Mapping of the HhaI and HinfI cleavage sites on simian virus 40 DNA

RSITE: a computer program to predict the recognition sequence of a restriction enzyme

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).

Analysis of JC virus DNA purified directly from human progressive multifocal leukoencephalopathy brains

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.

The nucleotide sequence surrounding the replication terminus of R6K

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.

Specific association of simian virus 40 tumor antigen with simian virus 40 chromatin

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.

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

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.

A study of an endogenous nucleolytic reaction and of the action micrococcal nuclease and DNAase I on a salt-soluble, compact form of chromatin

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.

Studies on the single-stranded discontinuities of the cauliflower mosaic virus genome

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.

Cleavage of type 2 adenovirus DNA by HaeIII endonuclease. I. Catalog of HaeIII fragments

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).

The early region of SV40 DNA may have more than one gene

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.