dna packaging

Summary

Summary: The folding of an organism's DNA molecule into a compact, orderly structure that fits within the limited space of a CELL or VIRUS PARTICLE.

Top Publications

  1. ncbi Interaction of the adenovirus major core protein precursor, pVII, with the viral DNA packaging machinery
    Wei Zhang
    Department of Pharmacology, University of Texas Health Science Center, San Antonio, TX 78229 3900, USA
    Virology 334:194-202. 2005
  2. ncbi Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number
    Christopher T Campbell
    Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
    Biochim Biophys Acta 1819:921-9. 2012
  3. pmc Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions
    Sherwood R Casjens
    Division of Cell Biology and Immunology, Department of Pathology, University of Utah Medical School, Salt Lake City, UT, USA
    Methods Mol Biol 502:91-111. 2009
  4. pmc Portal-large terminase interactions of the bacteriophage T4 DNA packaging machine implicate a molecular lever mechanism for coupling ATPase to DNA translocation
    Shylaja Hegde
    Department of Biology, The Catholic University of America, Washington, DC, USA
    J Virol 86:4046-57. 2012
  5. ncbi The bacteriophage DNA packaging machine
    Michael Feiss
    Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
    Adv Exp Med Biol 726:489-509. 2012
  6. pmc In vitro and in vivo delivery of genes and proteins using the bacteriophage T4 DNA packaging machine
    Pan Tao
    Department of Biology, The Catholic University of America, Washington, DC 20064, USA
    Proc Natl Acad Sci U S A 110:5846-51. 2013
  7. pmc The adenovirus L4-33K protein regulates both late gene expression patterns and viral DNA packaging
    Kai Wu
    Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
    J Virol 87:6739-47. 2013
  8. ncbi Virus DNA translocation: progress towards a first ascent of mount pretty difficult
    Nasib K Maluf
    Department of Microbiology, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
    Mol Microbiol 61:1-4. 2006
  9. pmc DNA packaging motor assembly intermediate of bacteriophage phi29
    Jaya S Koti
    Department of Diagnostic Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
    J Mol Biol 381:1114-32. 2008
  10. pmc Construction of folate-conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells
    S Guo
    Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
    Gene Ther 13:814-20. 2006

Detail Information

Publications206 found, 100 shown here

  1. ncbi Interaction of the adenovirus major core protein precursor, pVII, with the viral DNA packaging machinery
    Wei Zhang
    Department of Pharmacology, University of Texas Health Science Center, San Antonio, TX 78229 3900, USA
    Virology 334:194-202. 2005
    Adenovirus is one of the well-studied double-stranded DNA viruses. However, the mechanisms of its DNA packaging and virion assembly are still not fully understood...
  2. ncbi Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number
    Christopher T Campbell
    Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
    Biochim Biophys Acta 1819:921-9. 2012
    ..This article is part of a Special Issue entitled: Mitochondrial Gene Expression...
  3. pmc Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions
    Sherwood R Casjens
    Division of Cell Biology and Immunology, Department of Pathology, University of Utah Medical School, Salt Lake City, UT, USA
    Methods Mol Biol 502:91-111. 2009
    ..types of ends reflect differing DNA replication strategies and especially differing terminase actions during DNA packaging. In general, complete genome sequence determination does not by itself elucidate the nature of these ends, so ..
  4. pmc Portal-large terminase interactions of the bacteriophage T4 DNA packaging machine implicate a molecular lever mechanism for coupling ATPase to DNA translocation
    Shylaja Hegde
    Department of Biology, The Catholic University of America, Washington, DC, USA
    J Virol 86:4046-57. 2012
    b>DNA packaging by double-stranded DNA bacteriophages and herpesviruses is driven by a powerful molecular machine assembled at the portal vertex of the empty prohead...
  5. ncbi The bacteriophage DNA packaging machine
    Michael Feiss
    Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
    Adv Exp Med Biol 726:489-509. 2012
    ..The phage packaging machine has emerged as an excellent model for understanding the molecular machines, given the mechanistic parallels between terminases, helicases, and numerous motor proteins...
  6. pmc In vitro and in vivo delivery of genes and proteins using the bacteriophage T4 DNA packaging machine
    Pan Tao
    Department of Biology, The Catholic University of America, Washington, DC 20064, USA
    Proc Natl Acad Sci U S A 110:5846-51. 2013
    The bacteriophage T4 DNA packaging machine consists of a molecular motor assembled at the portal vertex of an icosahedral head...
  7. pmc The adenovirus L4-33K protein regulates both late gene expression patterns and viral DNA packaging
    Kai Wu
    Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
    J Virol 87:6739-47. 2013
    ..The L4-33K mutant virus produces only empty capsids, indicating a defect in viral DNA packaging. We demonstrate that L4-33K does not preferentially bind to viral packaging sequences in vivo, and mutation of ..
  8. ncbi Virus DNA translocation: progress towards a first ascent of mount pretty difficult
    Nasib K Maluf
    Department of Microbiology, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
    Mol Microbiol 61:1-4. 2006
    ..between the fivefold symmetry of the shell vertex and the 12-fold symmetry of the portal protein has prompted DNA packaging models in which ATP-driven portal protein rotation drives DNA translocation...
  9. pmc DNA packaging motor assembly intermediate of bacteriophage phi29
    Jaya S Koti
    Department of Diagnostic Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
    J Mol Biol 381:1114-32. 2008
    Unraveling the structure and assembly of the DNA packaging ATPases of the tailed double-stranded DNA bacteriophages is integral to understanding the mechanism of DNA translocation...
  10. pmc Construction of folate-conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells
    S Guo
    Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
    Gene Ther 13:814-20. 2006
    ....
  11. pmc Integrative DNA methylation and gene expression analyses identify DNA packaging and epigenetic regulatory genes associated with low motility sperm
    Sara E Pacheco
    Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 6:e20280. 2011
    ..We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function...
  12. pmc Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations
    Derek N Fuller
    Department of Physics, University of California, San Diego, Mail Code 0379, 9500 Gilman Drive, La Jolla, CA 92093, USA
    J Mol Biol 373:1113-22. 2007
    ....
  13. ncbi Paternal contributions: new functional insights for spermatozoal RNA
    Claudia Lalancette
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
    J Cell Biochem 104:1570-9. 2008
    ..This review presents and discusses the functional significance of spermatozoal RNA in relation to some recent advances in the field...
  14. ncbi In vitro DNA packaging of PRD1: a common mechanism for internal-membrane viruses
    Nelli J Strömsten
    Department of Biological and Environmental Sciences and Institute of Biotechnology, Biocenter 2, P O Box 56 Viikinkaari 5, FIN 00014, University of Helsinki, Helsinki, Finland
    J Mol Biol 348:617-29. 2005
    ..Our finding here strongly supports the idea that all these viruses infecting hosts in all domains of life had a common ancestor...
  15. pmc Role of channel lysines and the "push through a one-way valve" mechanism of the viral DNA packaging motor
    Huaming Fang
    Nanobiomedical Center, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, Ohio, USA
    Biophys J 102:127-35. 2012
    ..The results support our recent findings regarding the dsDNA packaging mechanism known as the "push through a one-way valve"...
  16. ncbi Genome gating in tailed bacteriophage capsids
    Paulo Tavares
    Unité de Virologie Moléculaire et Structurale, Gif sur Yvette, France
    Adv Exp Med Biol 726:585-600. 2012
    ..Recent exciting advances are providing new molecular insights on the mechanisms that ensure precise coordination of these critical steps required both for stable viral genome packaging and for its efficient release to initiate infection...
  17. ncbi DNA packaging proteins Glom and Glom2 coordinately organize the mitochondrial nucleoid of Physarum polycephalum
    Kie Itoh
    Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464 8602, Japan
    Mitochondrion 11:575-86. 2011
    ..These data suggest that Glom2 may organize the mt-nucleoid coordinately with Glom...
  18. ncbi Challenging packaging limits and infectivity of phage λ
    Elmar Nurmemmedov
    Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE 221 00, Lund, Sweden
    J Mol Biol 415:263-73. 2012
    ..Further, we demonstrated that the phage production rate is modulated by the presence of multivalent ionic species. The biological consequences of these findings are discussed...
  19. pmc Real-time sensing and discrimination of single chemicals using the channel of phi29 DNA packaging nanomotor
    Farzin Haque
    Nanobiotechnology Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
    ACS Nano 6:3251-61. 2012
    ..This article reports a method for precise detection of single chemicals. The hub of the bacteriophage phi29 DNA packaging motor is a connector consisting of 12 protein subunits encircled into a 3...
  20. pmc Staphylococcal pathogenicity island DNA packaging system involving cos-site packaging and phage-encoded HNH endonucleases
    Nuria Quiles-Puchalt
    Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
    Proc Natl Acad Sci U S A 111:6016-21. 2014
    ..Cos-site packaging in Staphylococcus aureus is additionally unique in that it requires the HNH nuclease, carried only by cos phages, in addition to the large terminase subunit, for cos-site cleavage and melting...
  21. ncbi "Push through one-way valve" mechanism of viral DNA packaging
    Hui Zhang
    Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY, USA
    Adv Virus Res 83:415-65. 2012
    ..Viral DNA packaging motors are mainly composed of the connector channel and two DNA packaging enzymes...
  22. pmc The ATPase of the phi29 DNA packaging motor is a member of the hexameric AAA+ superfamily
    Chad Schwartz
    Nanobiotechnology Center, College of Pharmacy and Markey Cancer Center, University of Kentucky, Lexington, KY, USA
    Virology 443:20-7. 2013
    ..The ATPase of phi29 DNA packaging motor has long been a subject of debate in terms of stoichiometry and mechanism of action...
  23. pmc The structure of the NTPase that powers DNA packaging into Sulfolobus turreted icosahedral virus 2
    Lotta J Happonen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    J Virol 87:8388-98. 2013
    ..5. The overall fold of B204 places it in the FtsK-HerA superfamily of P-loop ATPases, whose cellular and viral members have been suggested to share a DNA-translocating mechanism. ..
  24. pmc Three reversible and controllable discrete steps of channel gating of a viral DNA packaging motor
    Jia Geng
    Nanobiomedical Center, SEEBME, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45267, USA
    Biomaterials 32:8234-42. 2011
    The channel of the viral DNA packaging motor allows dsDNA to enter the protein procapsid shell during maturation and to exit during infection...
  25. ncbi Herpes simplex virus capsid assembly and DNA packaging: a present and future antiviral drug target
    Joel D Baines
    Department of Microbiology and Immunology, New York State College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
    Trends Microbiol 19:606-13. 2011
    ..The goal of this review is to outline these intranuclear assembly steps and illustrate potential and existing antiviral strategies that exploit them...
  26. pmc Structure and assembly of the essential RNA ring component of a viral DNA packaging motor
    Fang Ding
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 108:7357-62. 2011
    Prohead RNA (pRNA) is an essential component in the assembly and operation of the powerful bacteriophage 29 DNA packaging motor...
  27. pmc Role of φ29 connector channel loops in late-stage DNA packaging
    Shelley Grimes
    Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
    J Mol Biol 410:50-9. 2011
    ..This vertex is the site of assembly of the DNA packaging motor, and the connector has a central channel through which viral DNA passes during genome packaging and ..
  28. ncbi Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process
    Luis R Comolli
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Virology 371:267-77. 2008
    The goal of the work reported here is to understand the precise molecular mechanism of the process of DNA packaging in dsDNA bacteriophages...
  29. pmc Genome packaging in viruses
    Siyang Sun
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 2054, USA
    Curr Opin Struct Biol 20:114-20. 2010
    ..Here we discuss various aspects of genome packaging and compare the mechanisms proposed for packaging motors on the basis of structural information...
  30. ncbi Mechanochemistry of a viral DNA packaging motor
    Jin Yu
    Department of Physics, University of California, Berkeley, CA 94720, USA
    J Mol Biol 400:186-203. 2010
    ..The push and roll model provides a new perspective on how a multimeric ATPase transports DNA, and it might apply to other ring motors as well...
  31. ncbi The portal protein plays essential roles at different steps of the SPP1 DNA packaging process
    Anabela Isidro
    Instituto de Tecnologia Quimica e Biologica, 2781 901 Oeiras, Portugal
    Virology 322:253-63. 2004
    ..The portal protein is an essential component of this DNA packaging machine...
  32. pmc Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein
    Leonor Oliveira
    Unité de Virologie Moléculaire et Structurale, Unite Mixte de Recherche, CNRS 2472, Institut Fédératif de Recherche 1157, and IFR 115, Bâtiment 14B, Avenue de la Terrasse, 91190 Gif sur Yvette, France
    J Biol Chem 285:7366-73. 2010
    b>DNA packaging in tailed bacteriophages and other viruses requires assembly of a complex molecular machine at a specific vertex of the procapsid...
  33. ncbi The bacteriophage DNA packaging motor
    Venigalla B Rao
    Department of Biology, The Catholic University of America, Washington, D C 20064, USA
    Annu Rev Genet 42:647-81. 2008
    ..Recent advances permit experiments that can critically test the packaging models. The viral genome translocation mechanism is of general interest, given the parallels between terminases, helicases, and other motor proteins...
  34. ncbi The DNA-packaging nanomotor of tailed bacteriophages
    Sherwood R Casjens
    Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, 15 North Medical Drive East, Salt Lake City, Utah 84112, USA
    Nat Rev Microbiol 9:647-57. 2011
    ....
  35. pmc The herpes simplex virus 1 UL17 protein is the second constituent of the capsid vertex-specific component required for DNA packaging and retention
    Katerina Toropova
    Department of Structural Biology, University of Pittsburgh, Biomedical Science Tower 3, 3501 5th Ave, Pittsburgh, PA 15260, USA
    J Virol 85:7513-22. 2011
    The herpes simplex virus (HSV) UL17 and UL25 minor capsid proteins are essential for DNA packaging. They are thought to comprise a molecule arrayed in five copies around each of the capsid vertices...
  36. pmc Strand and nucleotide-dependent ATPase activity of gp16 of bacterial virus phi29 DNA packaging motor
    Tae Jin Lee
    Department of Biomedical Engineering, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
    Virology 380:69-74. 2008
    ..The results suggest that pRNA accelerates gp16 ATPase activity more significantly than genomic dsDNA, albeit both pRNA and genomic DNA are involved in the contact with gp16 during DNA packaging.
  37. pmc Specificity of staphylococcal phage and SaPI DNA packaging as revealed by integrase and terminase mutations
    Carles Ubeda
    Kimmel Center for Biology and Medicine, Skirball Institute, Department of Microbiology, New York University Medical Center, New York, NY 10016, USA
    Mol Microbiol 72:98-108. 2009
    ..TerS, however, determines DNA packaging specificity but not the choice of large versus small capsids...
  38. pmc Revolution rather than rotation of AAA+ hexameric phi29 nanomotor for viral dsDNA packaging without coiling
    Chad Schwartz
    Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
    Virology 443:28-39. 2013
    ..Here we report a revolution rather than rotation mechanism for the bacteriophage phi29 DNA packaging motor. The phi29 motor contains six copies of the ATPase (Schwartz et al...
  39. pmc The C-terminal domain of the bacteriophage T4 terminase docks on the prohead portal clip region during DNA packaging
    Aparna Banerjee Dixit
    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108N Greene St, Baltimore, MD 21201, USA
    Virology 446:293-302. 2013
    ..Such a terminase-portal orientation fits better to a proposed "DNA crunching" compression packaging motor and to portal determined DNA headful cutting. ..
  40. ncbi Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29
    Nicholas Keller
    Department of Physics, University of California, San Diego, 9500 Gilman Dr, La Jolla, California 92093, USA
    Phys Rev Lett 112:248101. 2014
    ..Thus, repulsive interactions facilitate packaging despite increasing the energy of the theoretical optimum spooled DNA conformation...
  41. pmc The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4
    Vishal I Kottadiel
    Department of Biology, The Catholic University of America, Washington, DC 20064, USA
    Proc Natl Acad Sci U S A 109:20000-5. 2012
    ..These results lead to a four-state mechanochemical model that provides insights into the mechanisms of translocation of an intricately branched concatemeric viral genome...
  42. ncbi Single-molecule studies of viral DNA packaging
    Douglas E Smith
    Department of Physics, University of California, San Diego, La Jolla, United States
    Curr Opin Virol 1:134-41. 2011
    ..Single-molecule fluorescence methods have also been used to measure packaging kinetics and motor conformations. Here we review recent discoveries made using these new techniques...
  43. ncbi DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA
    Alexander P Hynes
    Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St John s, NL, A1B 3X9, Canada
    Mol Microbiol 85:314-25. 2012
    ..This subpopulation's role in producing and releasing the RcGTA particles explains the lack of observed cell lysis in cultures...
  44. pmc Functional identification of the DNA packaging terminase from Pseudomonas aeruginosa phage PaP3
    Xiaodong Shen
    Department of Microbiology, Third Military Medical University, Chongqing, China
    Arch Virol 157:2133-41. 2012
    Terminase proteins are responsible for DNA recognition and initiation of DNA packaging in phages...
  45. pmc Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation
    Aparna Banerjee Dixit
    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 109:20419-24. 2012
    ....
  46. pmc Channel size conversion of Phi29 DNA-packaging nanomotor for discrimination of single- and double-stranded nucleic acids
    Jia Geng
    Nanobiotechnology Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
    ACS Nano 7:3315-23. 2013
    ..This finding of size alterations in reengineered motor channels expands the potential application of the phi29 DNA-packaging motor in nanomedicine, nanobiotechnology, and high-throughput single-pore DNA sequencing...
  47. pmc Mechanism of one-way traffic of hexameric phi29 DNA packaging motor with four electropositive relaying layers facilitating antiparallel revolution
    Zhengyi Zhao
    Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
    ACS Nano 7:4082-92. 2013
    ..The viral DNA packaging motor has been believed to be a rotational machine...
  48. pmc A promiscuous DNA packaging machine from bacteriophage T4
    Zhihong Zhang
    Department of Biology, The Catholic University of America, Washington, District of Columbia, United States of America
    PLoS Biol 9:e1000592. 2011
    ..These results suggest that the phage DNA packaging machine has unusual conformational plasticity, powering DNA into an apparently passive capsid receptacle, ..
  49. pmc Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4
    Anton S Petrov
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    J Struct Biol 174:137-46. 2011
    ..In all cases packaging in a specific conformation occurs as a result of interplay between bending stresses experienced by the confined polymer and interactions between the strands...
  50. pmc Role of the CCA bulge of prohead RNA of bacteriophage ø29 in DNA packaging
    Wei Zhao
    Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
    J Mol Biol 383:520-8. 2008
    The oligomeric ring of prohead RNA (pRNA) is an essential component of the ATP-driven DNA packaging motor of bacteriophage ø29...
  51. pmc Robust properties of membrane-embedded connector channel of bacterial virus phi29 DNA packaging motor
    Peng Jing
    Department of Biomedical Engineering, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
    Mol Biosyst 6:1844-52. 2010
    ..Herein, we demonstrate the robust characteristics of the connector of the bacteriophage phi29 DNA packaging motor by single pore electrophysiological assays...
  52. pmc Structural changes of bacteriophage phi29 upon DNA packaging and release
    Ye Xiang
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 2054, USA
    EMBO J 25:5229-39. 2006
    ..Gene product 3, bound to the 5' ends of the genome, appears to be positioned within the expanded connector, which may potentiate the release of DNA-packaging machine components, creating a binding site for attachment of the tail...
  53. pmc DNA ejection from bacteriophage T5: analysis of the kinetics and energetics
    Marta de Frutos
    Laboratoire de Physique des Solides, UMR CNRS 8502, Universite Paris Sud, 91405 Orsay, Cedex, France
    Biophys J 88:1364-70. 2005
    ..Both effects contribute to shorten or to lengthen the pause time between the different stages explaining why the T5 DNA ejection is so slow compared to other types of phage...
  54. ncbi Structure, assembly, and DNA packaging of the bacteriophage T4 head
    Lindsay W Black
    Department of Biochemistry and Molecular Biology, University of Maryland Medical School, Baltimore, Maryland, USA
    Adv Virus Res 82:119-53. 2012
    ..Extensive mutagenesis, combined with atomic structures of the DNA packaging/terminase proteins gp16 and gp17, elucidated the ATPase and nuclease functional motifs involved in DNA ..
  55. pmc Adjustable ellipsoid nanoparticles assembled from re-engineered connectors of the bacteriophage phi29 DNA packaging motor
    Feng Xiao
    Department of Biomedical Engineering, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45221, USA
    ACS Nano 3:2163-70. 2009
    ..containing 84 subunits or 7 dodecamers of the re-engineered core protein of the bacteriophage phi29 DNA packaging motor was constructed. Homogeneous nanoparticles were obtained with simple one-step purification...
  56. pmc Mutational analysis of the herpes simplex virus type 1 DNA packaging protein UL33
    Frauke Beilstein
    MRC Virology Unit, University of Glasgow, Church Street, Glasgow G11 5JR, United Kingdom
    J Virol 83:8938-45. 2009
    ..These data indicate that the ability of UL33 to interact with UL28 is probably necessary, but not sufficient, to support viral growth and DNA packaging.
  57. ncbi The phiX174 protein J mediates DNA packaging and viral attachment to host cells
    Ricardo A Bernal
    Department of Biological Sciences, Purdue University, Lilly Hall, 915 W State Street, West Lafayette, IN 47907 2054, USA
    J Mol Biol 337:1109-22. 2004
    ..particles containing the smaller DNA-binding protein cannot be generated due to procapsid instability during DNA packaging. However, chimeric alpha3 and G4 phages, containing the phiX174 DNA-binding protein in place of the endogenous ..
  58. pmc Analysis of intermolecular base pair formation of prohead RNA of the phage phi29 DNA packaging motor using NMR spectroscopy
    Aya Kitamura
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Nucleic Acids Res 36:839-48. 2008
    The bacteriophage ø29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers...
  59. pmc Fabrication of stable and RNase-resistant RNA nanoparticles active in gearing the nanomotors for viral DNA packaging
    Jing Liu
    Nanobiomedical Center, SEEBME, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
    ACS Nano 5:237-46. 2011
    ..Our results demonstrate that it is practical to produce RNase-resistant, biologically active, and stable RNA for application in nanotechnology...
  60. pmc A-tract clusters may facilitate DNA packaging in bacterial nucleoid
    Michael Y Tolstorukov
    Laboratory of Experimental and Computational Biology, National Cancer Institute Bethesda, MD 20892, USA
    Nucleic Acids Res 33:3907-18. 2005
    ....
  61. ncbi Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems
    A M Burroughs
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Dyn 3:48-65. 2007
    We present an overview of comparative genomics of ATP-dependent DNA packaging systems of viruses...
  62. pmc Single-molecule and FRET fluorescence correlation spectroscopy analyses of phage DNA packaging: colocalization of packaged phage T4 DNA ends within the capsid
    Krishanu Ray
    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
    J Mol Biol 395:1102-13. 2010
    ..The analysis suggests that a DNA loop, rather than a DNA end, is translocated by the packaging motor to fill the procapsid...
  63. pmc Portal control of viral prohead expansion and DNA packaging
    Krishanu Ray
    Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Virology 391:44-50. 2009
    ..These data suggest the portal controls the expansion of the major capsid protein lattice during prohead maturation, and that this expansion is necessary for DNA protection but not for packaging...
  64. ncbi DNA packaging and delivery machines in tailed bacteriophages
    John E Johnson
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Curr Opin Struct Biol 17:237-43. 2007
    ..epsilon15, P22 and phi29, were determined at resolutions sufficient to visualize details of the machinery for DNA packaging and delivery, as well as the organization of the double-stranded DNA within the particles...
  65. pmc The DNA maturation domain of gpA, the DNA packaging motor protein of bacteriophage lambda, contains an ATPase site associated with endonuclease activity
    Marcos E Ortega
    Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, CO 80262, USA
    J Mol Biol 373:851-65. 2007
    ..b>DNA packaging requires an ATPase catalytic site situated in the N terminus of the protein...
  66. pmc Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain
    Marta Nadal
    Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
    Proc Natl Acad Sci U S A 107:16078-83. 2010
    ..We also show that the nuclease function can be inactivated by raltegravir, a recently approved anti-AIDS drug that targets the HIV integrase...
  67. ncbi The headful packaging nuclease of bacteriophage T4
    Tanfis I Alam
    Department of Biology, The Catholic University of America, Washington, DC 20064, USA
    Mol Microbiol 69:1180-90. 2008
    ..These results lead to hypotheses concerning how phage headful nucleases cut the viral genomes before and after, but not during, DNA packaging.
  68. ncbi The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces
    Siyang Sun
    Department of Biological Sciences, Purdue University, 915 W State Street, West Lafayette, IN 47907 2054, USA
    Cell 135:1251-62. 2008
    ..We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4...
  69. pmc Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability
    Derek N Fuller
    Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:16868-73. 2007
    Terminase enzyme complexes, which facilitate ATP-driven DNA packaging in phages and in many eukaryotic viruses, constitute a wide and potentially diverse family of molecular motors about which little dynamic or mechanistic information is ..
  70. ncbi The DNA translocating ATPase of bacteriophage T4 packaging motor
    Kiran R Kondabagil
    Department of Biology, The Catholic University of America, Washington, DC 20064, USA
    J Mol Biol 363:786-99. 2006
    ..An ATPase activity is stimulated when proheads, gp17, and DNA are actively engaged in the DNA packaging mode...
  71. pmc Efficient DNA packaging of bacteriophage PRD1 requires the unique vertex protein P6
    Nelli J Karhu
    Department of Biological and Environmental Science, Institute of Biotechnology, University of Helsinki, Biocenter 2, Viikinkaari 5, FIN 00014 University of Helsinki, Finland
    J Virol 81:2970-9. 2007
    ..A packaging model for bacteriophage PRD1, based on previous results and those obtained in this study, is presented...
  72. pmc Langevin dynamics simulations of genome packing in bacteriophage
    Christopher Forrey
    Department of Polymer Science and Engineering, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA
    Biophys J 91:25-41. 2006
    ..Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general...
  73. pmc Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging
    Feng Xiao
    Department of Biomedical Engineering, College of Engineering College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA
    Nucleic Acids Res 36:6620-32. 2008
    ..This new mechanism was tested by redesigning two artificial RNAs that formed hexamer and packaged DNA. The results confirmed the stoichiometry of pRNA on the motor was the common multiple of two and three, thus, a hexamer...
  74. ncbi Mechanistic coupling of bacteriophage T4 DNA packaging to components of the replication-dependent late transcription machinery
    Lindsay W Black
    Department of Biochemistry and Molecular Biology, University of Maryland Medical School, Baltimore, Maryland 21201 1503, USA
    J Biol Chem 281:25635-43. 2006
    Regulation of the terminal stage of viral DNA development, DNA packaging, is poorly understood...
  75. pmc Mutational analysis of the herpes simplex virus type 1 UL25 DNA packaging protein reveals regions that are important after the viral DNA has been packaged
    Maureen O'Hara
    MRC Virology Unit, University of Glasgow, Church Street, Glasgow G11 5JR, United Kingdom
    J Virol 84:4252-63. 2010
    ..The impacts of these mutations on viral DNA packaging, virus assembly, and growth were examined...
  76. pmc Structural characterization of the UL25 DNA-packaging protein from herpes simplex virus type 1
    Brian R Bowman
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    J Virol 80:2309-17. 2006
    ..The herpes simplex virus type 1 UL25 protein is incorporated into the capsid during DNA packaging, and previous studies of a null mutant have demonstrated that its function is essential at the late stages of ..
  77. pmc Construction of bacteriophage phi29 DNA packaging motor and its applications in nanotechnology and therapy
    Tae Jin Lee
    Department of Biomedical Engineering, The Vontz Center for Molecular Studies, College of Engineering and College of Medicine, University of Cincinnati, Room 1301, Cincinnati, OH 45267, USA
    Ann Biomed Eng 37:2064-81. 2009
    ..The novelty and ingenious design of the bacterial virus phi29 DNA packaging motor and its parts inspired the synthesis of this motor and its components as biomimetics...
  78. ncbi Self-association properties of the bacteriophage lambda terminase holoenzyme: implications for the DNA packaging motor
    Nasib K Maluf
    Department of Pharmaceutical Sciences, University of Colorado Health Sciences Center, 4200 East Ninth Ave, C238, Denver, CO 80262, USA
    J Mol Biol 347:523-42. 2005
    ..Both the heterotrimer and the higher-order species possess site-specific cos cleavage activity, as well as DNA packaging activity; however, the heterotrimer is dependent upon Escherichia coli integration host factor (IHF) for these ..
  79. pmc Linker insertion mutations in the herpes simplex virus type 1 UL28 gene: effects on UL28 interaction with UL15 and UL33 and identification of a second-site mutation in the UL15 gene that suppresses a lethal UL28 mutation
    Jennie G Jacobson
    Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, W1256 Biomedical Science Tower, Pittsburgh, PA 15261, USA
    J Virol 80:12312-23. 2006
    ..The isolation of an intergenic suppressor mutant provides direct genetic evidence of an association between the UL28 and UL15 proteins and demonstrates that this association is essential for DNA cleavage and packaging...
  80. pmc Defining molecular and domain boundaries in the bacteriophage phi29 DNA packaging motor
    Marc C Morais
    Department of Biochemistry and Molecular Biology, 301 University Boulevard, University of Texas Medical Branch, Galveston, TX 77555 0647, USA
    Structure 16:1267-74. 2008
    Cryo-electron microscopy (cryo-EM) studies of the bacteriophage phi29 DNA packaging motor have delineated the relative positions and molecular boundaries of the 12-fold symmetric head-tail connector, the 5-fold symmetric prohead RNA (..
  81. pmc DNA packaging-associated hyper-capsid expansion of bacteriophage t3
    Philip Serwer
    Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229 3900, USA
    J Mol Biol 397:361-74. 2010
    Evidence that in vivo bacteriophage T3 DNA packaging includes capsid hyper-expansion that is triggered by lengthening of incompletely packaged DNA (ipDNA) is presented here...
  82. ncbi An ATP hydrolysis sensor in the DNA packaging motor from bacteriophage T4 suggests an inchworm-type translocation mechanism
    Bonnie Draper
    Department of Biology, The Catholic University of America, Washington, DC 20064, USA
    J Mol Biol 369:79-94. 2007
    ..We suggest that the C-motif is an ATP hydrolysis sensor, linking product release to mechanical motion. A novel terminase-driven mechanism is proposed for translocation of dsDNA in viruses...
  83. pmc Alanine scanning and Fe-BABE probing of the bacteriophage ø29 prohead RNA-connector interaction
    Rockney Atz
    Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
    J Mol Biol 369:239-48. 2007
    The DNA packaging motor of the Bacillus subtilis bacteriophage ø29 prohead is comprised in part of an oligomeric ring of 174 base RNA molecules (pRNA) positioned near the N termini of subunits of the dodecameric head-tail connector...
  84. pmc Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage phi29
    John Peter Rickgauer
    Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
    Biophys J 94:159-67. 2008
    ..Here, we present measurements of viral DNA packaging in bacteriophage phi29 using an improved optical tweezers method that allows DNA translocation to be measured ..
  85. pmc Counting of six pRNAs of phi29 DNA-packaging motor with customized single-molecule dual-view system
    Dan Shu
    Department of Comparative Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
    EMBO J 26:527-37. 2007
    ..The stalled motors were restarted to observe the motion of DNA packaging in real time...
  86. pmc Viral DNA packaging studied by fluorescence correlation spectroscopy
    Chandran R Sabanayagam
    Biophys J 93:L17-9. 2007
    The DNA packaging machinery of bacteriophage T4 was studied in vitro using fluorescence correlation spectroscopy...
  87. ncbi Structure and morphogenesis of bacteriophage T4
    P G Leiman
    Department of Biological Sciences, Purdue University, 915 W State Street, West Lafayette, Indiana 47907 2054, USA
    Cell Mol Life Sci 60:2356-70. 2003
    ..Similar to other phages, and also herpes viruses, the unique vertex is occupied by a dodecameric portal protein, which is involved in DNA packaging.
  88. pmc Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging
    Yun Fang
    Department of Chemistry, University of Southern California, LJS 251, 840 Downey Way, Los Angeles, CA 90089 0744, USA
    Biochem Biophys Res Commun 372:589-94. 2008
    The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double-stranded DNA genome into a pre-formed protein capsid...
  89. pmc Forces during bacteriophage DNA packaging and ejection
    Prashant K Purohit
    Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California, USA
    Biophys J 88:851-66. 2005
    ..The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure...
  90. pmc The effect of N- or C-terminal alterations of the connector of bacteriophage phi29 DNA packaging motor on procapsid assembly, pRNA binding, and DNA packaging
    Ying Cai
    Department of Biomedical Engineering, The Vontz Center for Molecular Studies, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA
    Nanomedicine 4:8-18. 2008
    ..motor modification, conjugation, labeling, and manufacturing, the connector protein gp10 of the varphi29 DNA packaging motor was truncated, mutated, and extended...
  91. ncbi Translocation of nicked but not gapped DNA by the packaging motor of bacteriophage phi29
    Wulf Dieter Moll
    Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
    J Mol Biol 351:100-7. 2005
    ..Thus the phi29 DNA packaging machinery tolerated nicks, but stopped at gaps...
  92. ncbi The ATPase domain of the large terminase protein, gp17, from bacteriophage T4 binds DNA: implications to the DNA packaging mechanism
    Tanfis I Alam
    Department of Biology, The Catholic University of America, 103 McCort Ward Hall, 620 Michigan Avenue, N E, Washington, DC 20064, USA
    J Mol Biol 376:1272-81. 2008
    ..The small terminase protein, gp16, inhibited DNA binding, which was further accentuated by ATP. The presence of a DNA binding site in the ATPase domain and its binding properties implicate a role in the DNA packaging mechanism.
  93. pmc REDOR NMR characterization of DNA packaging in bacteriophage T4
    Tsyr Yan Yu
    Department of Chemistry, Washington University, St Louis, MO 63130, USA
    J Mol Biol 382:1031-42. 2008
    Bacteriophage T4 is a large-tailed Escherichia coli virus whose capsid is 120x86 nm. ATP-driven DNA packaging of the T4 capsid results in the loading of a 171-kb genome in less than 5 min during viral infection...
  94. ncbi Modulation of the viral ATPase activity by the portal protein correlates with DNA packaging efficiency
    Leonor Oliveira
    Unité de Virologie Moléculaire et Structurale, Unité Mixte de Recherche CNRS 2472, UMR INRA 1157 and Institut Fédératif de Recherche 115, Bâtiment 14B, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
    J Biol Chem 281:21914-23. 2006
    b>DNA packaging in tailed bacteriophages and herpesviruses requires assembly of a complex molecular machine at a specific vertex of a preformed procapsid...
  95. ncbi Portal fusion protein constraints on function in DNA packaging of bacteriophage T4
    Richard G Baumann
    USNA, Department of Chemistry, Mailstop 9B, 572 Holloway Road, Annapolis, MD 21402 5070, USA
    Mol Microbiol 61:16-32. 2006
    Architecturally conserved viral portal dodecamers are central to capsid assembly and DNA packaging. To examine bacteriophage T4 portal functions, we constructed, expressed and assembled portal gene 20 fusion proteins...
  96. ncbi Effect of spermine and DNase on DNA release from bacteriophage T5
    M de Frutos
    Laboratoire de Physique des Solides, UMR CNRS 8502, Bat 510, Universite Paris Sud, 91405 Orsay Cedex, France
    Eur Phys J E Soft Matter 17:429-34. 2005
    ..We discuss the results in terms of free energy minimization and we demonstrate that the presence of a DNA condensate outside the phage generates an additional force pulling passively on the DNA remaining inside the capsid...
  97. ncbi Construction and 3-D computer modeling of connector arrays with tetragonal to decagonal transition induced by pRNA of phi29 DNA-packaging motor
    Yin Yin Guo
    Department of Pathobiology and Wildon School of Bioengineering, Purdue University, West Lafayette, IN 47907, USA
    J Nanosci Nanotechnol 5:856-63. 2005
    ..Both the connector array and the decagon are ideal candidates to be used as templates to build patterned suprastructures in nanotechnology...
  98. ncbi Interaction of gp16 with pRNA and DNA for genome packaging by the motor of bacterial virus phi29
    Tae Jin Lee
    Department of Pathobiology, Weldon School of Biomedical Engineering, and Cancer Center, Purdue University, West Lafayette, IN 47907, USA
    J Mol Biol 356:589-99. 2006
    ..The C18C19A20 bulge that is essential for DNA packaging was found to be dispensable for gp16 binding...
  99. ncbi Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery
    Juan Chang
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
    Structure 14:1073-82. 2006
    ..The coaxially packed DNA genome is encapsidated by the icosahedral shell. This complete structure unifies various biochemical, genetic, and crystallographic data of its components from the past several decades...
  100. ncbi Mutations in the temperature-sensitive murine cytomegalovirus (MCMV) mutants tsm5 and tsm30: a study of genes involved in immune evasion, DNA packaging and processing, and DNA replication
    Clive Sweet
    School of Biosciences, University of Birmingham, Birmingham, UK
    J Med Virol 79:285-99. 2007
    ..Sequencing of the herpesvirus conserved cis-acting elements, pac1 and pac2, and genes involved in DNA packaging and cleavage located in the central core region of the genome identified few point mutations...
  101. pmc Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids
    Thorsten Hugel
    Department of Physics, Technical University, Munich, Germany
    PLoS Biol 5:e59. 2007
    ..From our data, we can exclude connector rotation with greater than 99% probability and therefore answer a long-standing mechanistic question...

Research Grants64

  1. Mechanistic Studies on a Viral DNA Packaging Machine
    CARLOS CATALANO; Fiscal Year: 2009
    Our long-range goal is to understand virus assembly at the molecular level. DNA packaging is a critical step in the assembly of many double-stranded DNA viruses, including poxvirus, adenovirus, herpesviruses, and many bacteriophages...
  2. DNA REPAIR IN A HORMONE RESPONSIVE GENE
    Michael J Smerdon; Fiscal Year: 2013
    ..objective of this proposal is to understand the molecular details of DNA excision repair in the context of DNA packaging and gene transcription in chromatin...
  3. Evaluating the role of histone H3K79 methylation states in DNA damage repair in S
    Jeffrey S Thompson; Fiscal Year: 2010
    ..The proposal outlined in this application examines the role by which DNA packaging proteins, known as histones, participate in DNA repair...
  4. ANALYSIS OF CHROMATIN REMODELING IN MAMMARY GLAND DEVELOPMENT USING TILING ARRAYS
    Monique Rijnkels; Fiscal Year: 2009
    ..In particular the role DNA packaging plays is not well established...
  5. REPAIR OF CARCINOGEN DAMAGED DNA IN HUMAN CHROMATIN
    John J Wyrick; Fiscal Year: 2013
    ..The broad objective of this proposal is to understand the molecular details of DNA packaging in both DNA damage and its repair, and the response of DNA packaging to these events...
  6. Mechanisms of Viral DNA Packaging
    CARLOS JOSE BUSTAMANTE; Fiscal Year: 2013
    ..b>DNA packaging occurs in many phages, herpesviruses, adenoviruses and poxvirues and it is therefore an important target for ..
  7. Biochemical and Genetic Analysis of yFACT, A Novel Nucleosome Reorganizing Factor
    TIMOTHY G FORMOSA; Fiscal Year: 2013
    ..Nucleosomes are the fundamental subunit of chromatin, which is the DNA packaging in eukaryotes. Their properties govern the flow of information from the genome...
  8. Engineering a packaging nanomotor for delivery of RNA and other molecules
    Venigalla B Rao; Fiscal Year: 2010
    ..The goal of this application is to engineer the bacteriophage T4 DNA packaging motor to translocate double stranded RNA and RNA:DNA hybrid molecules...
  9. Role of Set2 and H3 methylation in chromatin function
    Brian D Strahl; Fiscal Year: 2013
    ..PUBLIC HEALTH RELEVANCE: Defects in chromatin organization, DNA packaging and its accessibility is a major cause of human disease, including cancer and numerous developmental defects...
  10. PHAGE T4 HEAD ASSEMBLY AND INITIATION OF INFECTION
    Lindsay W Black; Fiscal Year: 2013
    ..research toward two long term objectives: understanding 1) the translocation mechanism of the conserved viral DNA packaging motor and its regulation;and 2) the evolution of the internal proteins injected to counter novel DNA ..
  11. Helper phage mobilization of S. aureus superantigen pathogenicity islands
    Gail E Christie; Fiscal Year: 2010
    ..In addition, the SaPIs redirect the specificity of the phage DNA packaging machinery so that SaPI DNA is preferentially encapsidated...
  12. ASSEMBLY OF THE HERPES SIMPLEX VIRUS CAPSID
    Jay C Brown; Fiscal Year: 2012
    ..Studies will also be performed to identify how components of the DNA packaging machinery are assembled on the capsid surface prior to their functioning in DNA translocation (aim 4)...
  13. Behavioral and Molecular Analysis of Chromatin Modifications in Memory Retrieval
    James M Stafford; Fiscal Year: 2012
    ..Recent research indicates that chromatin (DNA packaging complexes) modifications via histone acetylation (HA) results in networks of molecular changes (e.g...
  14. Encapsidation of Adenovirus DNA
    Michael J Imperiale; Fiscal Year: 2010
    ..The mechanism by which the IVa2 protein facilitates capsid assembly and DNA packaging will be studied by examining the structure of complexes containing the IVa2 and L4 22 kDa proteins and by ..
  15. Dynamics of nucleosome assembly/disassembly affected by chromatin modifications
    Tae Hee Lee; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Nucleosomes are the fundamental DNA packaging units of eukaryotic chromatin...
  16. Mechanisms of Viral DNA Packaging: Biophysical, Biochemical, &Genetic Analysis
    Douglas E Smith; Fiscal Year: 2013
    ..abstract_text> ..
  17. Excision of Carcinogen-DNA Adducts in Nucleosomes
    Nicholas E Geacintov; Fiscal Year: 2013
    ..known whether in biologically more relevant protein environments of nucleosomes, the fundamental sub-units of DNA packaging in the cell, similar hierarchies of NER will be observed with DNA substrates containing the same single bay ..
  18. Structures of the portal vertex in dsDNA viruses and virus-infected cells
    Wah Chiu; Fiscal Year: 2011
    ..We put particular emphasis on capsid structures functioning in DNA packaging and ejection...
  19. Structural studies of bacteriophage T4 and their potential medical applications
    MICHAEL ROSSMANN; Fiscal Year: 2009
    ..The plan is to analyze the structure and assembly of the capsid (Specific Aim 1), the DNA packaging machine (Specific Aim 2), the tail assembly (Specific Aim 3), assembly of the tail with head (Specific Aim 4) ..
  20. SEQUENCE DETERMINANTS OF PROTEIN STRUCTURE AND STABILITY
    Robert T Sauer; Fiscal Year: 2013
    ..budding, cytokinesis, activation of apoptosis and the innate immune response, chromosome translocation, viral DNA packaging, peroxisome biogenesis, transcriptional activation, and clamp and helicase loading onto DNA...
  21. RNA IN VIRAL DNA PACKAGING
    Shelley Grimes; Fiscal Year: 2012
    ..Study of the structure and function of this RNA-dependent DNA packaging motor may have general significance in uncovering targets for antiviral agents...
  22. DNA confined by surfaces
    Bernard Montgomery Pettitt; Fiscal Year: 2013
    ..4, 5) Structural insight into DNA packaging is aided by cryo-electron microscopy asymmetric reconstructions done in the NCMI with our collaborator Chiu...
  23. Assembly of phi29 pRNA nanoparticles for siRNA delivery to prostate cancer cells
    Peixuan Guo; Fiscal Year: 2012
    ..The ingenious, novel design of the bacteriophage phi29 DNA packaging motor and its constituents has inspired the artificial synthesis and assembly of phi29 biomimetic motor and ..
  24. Structure and Function of the Herpesvirus Capsid and its DNA-Packaging Machinery
    James F Conway; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): This project focuses on herpesvirus capsid structure and the processes of DNA packaging and capsid completion...
  25. Structural studies of bacteriophage T4 and their potential medical applications
    Michael G Rossmann; Fiscal Year: 2013
    ..The plan is to analyze the structure and assembly of the capsid (Specific Aim 1), the DNA packaging machine (Specific Aim 2), the tail assembly (Specific Aim 3), assembly of the tail with head (Specific Aim 4) ..
  26. Phi29 Motor Nanopore for Single Molecule Sensing
    Peixuan Guo; Fiscal Year: 2013
    ..short-term objective of this proposal is to demonstrate the utility of the lipid-embedded channel of the phi29 DNA packaging motor as a highly sensitive device for capture and fingerprinting of chemicals and biopolymers in real time at ..
  27. Structural Characterization of Archaeal Virus Assembly and Host Interactions
    Chi Yu Fu; Fiscal Year: 2012
    ..We propose to test the hypothesis by uncoupling capsid assembly and DNA packaging. The model predicts that blocking DNA-packaging will block array formation...
  28. Establish and Apply In Vitro System for Human Cytomegalovirus Capsid Assembly
    D WADE GIBSON; Fiscal Year: 2013
    ..to develop virus- structure-based therapeutics, and as model systems for herpesvirus tegumentation and DNA packaging evolve...
  29. From DNA sequence to expression: A quantitative approach from yeast to human
    Eran Segal; Fiscal Year: 2013
    ..proteins, termed transcription factors, to their binding to regulatory regions, through the important role of DNA packaging in this process, and up to the gene activity patterns resulting from the DNA binding activity of the ..
  30. Structure-function based development of JC virion specific antagonists for PML
    Walter Atwood; Fiscal Year: 2013
    ..in the virus based on these structures and functionally characterize the mutants for defects in assembly, DNA packaging, cell binding, cell penetration, and infection...
  31. Mapping Adeno-associated Virus Capsid Structural and Dynamic Transitions
    Brian P Bothner; Fiscal Year: 2012
    ..their capsid structure, cellular tropism and interactions for entry, trafficking, uncoating, replication, DNA packaging, capsid assembly, and antibody neutralization...
  32. Control of Bacterial Nucleoid Structure
    John W Shriver; Fiscal Year: 2011
    ..This work is a necessary first step to understanding the role of these proteins in controlling bacteria gene expression, metabolism, growth and virulence through changes in both DNA packaging and gene regulation.
  33. Biology and Mechanism of the Single Subunit RNA Polymerases
    RUI J SOUSA; Fiscal Year: 2012
    ..we will: (1) Define the role of T7RNAP and its regulator T7 lysozyme in recruitment and assembly of the T7 DNA packaging machinery and, using both ensemble and single molecule experiments, describe the molecular details of the T7 ..
  34. DNA packaging and delivery by dsDNA viruses
    Sherwood R Casjens; Fiscal Year: 2012
    ..other focuses of the proposal are aimed at understanding the structure and function of the components of the DNA packaging/injection molecular machine which include the terminase DNA packaging motor and proteins that are injected ..
  35. The DNA Packaging Motor of Bacteriophage Phi29
    MARC MORAIS; Fiscal Year: 2013
    The mechanism of DNA packaging for double-stranded DNA viruses will be studied in the Bacillus subtilis bacteriophage [unreadable]29, the most efficient in vitro viral packaging system known...
  36. Probing the Universality and Function of Single dsDNA Viral Packaging Motors
    James M Tsay; Fiscal Year: 2010
    ..Specific Aims: 1. The universality of viral DNA packaging motors will be explored by developing a new optical tweezers assay for studying DNA packaging in bacteriophage ..
  37. Multisubunit viral ATPases that couple ATP-hydrolysis to genome translocation
    Gino Cingolani; Fiscal Year: 2011
    ..to determine the structure of the P22 terminase holoenzyme assembled at the portal protein vertex;2.) to define how small terminase subunit stimulates large terminase ATPase activity during DNA packaging.
  38. DNA Topology In TBP/DNA Complexes: Chromatin Connections
    Jason Kahn; Fiscal Year: 2004
    The control of gene expression is vital to development, homeostasis, and signal transduction. In eukaryotes, DNA packaging into chromatin generally represses transcription...
  39. Herpes Simples Virus Capsid Assembly and DNA Packaging
    FREDERICK L HOMA; Fiscal Year: 2011
    ..The long-term goal of this project is to understand the mechanism of herpesvirus capsid assembly and DNA packaging. Assembly of herpesvirus capsids involves highly specific interactions of at least five different proteins and ..
  40. MECHANISTIC STUDIES ON VIRAL ASSEMBLY
    CARLOS CATALANO; Fiscal Year: 1999
    ..Similar mechanisms for DNA packaging have been proposed for all of the double-stranded DNA bacteriophages and may also apply to mammalian viruses ..
  41. RNA Nanomotor Based Active Devices for Biology and Medicine
    Rashid Bashir; Fiscal Year: 2009
    ..Molecular motors, such as ATPase [Noji et al., 1997], bacterial flagellar [Sowa et al., 2005], or viral DNA packaging motors [Guo, 2002;Shu et al., 2003] can be utilized to synthesize power at the nano-scale...
  42. Structure, dynamics, and function of the packaging RNA
    Peter Z Qin; Fiscal Year: 2010
    ..phi29 packaging RNA (pRNA) that plays essential roles in the most powerful biological motor known today - the DNA packaging motor of the phi29 bacteriophage...
  43. Subunit Coupling on a DNA Packaging Machine
    BENJAMIN THOMAS ANDREWS; Fiscal Year: 2012
    ..These DNA packaging motors are required for infectivity, and operate as several individual subunits working together as a motor...
  44. Enhancing Gene Therapy by Designing Chimeric AAV Virions
    JARROD JOHNSON; Fiscal Year: 2009
    ..engineering chimeric AAV virions that incorporate altered VP1 proteins and then testing these virions for DNA packaging, cellular attachment, phospholipase activity, endosomal escape, nuclear targeting, and transgene expression ..
  45. ASSEMBLY OF THE HERPES SIMPLEX VIRUS CAPSID
    Jay Brown; Fiscal Year: 2007
    ..Studies will also be performed to identify how components of the DNA packaging machinery are assembled on the capsid surface prior to their functining in DNA translocation (aim 4)...
  46. DETERMINANTS OF PARVOVIRUS ASSEMBLY AND INFECTIVITY
    IAN MAXWELL; Fiscal Year: 2000
    ..Despite their structural simplicity the processes of virion assembly, including DNA packaging, and the role of the individual capsid proteins in assembly and infectivity are poorly understood...
  47. ADENOVIRUS NUCLEOPROTEINS
    SARAH FLINT; Fiscal Year: 1991
    ..Antibodies will be raised to a second, very basic core protein, Mu (Mr 3-6,000) so that its role in DNA packaging may be examined...
  48. Analytical Ultracentrifuge Purchase
    Robert Hodges; Fiscal Year: 2006
    ..L. Bain) [unreadable] [unreadable] Obtaining a mechanistic understanding of viral DNA packaging (C.E. Catalano)...
  49. GENETIC EXCHANGE BY A BACTERIOPHAGE FROM BARTONELLA
    MICHAEL MINNICK; Fiscal Year: 1999
    ..to initiate a genetic analysis of the BLP genome to better understand the mechanism of phage replication and DNA packaging, with the hope of eventually harnessing the BLP for phagemid production and genetic manipulation of Bartonella...
  50. Vaccinia Virus Genetics and Morphogenesis
    Richard Condit; Fiscal Year: 2003
    ..will include assays for virion temperature sensitivity, post-translational cleavage of virion proteins, DNA packaging, synthesis, virion localization and intracellular localization of the protein product of the affected gene, ..
  51. RNA LIGASE FUNCTION AND USE IN DNA SYNTHESIS
    Michael Botchan; Fiscal Year: 2006
    ..division of the chromosomes into topologically closed supercoiled regions limits damage to DNA and facilitates DNA packaging and unlinking. The key methods that will be used are the isolation and characterization of E...
  52. Structure and Function of Phi29 hexameric pRNA
    Peixuan Guo; Fiscal Year: 2009
    ..One of the most complex and intricate translocation processes is viral genomic DNA packaging. A strikingly common feature in the maturation of linear dsDNA viruses, including herpes viruses, adenoviruses,..
  53. LARGE DELETION ADENOVIRAL VECTORS FOR CYSTIC FIBROSIS
    WANDA O NEAL; Fiscal Year: 1999
    ..They are propagated in the presence of a helper virus, which supplies all necessary proteins vector DNA packaging. Recent results using intravenous delivery provide a strong indication that these vectors have great potential ..
  54. VIRUS CHROMOSOME STRUCTURE: ROLE IN DEVELOPMENT
    Michael Feiss; Fiscal Year: 1993
    ..Our work focusses on several virus assembly steps, dealing especially with DNA packaging. The first aspect of virus assembly we are studying is genome recognition...
  55. DNA PACKAGING IN BACTERIOPHAGE LAMBDA
    Helios Murialdo; Fiscal Year: 1990
    ..two lambda genes, - Nu1 and A - brings together DNA and proheads, thus serving as the recognition element for DNA packaging. The enzyme also generates the mature chromosomal ends by catalyzing the formation of the staggered nicks at ..
  56. TOPOLOGICAL MODIFICATION OF VIRAL DNA
    Dwight Anderson; Fiscal Year: 1991
    ..proposal is centered on an analysis of the topology of packaged DNA-gp3, and the structure and function of the DNA packaging protein gp16, a DNA-dependent ATPase that topologically modifies phi29 DNA- gp3 as a prerequisite for ..
  57. Structural Studies of Virus Assembly & DNA Packaging
    MARC MORAIS; Fiscal Year: 2004
    ..abstract_text> ..
  58. PHAGE T4 HEAD ASSEMBLY AND INITIATION OF INFECTION
    Lindsay Black; Fiscal Year: 2003
    ..As part of the first objective, the DNA packaging mechanism will be investigated by focusing on terminase and portal dodecamer structure and function...
  59. Mechanisms of Meiotic Gene Expression in the Testis
    Jeff DeJong; Fiscal Year: 2007
    ..This is especially interesting because expression from meiotic chromosomes may be influenced by changes in DNA packaging and organization that do not occur in somatic cells...
  60. Mechanism of Lambda Terminase DNA Processing
    NASIB MALUF; Fiscal Year: 2005
    ..Bacteriophage lambda is an ideal model system to study viral DNA packaging mechanisms due to the availability of a large amount of biochemical and genetic data...
  61. Phi29 DNA-Packaging Motor for Nanomedicine
    Peixuan Guo; Fiscal Year: 2009
    ..abstract_text> ..
  62. The Role of ATP Hydrolysis in HSV-1 Terminase Activity
    Carol Duffy; Fiscal Year: 2004
    ..The process of DNA packaging is both conserved among members of the Herpesviridae and distinct from cellular processes...
  63. SUBUNIT INTERACTIONS DURING ICOSAHEDRAL CAPSID ASSEMBLY
    Peter Prevelige; Fiscal Year: 2007
    ..b>DNA packaging requires an ATP dependent motor protein termed a portal or connector protein, and the process of packaging ..
  64. IDENTITY AND FUNCTION OF VERTEBRATE TELOMERE PROTEINS
    Carolyn Price; Fiscal Year: 2002
    ..We will examine the terminal DNA structure and ascertain if it is bound by hnRNPs. We will also examine the DNA packaging, and positioning of telomere proteins along the length of the telomeric tract...