Analysis and purification of synthetic DNA fragments with NuSieve agarose mini-gels.

We outline in this note a new method for analyzing the crude product from long (greater than 40 bp) DNA synthesis reactions. This procedure is quick, and provides direct visualization of the end product. As described here, this method is not quantitative. However, densitometry of the stained gel could be used to quantitate the amount of DNA in the full-length peak. Without quantitation, our experience indicates that if a full-length fragment in the size range of 60 to 106 bases cannot be visualized with up to 1 microgram of crude material, re-synthesis is indicated. The 1 microgram value will no doubt increase with longer fragments. This system has also been used to purify ligated fragments for cloning. We have not attempted to purify full-length single-stranded oligomers from the crude reaction mix using the agarose mini-gel system, because of the lack of resolution at the n-1 level, and also because of the small loading capacity of the gel.

Conserved epitopes on the hemagglutinin-neuraminidase proteins of human and bovine parainfluenza type 3 viruses: nucleotide sequence analysis of variants selected with monoclonal antibodies.

We have previously identified 11 epitopes located in two topologically nonoverlapping antigenic sites (A and B) and a third bridging site (C) on the human type 3 parainfluenza virus (PIV3) hemagglutinin-neuraminidase (HN) glycoprotein by using monoclonal antibodies (MAbs) which inhibit hemagglutination and virus infectivity (K. L. Coelingh, C. C. Winter, and B. R. Murphy, Virology 143:569-582, 1985). We have identified three additional antigenic sites (D, E, and F) on the HN molecule by competitive-binding assays of anti-HN MAbs which have no known biological activity. Epitopes in sites A, D, and F are conserved on the bovine PIV3 HN glycoprotein and also among a wide range of human isolates. The dideoxy method was used to identify nucleotide substitutions in the HN genes of antigenic variants selected with neutralizing MAbs representing epitopes in site A which are shared by human and bovine PIV3. The deduced amino acid substitutions in the variants were located in separate hydrophilic stretches of HN residues which are conserved in the primary structures of the HN proteins of both human and bovine PIV3 strains.

Three sizes of subunits in RNAs from feline sarcoma-leukaemia virus mixtures.

RNA from the Snyder-Theilen feline sarcoma-leukaemia virus complex (ST-FeSV-FeLV) sedimented in a double-peaked band between 50 and 70S, but Gardner-Arnstein (GA) FeSV-FeLV RNA sedimented in a single 70S peak. FeLV isolated from the ST virus mixture contained RNA which sedimented in a 70S band like GA-FeSV-FeLV RNA, but F422 FeLV RNA sedimented more slowly, at 50 to 60S. After thermal denaturation, resedimentation revealed three classes of RNA subunits in ST-FeSV-FeLV RNA: the first class, 35 to 37S, was also found in ST-FeLV and other FeLVs (except F422 FeLV), in the endogenous feline virus, RD114 and in GA-FeSV-FeLV; the second class, 32 to 34S, was similar to subunits in F422 FeLV and minor components of GA-FeSV-FeLV and ST-FeLV; the third class, 25S, was detected only in ST-FeSV-FeLV RNA. Electrophoresis of RNA species in buffered formamide provided evidence that the three classes of RNA subunits distinguishable on the basis of sedimentation rates actually represent three size classes of subunits. The ST virus mixture was shown to contain about equal titres of infectious FeLV and transforming FeSV whereas GA-FeSV-FeLV had at least a 10-fold excess fo FeLV over FeSV. These observations are discussed in terms of possible origins of the three sizes of FeSV-FeLV RNA subunits and their relationships to three species of FeSV-FeLV proviral DNA described recently (Sherr et al. 1979).

Toward a model for the molecular genetics of carcinogenesis in rats.

Cultured rat embryo cells are resistant to neoplastic transformation by chemical carcinogens unless they are extensively subcultured or infected with a murine leukemia virus (MuLV) first. We found that, in normal cultured cells, MuLV activates expression of rat genes that are the progenitors of sarcoma virus genes, but not those of endogenous "leukemia" virus. Elevated levels of sarcoma virus-related RNA in normal cells infected with MuLV were indistinguishable from the levels in cells transformed spontaneously or by a carcinogen or a sarcoma virus. Because of previous reports that some carcinomas in rats also contain elevated levels of sarcoma virus-related RNA, we believe these events can be explained by a molecular genetic model which may be generally valid for initiation of carcinogenesis. The basic elements of the model are: transcriptional activation of all the multiple copies of normal rat progenitors of sarcoma virus genes is required before cellular transformation can be initiated, and initiation occurs when a spontaneous or induced mutation in any one active copy of these same genes generates a dominant transforming function.

Efficient production of mammalian RNA tumor viruses in serum-free culture medium allows rapid RNA subunit purification.

A wide variety of infected mammalian cell cultures were observed to produce high levels of RNA tumor virus particles in the absence of serum for at least 12 h. Virus production was measured by yields of 50-70 S virus RNAs isolated directly from serum-free culture media by chromatography on oligo(dT)-cellulose. Yields of RNAs from viruses produced in serum-free medium were comparable to yields obtained from purified viruses produced in serum-containing medium. Subunits of viral RNAs were thermally dissociated and separated by a new sedimentation system using sucrose gradients with resolving power (in the relevant size range) equivalent to that obtained with electrophoresis in polyacrylamide gels. RNA subunits isolated directly from serum-free medium appeared to be intact as judged by poly(A) content and resedimentation. The overall approach developed here represents dramatic savings in time and effort over previous ways of producing purified RNA subunits from tumor viruses.

Characterization of mouse mammary tumor viruses from primary tumor cell cultures.I. Immunologic and structural studies.

Primary cell cultures of mammary tumors from Rill, GR, DD, BALB/cfC3H, and BALB/c mice were prepared by trypsin-EDTA dissociation of tumors. Cultures from these strains contained predominantly cells of epithelial morphology which formed three-dimensional domelike structures. Cultures from Rill, GR, DD, and BALB/cfC3H tumors produced extra-cellular type-B mouse mammary tumor virus(es) (MuMTV), either in the absence of detectable type-C virus or with less than 1% contamination with type-C virus. This was determined by radioimmunoassays for MuMTV and murine leukemia virus (MuLV) antigens. Only BALB/c cultures produced MuMTV with as much as 3% contaminating MuLV. High levels of MuMTV surface antigen were also found in soluble form in culture supernatants. Virus polypeptide analyses by electrophoresis on polyacrylamide gels showed that the Rill BALB/cfC3H, DD, and BALB/c viruses all contained polypeptides characteristic of MuMTV. Primary cultures of mammary tumor cells make available a source of purified MuMTV antigens, structural proteins, and nucleic acids for comparative studies of MuMTV from various mouse strains.

Characterization of mouse mammary tumor viruses from primary tumor cell cultures. II. Biochemical and biophysical studies.

Primary mammary tumor cultures of RIII, GR, DD, BALB/c, and BALB/cfC3H mice were examined for mouse mammary tumor virus (MuMTV) production. Levels of production of 12-32 mug virus protein/day/75-cm2 culture flask could be maintained for 30-50 days with daily virus harvests. The viruses from tumor cell cultures of these mouse strains contained DNA polymerase with a strong preference for Mg++ over Mn++ as the divalent cation, a characteristic of DNA polymerase of MuMTV from mouse milk. These viruses from tumor cell cultures were excellent sources of MuMTV 3H-complementary DNA (complexed to 60-70S RNA) and radioactive 60-70S RNA, sufficiently free of contaminating murine leukemia virus nucleic acids, that can be used in molecular hybridization experiments. The effects of several culture parameters on MuMTV production were also studied.

Separation of the infectious ribonucleic acid of potato spindle tuber virus from double-stranded ribonucleic acid of plant tissue extracts.

The infectious ribonucleic acid (RNA) of potato spindle tuber virus (PSTV) can be separated by hydroxyapatite chromatography from double-stranded RNA detectable in low amounts in both infected and uninfected plant tissue extracts. The chromatographic behavior of ribonuclease-sensitive PSTV RNA resembles that of transfer RNA.

Virus interference by cellular double-stranded ribonucleic acid.

Ribonuclease-resistant ribonucleic acid (RNA) was isolated from uridine-labeled cultures of rabbit kidney, chicken embryo, and HeLa cells. This RNA, regardless of its source, was found to induce interference with virus growth in either rabbit kidney or chicken embryo cultures. Nuclease-treated cellular nucleic acids exhibited interference-inducing activity which eluted with a small fraction of RNA in the exclusion volume of a 6% agarose gel column. Besides resistance to ribonucleases, the interference inducer and RNA isolated from partially digested nucleic acids have in common two properties of double-stranded RNA: (i) similar sharp melting profiles were obtained for inducer and ribonuclease-resistant RNA, with T(m) dependent on NaCl concentration; (ii) ribonuclease-resistant inducer and RNA banded together in Cs(2)SO(4) density gradients at a density characteristic of known double-stranded RNA. After melting at low ionic strength, the labeled RNA shifted to a higher density and its capacity to inhibit virus replication was lost. Velocity sedimentation analysis of the cellular ribonuclease-resistant RNA indicated that the majority sedimented between 7 and 11S, but only RNA sedimenting at >==8 to 20S had a high specific activity of interference induction. Without prior ribonuclease treatment, the ribonuclease-resistant RNA can be precipitated with 2 m LiCl and thus appears to exist in purified cellular nucleic acids as part of molecular complexes with both single- and double-stranded regions of RNA. The biosynthesis of cellular double-stranded RNA is inhibited by actinomycin D.