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Maruyama T, Yamamura H, Hiraki M, Kemori Y, Takata H, Goto M. Directed aggregation and fusion of lipid vesicles induced by DNA-surfactants. Colloids Surf B Biointerfaces 2008; 66:119-24. [DOI: 10.1016/j.colsurfb.2008.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 05/23/2008] [Accepted: 05/28/2008] [Indexed: 10/22/2022]
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2
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Tolstoshev CM, Blakesley RW. RSITE: a computer program to predict the recognition sequence of a restriction enzyme. Nucleic Acids Res 1982; 10:1-17. [PMID: 6278401 PMCID: PMC326108 DOI: 10.1093/nar/10.1.1] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A computer program (RSITE) was developed which predicts the recognition sequence of a restriction endonuclease. The sizes of fragments experimentally determined on cleavage of a DNA of known sequence were input. Possible recognition sequences producing fragments of sizes matching those determined empirically were printed out. The program faithfully predicted the specificity of restriction enzymes of known recognition sequence and also determined the recognition sequence of a new restriction enzyme from Haemophilus influenzae GU (HinGU II).
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3
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Rentier-Delrue F, Lubiniecki A, Howley PM. Analysis of JC virus DNA purified directly from human progressive multifocal leukoencephalopathy brains. J Virol 1981; 38:761-9. [PMID: 6264142 PMCID: PMC171206 DOI: 10.1128/jvi.38.2.761-769.1981] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Human polyomavirus JC DNA was purified directly from the diseased brain tissue of two patients with progressive multifocal leukoencephalopathy (PML) by a method employing differential salt precipitation (B. Hirt, J. Mol. Biol. 26:365-369, 1967). Each of the viral genomes (JC-NIH-1 and JC-NIH-2) was molecularly cloned intact in Escherichia coli, using pBR322, at their unique EcoRI (0.00 map unit) and BamHI (0.51 map unit) sites. The JC-NIH-1 genome was approximately 50 base pairs larger and the JC-NIH-2 genome was approximately 50 base pairs smaller than the prototype human polyomavirus JC (Mad-1) DNA. Analysis of the restriction endonuclease cleavage fragments of these two DNAs and the human polyomavirus JC (Mad-1) DNA revealed only slight differences which mapped in a region of the genome extending from 0.67 to 0.74 map unit. From previous homology studies, this region of variance corresponds to the noncoding region to the late side of the origin of DNA replication.
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4
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Bastia D, Germino J, Crosa JH, Ram J. The nucleotide sequence surrounding the replication terminus of R6K. Proc Natl Acad Sci U S A 1981; 78:2095-9. [PMID: 6941271 PMCID: PMC319290 DOI: 10.1073/pnas.78.4.2095] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The replication terminus of the plasmid R6K has been cloned into the single-stranded DNA phage vector M13mp5 and also into the plasmid vectors pBR313 and PBR322. By using single-stranded DNA templates prepared from the recombinant DNA clones, the sequence of 215 base pairs of DNA containing the replication terminus has been determined. The DNA sequence of the region of the terminus does not contain any 2-fold rotational symmetry. Therefore, folding of the DNA at the region of the terminus is unlikely to be a cause for replication termination. Interaction of a host-specified protein(s) with the sequence of the replication terminus is probably the basis of the mechanism of replicaion termination.
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5
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Reiser J, Renart J, Crawford LV, Stark GR. Specific association of simian virus 40 tumor antigen with simian virus 40 chromatin. J Virol 1980; 33:78-87. [PMID: 6245256 PMCID: PMC288525 DOI: 10.1128/jvi.33.1.78-87.1980] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Simian virus 40 tumor antigen (SV40 T antigen) was bound to both replicating and fully replicated SV40 chromatin extracted with a low-salt buffer from the nuclei of infected cells, and at least a part of the association was tight specific. T antigen cosedimented on sucrose gradients with SV40 chromatin, and T antigen-chromatin complexes could be precipitated from the nuclear extract specifically with anti-T serum. From 10 to 20% of viral DNA labeled to steady state with [3H]thymidine for 12 h late in infection or 40 to 50% of replicating viral DNA pulse-labeled for 5 min was associated with T antigen in such immunoprecipitates. After reaction with antibody, most of the T antigen-chromatin complex was stable to washing with 0.5 M NaCl, but only about 20% of the DNA label remained in the precipitate after washing with 0.5 M NaCl-0.4% Sarkosyl. This tightly bound class of T antigen was associated preferentially with a subfraction of pulse-labeled replicating DNA which comigrated with an SV40 form I marker. A tight binding site for T antigen was identified tentatively by removing the histones with dextran sulfate and heparin from immunoprecipitated chromatin labeled with [32P]phosphate to steady state and then digesting the DNA with restriction endonucleases HinfI and HpaII. The site was within the fragment spanning the origin of replication, 0.641 to 0.725 on the SV40 map.
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6
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Smith GE, Summers MD. Restriction Maps of Five
Autographa californica M
NPV Variants,
Trichoplusia ni M
NPV, and
Galleria mellonella M
NPV DNAs with Endonucleases
Sma
I,
Kpn
I,
Bam
HI,
Sac
I,
Xho
I, and
Eco
RI. J Virol 1979; 30:828-38. [PMID: 16789179 PMCID: PMC353393 DOI: 10.1128/jvi.30.3.828-838.1979] [Citation(s) in RCA: 126] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The restriction sites of
Autographa californica
nuclear polyhedrosis virus (Ac
M
NPV) E2 DNA were mapped for the endonucleases
Sma
I,
Kpn
I,
Bam
HI,
Sac
I,
Xho
I, and
Eco
RI. The restriction maps of four other Ac
M
NPV variants,
Trichoplusia ni
(Tn
M
NPV), and
Galleria mellonella
(Gm
M
NPV) genomes were determined and compared to the endonuclease cleavage maps of Ac
M
NPV E2 DNA. The viral structural polypeptides of Ac
M
NPV variants S3, E2, S1, M3, and R9 were the same when analyzed by polyacrylamide gel electrophoresis. The major structural polypeptides of Gm
M
NPV and Tn
M
NPV had the same pattern in polyacrylamide gels as did Ac
M
NPV structural polypeptides. Gm
M
NPV and Tn
M
NPV had several minor structural protein differences as compared with Ac
M
NPV. Ac
M
NPV variants, Tn
M
NPV, and Gm
M
NPV were distinct but with very similar genomes and protein structures.
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Affiliation(s)
- G E Smith
- Department of Entomology, Texas A&M University, College Station, Texas 77843
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7
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Devos R, van Emmelo J, Contreras R, Fiers W. Construction and characterization of a plasmid containing a nearly full-size DNA copy of bacteriophage MS2 RNA. J Mol Biol 1979; 128:595-619. [PMID: 374745 DOI: 10.1016/0022-2836(79)90295-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Bächi B, Reiser J, Pirrotta V. Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme. J Mol Biol 1979; 128:143-63. [PMID: 219202 DOI: 10.1016/0022-2836(79)90123-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Reiser J, Renart J, Stark GR. Transfer of small DNA fragments from polyacrylamide gels to diazobenzyloxymethyl-paper and detection by hybridization with DNA probes. Biochem Biophys Res Commun 1978; 85:1104-12. [PMID: 216362 DOI: 10.1016/0006-291x(78)90656-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Gutai MW, Nathans D. Evolutionary variants of simian virus 40: Nucleotide sequence of a conserved SV40 DNA segment containing the origin of viral DNA replication as an inverted repetition. J Mol Biol 1978; 126:259-74. [PMID: 216810 DOI: 10.1016/0022-2836(78)90362-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Krueger RC. A study of an endogenous nucleolytic reaction and of the action micrococcal nuclease and DNAase I on a salt-soluble, compact form of chromatin. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 520:358-67. [PMID: 708740 DOI: 10.1016/0005-2787(78)90233-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The endogenous nucleolytic reaction occurring in rabbit thymus nuclear lysates has been studied at extended incubation times (up to 4 h). Production of nucleosomal polymers containing multiples of 205 base pairs of DNA was observed. The stability of the bands and the low release (1%) of acid-soluble nucleotides indicated there was only a small fraction of sensitive DNA between the subunits. The salt-soluble chromatin formed in the endogenous reaction at short incubation times (14--24 min) and purified over Sephadex G-200 has been treated with micrococcal nuclease and DNAase I. With micrococcal nuclease, nucleosomal polymers containing multiples of 201 base pairs of DNA were formed. Extensive digestion reaveled a core subunit containing 145 base pairs of DNA. With DNAase I only random degradation was observed and nucleosomal complexes were not produced.
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12
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Volovitch M, Drugeon C, Yot P. Studies on the single-stranded discontinuities of the cauliflower mosaic virus genome. Nucleic Acids Res 1978; 5:2913-25. [PMID: 693323 PMCID: PMC342215 DOI: 10.1093/nar/5.8.2913] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Cauliflower Mosaic Virus (CaMV) genome is a double-stranded DNA molecule of about 5 million daltons. Native DNA molecules appear heterogeneous when analysed by gel electrophoresis. We have examined the nature of this apparent heterogeneity. Besides, this genome is shown here to contain three single-stranded breaks, as revealed by different denaturation experiments: heating at 75 degrees C, treatment with NaOH or dimethyl sulfoxide (DMSO). Labelling with terminal transferase proves that the 3' ends at these interruptions all have free hydroxyl groups. Electron microscopy and alkaline gel electrophoresis indicate that these three discontinuities are shared by both strands, and that they are not randomly located. S1 nuclease is active on CaMV DNA and generates three fragments. The comparison between the sizes of these fragments and of the products of denaturation leads us to consider that S1 acts at the level of the interruptions. We have determined that two of them, distant by one third genome unit, are in the same strand; the other is in the opposite strand, distant by one sixth genome unit from the nearest other one. The combined use of restriction enzymes and S1 nuclease has enabled us to locate these three discontinuities on the restriction map of the CaMV genome that we have otherwise established.
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13
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Carroll D, O'Neill FJ. Genome maps of simian virus 40 defectives propagated in human glioblastoma cells. Virology 1978; 87:120-9. [PMID: 208262 DOI: 10.1016/0042-6822(78)90164-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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McParland RH, Engelking HM, Pearson GD. Cleavage of type 2 adenovirus DNA by HaeIII endonuclease. I. Catalog of HaeIII fragments. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 518:413-23. [PMID: 656425 DOI: 10.1016/0005-2787(78)90160-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tye 2 adenovirus DNA was divided into 14 fragments by sequential use of BamI, HsuI, SmaI, anc EcoRI endonuclease. Each fragment was purified by gel electrophoresis and subsequently cleaved with HaeIII endonuclease. From the number of fragments produced, we could calculate the number of HaeIII cleavage sites: there are a total of 187 sites. HaeIII sites were not randomly distributed along the adenovirus chromosome. Most sites were clustered in the G + C-rich left half of the chromosome. The sum of the molecular weights of the HaeIII fragments is 22.4 . 10(6), within 2 % of the molecular weight of adenovirus DNA (22.9 . 10(6).
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15
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van Heuverswyn H, van de Voorde A, Fiers W. Nucleotide sequence of the simian-virus-40 DNA region coding for the carboxyl-terminal part of the T antigen. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 86:335-44. [PMID: 207522 DOI: 10.1111/j.1432-1033.1978.tb12315.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Hassell JA, Lukanidin E, Fey G, Sambrook J. The structure and expression of two defective adenovirus 2/simian virus 40 hybrids. J Mol Biol 1978; 120:209-47. [PMID: 205653 DOI: 10.1016/0022-2836(78)90065-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Zain B, Thimmappaya B, Dhar R, Weissman S. Nucleotide sequences of DNA encoding the 3' ends of SV40 mRNA. I. The sequence of the DNA fragment Hi-DII,III-G. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34908-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Nucleotide sequence of the DNA encoding the 5'-terminal sequences of simian virus 40 late mRNA. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38252-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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19
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Abstract
The nucleotide sequence of 70 base pairs (bp) around 0.545 map units (Alu I C and B junction) of the genome from the single Eco RI cleavage site within SV40 DNA is presented. The mRNA transcribed from the early strand template from this stretch contains two copies of the nonsense triplet UAA in each of the three reading frames. Thus at least 25% of the early region of SV40 DNA does not code for the SV40 "A" protein, and the viral contribution to events in the lytic cycle and transformation may be more complex than is generally appreciated.
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