure of the DNA substrate (circular DNA versus linear DNA) in the PCNA-dependent reaction in vitro, the effect of end-capping of linear DNA on the ..
  19. B CELL ONTOGENY AND ANTIBODY REPERTOIRE
    Katherine Knight; Fiscal Year: 1999
    ..pre-B cells, searching for V-D and D4 heavy chain gene rearrangements by analyzing intrachromosomally-derived circular DNA, developing Rb-SCID mice to determine if rabbit B cells are self-renewing, examining VDJ genes of germfree ..
  20. CONJUGATIVE TRANSPOSON TN 916
    DON CLEWELL; Fiscal Year: 1999
    ..for two hypothetical products, TraO and TraP, proposed to act in regulating the extent to which intermediate circular DNA can integrate into targets within the donor; 6...
  21. HISTONE LIKE PROTEINS ASSOCIATED WITH KINETOPLAST DNA
    DAN RAY; Fiscal Year: 2002
    ..b>Circular DNA molecules are released individually from the network, replicated and then rejoined to the network which ..
  22. BACULOVIRUS MEDIATED GENE DELIVERY OF HEPATITIS C VIRUS
    Harriet Isom; Fiscal Year: 2002
    ..Covalently closed circular DNA is present indicating that, in this system, HBV core particles are capable of delivering newly synthesized HBV ..
  23. STUDIES OF POLYNUCLEOTIDES AND NUCLEIC ACIDS
    Robert Warner; Fiscal Year: 1980
    The relation of dimer size, double-stranded, circular DNA of the replicative form of the bacterial viruses phi X174 and G4 to genetic recombination is being investigated...
  24. INHIBITION OF HUMAN DNA POLYMERASES BY ANTIVIRAL DRUGS
    MARIETTA LEE; Fiscal Year: 1992
    ..DNA sequencing gel methods and model template-primers in the form of oligonucleotide primed ss-circular DNA will be used to analyze the mechanisms involved...
  25. ANALYSIS OF RECOMBINATION IN TRANSFORMATION OF USTILAGO
    William Holloman; Fiscal Year: 1992
    ..Thus, DNA conformation directs the mole of plasmid integration. Gene conversion was observed when circular DNA was used, but was not associated with crossing over...
  26. SYNTHESIS OF NOVEL ANTITUMOR AGENTS
    AMOS SMITH; Fiscal Year: 1991
    ..aphidicolin markedly inhibits the production of progeny retroviruses by interfering with the synthesis of circular DNA. As such aphidicolin may have some efficacy in the area of Acquired Immune Deficiency Syndrome...
  27. True-Isothermal Plasmid Amplication System
    Huimin Kong; Fiscal Year: 2005
    ..Second, our method can amplify both the specific target sequence flanked by two primers and the entire circular DNA. Plasmid DNA purification and analysis is an essential step for DNA cloning, sequencing and screening...
  28. A GENETIC ANALYSIS OF HIV-1 INTEGRATION
    Mark Muesing; Fiscal Year: 2004
    ..An HIV shuttle vector system has been developed which allows direct cloning of circular DNA forms into bacteria, and which will facilitate recovery and characterization of these suppressor mutants...
  29. MAMMALIAN DNA REPLICATION ORIGINS
    Joel Huberman; Fiscal Year: 1990
    ..Third, the origin regions will be tested for their ability to allow circular DNA molecules containing them to replicate autonomously in mammalian cells...
  30. LINEAR AND CIRCULAR POLYMER GELL ELECTROPHORESIS
    Monica Olvera de la Cruz; Fiscal Year: 1992
    ..In particular gel electrophoresis of configurations occurring in closed circular DNA will be analyzed...
  31. TOPOLOGY GEOMETRY AND ENERGETICS OF CLOSED CIRCULAR DNA
    William Bauer; Fiscal Year: 1992
    ..Writhe and surface twist will be calculated for wrapping of closed circular DNA on a connected series of proteins of various geometric shapes...
  32. DROSOPHILA GENE DISRUPTION
    KENT GOLIC; Fiscal Year: 1999
    ..The rationale is that the linear fragment should be more recombinogenic that circular DNA. Two different variants of this strategy will be tried, though both eventually will use the beta2 tubulin ..
  33. THE ENZYMOLOGY OF DNA REPLICATION IN YEAST
    John Scott; Fiscal Year: 1980
    ..The object of the study will be small circular DNA plasmids which replicate in yeast under nuclear control...
  34. Massively Parallel Cloning and Sequencing of DNA
    Xiaohua Huang; Fiscal Year: 2007
    ..We have demonstrated that hundreds of millions of single circular DNA molecules can be separated and cloned in massive parallel on solid supports using a powerful isothermal DNA ..
  35. DIRECTOR REARRANGEMENT OF THE MAMMALIAN GENOME IN VIVO
    Philip Youderian; Fiscal Year: 1991
    ..These include whether FLP can mediate (1) reciprocal translocations, (2) the integration of a circular DNa carrying a FLP site into an FSV, (3) chromosome loss, and (4) efficient ring (or deficiency) chromosome ..
  36. UNDERSTANDING THE ROLE OF THE RAD12 HELICASE IN S POMBE
    JUSTIN HOPE; Fiscal Year: 2003
    ..e. they add positive supercoils to relaxed covalently closed circular DNA. I will also use both microarrays and DNA affinity binding to identify genes whose expression is rad12 ..
  37. CONFORMATIONAL PROPERTIES OF DNA CATENANES
    Alexander V Vologodskii; Fiscal Year: 2010
    ..Combining computer simulations and experiments, we will try to understand the mechanism of high topological selectivity of DNA resolvases. ..
  38. Mechanisms of Avian Hepadnavirus Replication
    DANIEL LOEB; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  39. Anti-cancer activity of Scutellaria baicalensis
    David Zhang; Fiscal Year: 2003
    ....
  40. Tangle Analysis of DNA Recombinases & Related Proteins
    ISABEL DARCY; Fiscal Year: 2005
    ..Apart from the recombination systems investigated in this proposal, the tangle-analysis tools that we develop will be extended to other recombinases and used to investigate related systems such as topoisomerases. ..
  41. CELLULAR BIOLOGY OF THE TRABECULAR MESHWORK
    Michael P Fautsch; Fiscal Year: 2010
    ..These regions will be "preferential flow" regions, and aqueous tracers should appear in these regions first. If this occurs, it would change our basic understanding of how aqueous passes through the TM (aim 5). ..
  42. Structural mechanism of DNA segregation by the pSK41 par system
    Maria Schumacher; Fiscal Year: 2010
    ..Thus, understanding the structural basis for DNA segregation by this par system will provide several points of potential therapeutic intervention against pSK41 harboring multidrug resistant S. aureus strains. ..
  43. Human Polyclonal Antibody Production in Chickens
    Philip Leighton; Fiscal Year: 2002
    ..The proposed technology will offer several advantages over current antibody production methods and thus will easily capture a share of this market. ..
  44. NONPOLAR NUCLEOSIDE ISOSTERES AS BIOMOLECULAR PROBES
    ERIC KOOL; Fiscal Year: 2002
    ..abstract_text> ..
  45. NOVEL PROBE TOPOLOGIES IN BIOMEDICAL DIAGNOSTICS
    ERIC KOOL; Fiscal Year: 2002
    ..Over the long term, it is hoped that this approach will give rise to clinically useful methods for the early diagnosis of diseases. ..
  46. TRAINING GRANT IN MOLECULAR BIOPHYSICS
    WILMA OLSON; Fiscal Year: 2003
    ..The requested funds help to attract a pool of outstanding predoctoral students, to unify existing graduate offerings, and to offer an independent graduate curriculum in molecular biophysics. ..
  47. Mechanistic Studies of Somatic Hypermutation
    ERIK LARSON; Fiscal Year: 2004
    ..In addition, identification of critical hypermutation molecules and their repair roles will provide new therapeutics that could enhance the efficiency of immunization and decrease the genomic instability associated with cancer. ..
  48. Pulmonary delivery of nicotine using the AERx System
    Stephen Farr; Fiscal Year: 2005
    ..The long-term goal of this proposed project is to develop an inhalation product (the AERx-nicotine) as a therapy for smoking cessation. ..
  49. Gene Expression Analyses During IFN Antiviral Therapy
    Robert Lanford; Fiscal Year: 2005
    ..These data will help determine why interferon therapy is often unsuccessful for chronic HCV infections and provide cellular targets for future therapies. ..
  50. Control of nematode development
    Eric Lambie; Fiscal Year: 2005
    ..Therefore, the results of this work are likely to be highly significant with regard to the etiology of human disease. ..
  51. Nanomedicine Center for Protein Deposition Diseases(RMI)
    Yuri Lyubchenko; Fiscal Year: 2004
    ..We assembled a multidisciplinary team of 12 investigators with broad expertise in nanobiology, imaging, spectroscopy, single molecule biophysics, proteomics, drug delivery and medicine. ..
  52. Genetic Analysis of Amplified Genomic DNA Archives
    Paul Lizardi; Fiscal Year: 2005
    ..abstract_text> ..
  53. DNA/RNA Quadruplexes: Structure, Stability, Interactions
    RICHARD SHAFER; Fiscal Year: 2006
    ..This combination of approaches will afford a detailed examination of the conformation and interaction properties of the very important nucleic acid species. [unreadable] [unreadable]..
  54. CHEMICAL AND BIOLOGICAL MIMICRY OF TELOMERASE
    ERIC KOOL; Fiscal Year: 2007
    ..Chemical approaches to telomere elongation have the long-term potential to solve important problems in transplantation medicine, and to lead to new treatments for senescence-related diseases. ..
  55. 2007 Molecular Biology of Hepatitis B Viruses Meeting
    William Mason; Fiscal Year: 2007
    ..Limited support for meeting materials and organizational[unreadable] functions is also needed. ..
  56. Senescence and Longevity Modulating Genes, WRN and BLM
    Judith Campisi; Fiscal Year: 2008
    ..Our studies will provide important insights into how WRN and BLM postpone the development of aging phenotypes and the development of cancer in humans. ..
  57. Structural studies on the P1 plasmid partition apparatus
    Maria Schumacher; Fiscal Year: 2009
    ....
  58. Probes for detection of DNA accessibility in chromatin
    Paul Lizardi; Fiscal Year: 2009
    ..Evaluation criteria will include signal/noise, signal persistence, spatial resolution, time resolution, and robustness for use in routine biological experiments. ..
  59. PATHOGENESIS OF HEPATITIS B VIRUS IN TRANSGENIC MICE
    FRANCIS VINCENT CHISARI; Fiscal Year: 2010
    ..Their impact on public health could be substantial, since more than 350 million people are chronically infected by HBV and 1million people die each year of this infection. ..