Clones of cauliflower mosaic virus identified by molecular hybridization in turnip leaves

Mechanical inoculation of turnip leaves with cauliflower mosaic virus (CaMV) results after one to two weeks in the appearance on these leaves of local lesions. Local lesions were detected by hybridization of radioactive CaMV DNA with nucleic acid immobilized in leaf skeletons by solvent extraction, proteinase digestion, and alkali treatment. The pattern of lesions detected as dark circles on autoradiographs of the washed leaf skeletons was the same as that detected by staining of solvent-extracted leaves for starch. Starch lesions appeared as white areas against a dark purple back-ground. These lesions were first detected between 5 and 8 days after inoculation and grew in size until 10 days after inoculation. Lesions were also detected by staining solvent-extracted and proteinase digested leaves with ethidium bromide. The lesions appeared as dark areas in a bright fluorescent background, and were found in the same positions as the starch lesions.     

Selective allele loss and interference between cauliflower mosaic virus DNAs

Summary Some cauliflower mosaic virus (CaMV) alleles are selectively lost during growth of the virus in mixedly infected turnip plants. Viral DNA from plants co-inoculated with DNA of the cabbage S isolate and infectious cabbage S DNA with an extra EcoRI restriciion site lacked the extra site. The EcoRI allele was also lost in most plants co-inoculated with a non-infectious mutant of cabbage S DNA while little selective allele loss was observed with two other non-infectious mutant DNAs. Plants co-inoculated with DNAs of closely-related isolates (CM4-184 and W) contained both parental viral DNAs and some DNAs with characteristics of both parents. Interference, scored as a reduced frequency of infection or a delay in symptom appearance relative to plants inoculated with wild-type DNA, occurred when plants were inoculated with wild-type and mutant DNAs covalently attached to one another in partial dimer plasmid DNAs. Similarities in the conditions leading to selective allele loss and those leading to interference suggest that both may have been due to active gene conversion between CaMV DNA molecules.     

Rapid purification of covalently closed circular DNAs of bacterial plasmids and animal tumor viruses

A rapid and simple purification of covalently closed circular (supercoiled) DNA from both bacterial clones (plasmids) and African green monkey cells (SV40) is presented. The method involves immediate treatment of lysed cells with sodium hydroxide, followed by neutralization and phenol extraction in high salt. After the extraction mixture is centrifuged, supercoiled DNA is found in the aqueous phase, the noncovalently closed DNA molecules form a white precipitate at the interphase, and proteins pellet. Contaminating RNA is eliminated from the aqueous phase by RNAse treatment and precipitation of the supercoiled DNA with polyethylene glycol. Residual polyethylene glycol is removed from the resuspended DNA by chloroform extraction. The purified supercoiled DNA is compatible with restriction enzymes, and is efficient at transforming both _χ1776 and HB101 bacterial hosts. Centrifugation in ethidium bromide-cesium chloride or sucrose gradients is not necessary. The method is virtually independent of the molecular size and gives good yields of supercoiled DNA. The technique is applicable to large-scale preparations and as a rapid “screening” procedure in which 20 to 30 samples can be easily purified within 5 to 6 h.     

Biophysical studies on double-stranded RNA from turnip yellow mosaic virus-infected plants

Summary Double-stranded RNA was isolated in mg quantities from TYMV-infected cabbage plants by a modified phenol procedure. Chromatography of the RNA on methylated albumin and hydroxyapatite is described. The base composition (A=21.3; U=21.2; G=28.8; C=28.7) was in good agreement with the values expected for a double-stranded RNA consisting of TYMV RNA and a strand complementary to it. The buoyant density of the RNA in Cs₂SO₄ was 1.617 g/cm³. Single-stranded TYMV RNA banded at 1.642 g/cm³ in Cs₂SO₄. The RNA sedimented in the analytical ultracentrifuge with an average sedimentation coefficient of 10–11 s. Absorbance as a function of temperature was determined in several different media. The absorbance-temperature profiles were typical of those expected for double-stranded RNA. Denatured RNA was examined by equilibrium density gradient centrifugation.     

Melting behavior of a covalently closed, single-stranded, circular DNA

We synthesized the 26-residue deoxynucleotide sequence d(TTCCT5GGAATTCCT5GGAA) which folds intramolecularly to form a dumbbell-shaped, double-hairpin structure with a gap between the 3' and the 5' ends. We used T4 polynucleotide kinase to phosphorylate the 5' end followed by T4 DNA ligase to close the 3' and 5' ends. Melting of the dumbbell structure formed by this ligated sequence produces a covalently closed, single-stranded, circular final state. We employed calorimetric and spectroscopic techniques to characterize thermodynamically the melting behavior of the ligated molecule and compared it with the corresponding melting behavior of its unligated precursor. This comparison allowed us to characterize uniquely the influence of single-stranded ring closure on intramolecular duplex melting. The data reveal that ring closure produces a thermally more stable structure which exhibits significantly altered melting thermodynamics. We rationalize these thermodynamic differences in terms of differential solvation and differential counterion association between the ligated and unligated molecules. We also note the importance of such constrained dumbbell structures as models for hairpins, cruciforms, and locally melted domains within naturally occurring DNA polymers.     

Replication of cauliflower mosaic virus DNA in leaves and suspension culture protoplasts of cotton

Cauliflower mosaic virus (CaMV) replicated in protoplasts and in inoculated leaves of the non-host, cotton (Gossypium hirsutum, L.). Protoplasts prepared from suspension-cultured cotton cells were infected by incubation with liposome-encapsulated CaMV virions. During a 1-week culture period the amount of CaMV nucleic acid as detected by nucleic acid hybridization in the protoplasts increased significantly regardless of whether or not the protoplasts contained vacuoles. In leaves inoculated with CaMV virions or CaMV DNA, viral DNA sequences were found by leaf skeleton hybridization to be located in small circular areas. DNA extracted from ultracentrifugal pellets of homogenates of inoculated leaves contained circular, gapped CaMV DNA only when inocula contained CaMV virions, CaMV DNA, or partial nested dimer CaMV plasmid DNA. When plants had been heavily watered, the CaMV DNA recovered contained degraded CaMV DNA. The results suggest that the host range limitation for CaMV is not due to an inability to replicate or spread locally in inoculated leaves.     

Epigenetic regulation of covalently closed circular DNA minichromosome in hepatitis B virus infection

Hepatitis B is caused by hepatitis B virus (HBV),and persistent HBV infection is a global public health problem,with 257 million people as HBV chronic carriers....     

Monomer and multimer covalently closed circular forms of Rous sarcoma virus DNA.

Covalently closed circular molecules of viral DNA synthesized in virus-infected cells are composed mainly of monomers sedimenting at 22 to 27S in neutral sucrose gradients. These monomers are detected by annealing with complementary DNA or transfection assay. However, 11% of the infectious circles sediment faster than monomers. There is a peak at 32S which may correspond to dimer molecules. Traces of infectivity (about 3%) found between 32S and 65S suggest the presence of higher oligomers. In alkaline sucrose gradients, covalently closed monomers are found at 64 to 71S. Infectivity of these monomers is reduced by alkali treatment to less than one-tenth, and, perhaps for this reason, no infectious dimers or higher oligomers are observed. It has been shown that upon resedimentation the dimers of 95 can be separated from monomers and detected by hybridization.     

Physical map of DNA from a new cauliflower mosaic virus strain

The restriction enzymes AluI, BamHI, BglII, EcoRI, HindIII, and SalI have been used to characterize and map a new cauliflower mosaic virus strain (Cabb-S). These fragments have been ordered by examining their overlapping regions after double enzymatic digestion. The single SalI cleavage site was chosen as the point of origin. We compare this strain with those already described.     

Optical investigations on double stranded ribonucleic acid from turnip yellow mosaic virus

Summary TYMV-dsRNA has been studied by ORD and CD. The spectra indicate a highly ordered secondary structure which disappears upon heating or titrating to acid pH. No distinct acid structure as found for DNA could be observed.Melting profiles of TYMV-dsRNA show a strong dependence on ionic strength which is analogous to synthetic polynucleotide complexes. Upon storage for several months the melting points drop considerably, without change in the ORD spectra. The two sets of melting points obtained for TYMV-dsRNA compare well with the results obtained in the literature: two series of melting points have been found for ds-RNA of a wide variety of origins. If plotted as a function of their G-C content, these data fall on two different lines with different slopes.It is suggested that ds-RNA might exist in two different helical forms and that TYMV-dsRNA might undergo a conformational change in solution upon storage.Boursier du Commissariat à l'Energie Atomique.     

Detection, purification, and characterization of two species of covalently closed circular proviral DNA molecules of bovine leukemia virus

Cocultivation of uninfected and bovine leukemia virus-producing bat cells yielded, in addition to the unintegrated linear DNA duplex, DNA molecules that migrated as 4.4- and 4.8-kilobase-pair DNA fragments in gel electrophoresis. These DNA molecules were purified by acid-phenol extraction and cleaved with restriction endonucleases EcoRI, and HindIII, which have one recognition site each on the bovine leukemia virus proviral DNA. Such cleavage generated DNA molecules of approximately 10.0 and 9.4 kilobase pairs, thus indicating the existence of two species of covalently closed circular molecules of bovine leukemia virus proviral DNA.