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At least 19 recordsLinked to original sources
PubMed1978

Induction of infectious virus DNA and virus particles by mitomycin C in SV40-transformed mouse cells.

A line of SV40-transformed mouse cells (SV/3T3-4E) was isolated and four clones were derived from this line. Spontaneous production of small amounts of infectious SV40 DNA was detected in the parental line and in three out of the four clones tested, although no synthesis of virions could be demonstrated. The yields of SV40 DNA were significantly enhanced following treatment of these cells with mitomycin C and infectious virus particles became detectable occasionally.

Cell Line↗
PubMed1979

Pheasant virus DNA polymerase is related to avian leukosis virus DNA polymerase at the active site.

The DNA polymerase from Amherst pheasant virus (APV), a member of the pheasant virus species of retroviruses, was compared to the DNA polymerases of avian leukosis viruses (ALV) and a reticuloendotheliosis virus (spleen necrosis virus (SNV)). Immunoglobulin inhibition tests and competition immunoassays showed that APV and ALV DNA polymerases are closely related at their active sites. The determinants common to their active sites are not shared by SNV DNA polymerase. Bu using a species-specific radioimmunoassay, it was shown that both APV and SNV DNA polymerases are grossly different from ALV DNA polymerase. The specificity of the relationship of the active sites of APV and ALV DNA polymerases was confirmed by a heterologous radioimmunoassay. Our data indicate that pheasant viruses are evolutionarily linked to ALV.

Avian Leukosis Virus↗
PubMed1975

Restriction enzyme digests of rapidly renaturing fragments of vaccinia virus DNA.

Vaccinia virus DNA fragments that have been denatured by alkali and then neutralized contain a fraction that rapidly reforms duplex structures. The fraction is enriched by fractionating on hydroxyapatite columns and serves as as substrate for digestion by two restriction endonucleases isolated from Hemophilus parainfluenzae, Hpa I and HPa II. The patterns obtained by gel electrophoresis of the digested fragments show the presence of three major bands after Hpa I digestion and four major bands after Hpa II digestion. The DNA that is isolated from some of these bands quickly reforms duplex regions after alkaline denaturation. The size of the DNA segments in the major bands has been estimated to be in the range of 0.44 X 10(6) to 3.2 X 10(6) daltons. The fragments which rapidly reform duplex chains after denaturation are sensitive to single-strand-specific nucleases. These results are consistent with a model of vaccinia virus DNA which has a covalent link connecting complementary chains.

Alkalies↗
PubMed1976

Preferential inhibition of herpes-group viruses by phosphonoacetic acid: effect on virus DNA synthesis and virus-induced DNA polymerase activity.

In tissue culture phosphonoacetic acid (PAA) specifically inhibited DNA synthesis of human cytomegalovirus (CMV), murine CMV, simian CMV, Epstein-Barr virus, and Herpesvirus saimiri. Fifty to one hundred micrograms per milliliter PAA completely inhibited viral DNA synthesis with no significant damage to host cell DNA synthesis. In vitro DNA polymerization assays showed that 10 μg/ml of PAA specifically inhibited partially purified human CMV-induced DNA polymerase, while little inhibition of host-cell DNA polymerase activity was found. The specific inhibition of herpes-group virus DNA synthesis with little toxicity to host cells suggests that PAA has great potential as an antiherpesvirus therapeutic agent.

Acetates↗
PubMed2026

Distinct YY dinucleotide periodicity in adeno-associated virus DNA.

Dinucleotide periodicity is a hallmark of genome organization, yet its role in single-stranded (ss)DNA viruses remains poorly understood. Here, we systematically analyzed dinucleotide spacing patterns in adeno-associated virus (AAV) genomes and other viruses. Across 13 primate AAV serotypes, we identified a pronounced and highly conserved ∼15-bp periodicity specific to pyrimidine-pyrimidine (YY) dinucleotides and their reverse complements (RR). Comparative analyses across >25,000 viral sequences demonstrate that this 15-bp YY/RR periodicity is unique to the genus Dependoparvovirus and absent from other ssDNA viruses, satellite viruses, and helper viruses, which predominantly exhibit canonical ∼10- to 11-bp periodicities. Upon disruption of the YY/RR pattern using DNA family shuffling of AAV capsid genes, and subsequent iterative selection for viral production or cell entry, we found that the pattern is under positive selection. Selected sequences display increased periodicity alongside reduced sequence diversity, supporting a functional role for this genomic feature. Finally, engineered recombinant AAV genomes containing YY periodic motifs exhibit enhanced production and, for some designs, improved transduction efficiency, demonstrating that YY periodicity can modulate viral replication and infectivity. Our findings uncover a unique DNA-encoded signal in dependoparvoviruses that contributes to AAV fitness, expands our knowledge of virus biology, and has implications for vector engineering.

Dependovirus↗
PubMed1979

DNA of Epstein-Barr virus. V. Direct repeats of the ends of Epstein-Barr virus DNA.

Previous data indicated that Epstein-Barr virus DNA is terminated at both ends by direct or inverted repeats of from 1 to 12 copies of a 3 X 10(5)-dalton sequence. Thus, restriction endonuclease fragments which include either terminus vary in size by 3 X 10(5)-dalton increments (D. Given and E. Kieff, J. Virol. 28:524--542, 1978; S. D. Hayward and E. Kieff, J. Virol. 23:421--429, 1977). Furthermore, defined fragments containing either terminus hybridize to each other (Given and Kieff, J. Virol. 28:524--542, 1978). The 5' ends of the DNA are susceptible to lambda exonuclease digestion (Hayward and Kieff, J. Virol. 23:421--429, 1977). To determine whether the terminal DNA is a direct or inverted repeat, the structures formed after denaturation and reannealing of the DNA from one terminus and after annealing of lambda exonuclease-treated DNA were examined in the electron microscope. The data were as follows. (i) No inverted repeats were detected within the SalI D or EcoRI D terminal fragments of Epstein-Barr virus DNA. The absence of "hairpin- or pan-handle-like" structures in denatured and partially reannealed preparations of the SalI D or EcoRI D fragment and the absence of repetitive hairpin- or pan-handle-like structures in the free 5' tails of DNA treated with lambda exonuclease indicate that there is no inverted repeat within the 3 X 10(5)-dalton terminal reiteration. (ii) Denatured SalI D or EcoRI D fragments reanneal to form circles ranging in size from 3 X 10(5) to 2.5 X 1O(6) daltons, indicating the presence of multiple direct repeats within this terminus. (iii) Lambda exonuclease treatment of the DNA extracted from virus that had accumulated in the extracellular fluid resulted in asynchronous digestion of ends and extensive internal digestion, probably a consequence of nicks and gaps in the DNA. Most full-length molecules, after 5 min of lambda exonuclease digestion, annealed to form circles, indicating that there exists a direct repeat at both ends of the DNA. (iv) The finding of several circularized molecules with small, largely double-strand circles at the juncture of the ends indicates that the direct repeat at both ends is directly repeated within each end. Hybridization between the direct repeats at the termini is likely to be the mechanism by which Epstein-Barr virus DNA circularizes within infected cells (T. Lindahl, A. Adams, G. Bjursell, G. W. Bornkamm, C. Kaschka-Dierich, and U. Jehn, J. Mol. Biol. 102:511-530, 1976).

Animals↗
PubMed1978

Interactions of Shope papilloma virus with some other DNA viruses.

The interactions of Shope papilloma virus (SPV) with primate and rabbit cells in tissue culture have been investigated. The rabbit cell cultures were derived from normal epidermis, from SPV-infected epidermis, from SPV-induced papillomas, and from an SPV-associated carcinoma. None of these cell cultures, whether infected in vitro with SPV or derived from tissues infected in vivo, ever produced infectious SPV or even detectable viral antigens. Some other DNA viruses behaved differently in cells which had been in previous contact with SPV either in vitro or in vivo. Adenovirus type 5 multiplies better in human cells infected 24 h previously with SPV than in the untreated controls. The production of infectious virions of either herpes simplex virus or Shope fibroma virus is reduced in cells derived from SPV-induced papillomas or carcinoma, due, apparently, to a defect in viral maturation. Of the rabbit cells, only those derived from in vivo infected tissue, or those previously infected in vitro with SPV, could be transformed by SV40. The rabbit cell lines derived from papillomas or carcinoma differed from their counterparts derived either from normal epidermis or from tissue infected 24 hrs before biopsy, in their karyotype, and in their ability to grow in soft agar. Similar karyotypic alterations were induced in cells derived from healthy epidermis by infection in vitro with SPV.

Adenoviruses, Human↗
PubMed1979

The kinetics of synthesis of infectious unintegrated virus DNA in rous sarcoma virus infected chicken cells.

Infectious virus nucleic acids were extracted from the Hirt supernatant of chicken embryo fibroblasts infected for different times with the Schmidt-Ruppin strain of Rous sarcoma virus (RSV). Infectious DNA and DNA-RNA hybrid molecules could be recovered from 6 h after infection in experiments using 1.5 X 10(9) infected cells. Only small amounts of infectious virus DNA could be purified 6 h after infection whereas at 24 h approximately one infectious DNA molecule could be recovered for each input virus infectious unit. At 24 h, both infectious supercoiled and non-supercoiled molecules were found. The specific infectivity of the supercoiled fraction was less than that of the non-supercoiled fraction. Infectious supercoiled DNA could be recovered from 16 h after infection. Evidence is presented that both forms of unintegrated virus DNA may rest unintegrated for at least 8 days in the cell, though chronically infected cells were shown to contain less than one unintegrated molecule per 10(2) to 10(3) cells.

Avian Sarcoma Viruses↗
PubMed1992

Detection of hepatitis B virus DNA by polymerase chain reaction in serum and liver of children with chronic hepatitis B negative for hepatitis B virus DNA by conventional hybridization tests.

Hepatitis B virus (HBV) DNA was detected by polymerase chain reaction in the serum of 87 and liver tissue of 40 children with chronic hepatitis B, negative for HBV DNA by dot blot and Southern blot hybridization, respectively. In sera HBV DNA could be detected in 73 hepatitis B surface antigen carriers; 14 were hepatitis B e antigen (HBeAg), 56 were anti-HBe-seropositive and 3 had neither HBeAg nor positive anti-HBe. In 14 anti-HBe-positive patients no HBV DNA could be found. Viral sequences in liver tissue were present in 33 specimens; 20 were HBeAg and 13 were anti-HBe-seropositive. All of the 7 negative children had anti-HBe. Our results confirm polymerase chain reaction to be a more sensitive method to detect HBV DNA in the liver compared with conventional hybridization techniques. Every HBeAg-positive carrier as well as the majority of anti-HBe-positive patients show ongoing viral replication. This is of special clinical relevance, because these children must be considered infectious.

Adolescent↗
PubMed1976

Observations on template-specific conditions for DNA synthesis by avian myeloblastosis virus DNA polymerase.

The effects of Mg++, Mn++, and KCl addition, individually and in combination, on the rate of DNA- and RNA-primed DNA synthesis by avian myeloblastosis virus DNA polymerase (reverse transcriptase) using a variety of natural and synthetic template-primer combinations were examined. Optimal divalent cation concentrations were found to vary by as much as 10-fold depending upon the template-primer used to direct synthesis. Addition of KCl to reaction mixtures containing optimal divalent cation concentrations produced stimulation or inhibition of DNA synthesis which was also template-specific. DNA synthesis on the modified template poly (2'-0-methylcytidylate) was uniquely stimulated by combinations of divalent cations. With Mg++ as divalent cation, deviations from classical Michaelis-Menten kinetics of substrate saturation were observed with all template-primers tested.

Avian Leukosis Virus↗
PubMed2026

Decoding sequence recognition code of nucleic acid-binding proteins of human-infecting DNA viruses.

Human-infecting DNA viruses remain major health threats, yet the DNA-recognition mechanisms of their nucleic acid-binding proteins (NBPs) are poorly understood. Here, we systematically profiled 103 viral NBPs from human-infecting DNA viruses, with three NBPs from non-human-infecting DNA viruses as controls, using high-throughput screening. This analysis identified diverse DNA-binding motifs and specificity modules, including convergent recognition of a conserved CCACC motif across phylogenetically distant viruses. Notably, viral NBP binding-site distributions varied with genome size, and several NBPs from small-genome viruses showed enrichment on mitochondrial DNA. Functional assays further supported their mitochondrial association and effects on mitochondrial membrane potential. By integrating an ivTRT-based ssDNA-SELEX workflow, we further found that ssDNA viral NBPs recognize dimer-like and inverted-repeat sequences with potential to form stem-loop structures. Collectively, this study constructs a comprehensive viral NBP DNA-recognition atlas, offering a fundamental resource for elucidating viral genome recognition mechanisms, virus-mitochondria interactions, and developing future antiviral strategies.

Letter↗
PubMed1979

Model RNA-directed DNA synthesis by avian myeloblastosis virus DNA polymerase and its associated RNase H.

A model RNA template-primer system is described for the study of RNA-directed double-stranded DNA synthesis by purified avian myeloblastosis virus DNA polymerase and its associated RNase H. In the presence of complementary RNA primer, oligo(rI), and the deoxyribonucleoside triphosphates dGTP, dTTP, and dATP, 3'-(rC)30-40-poly(rA) directs the sequential synthesis of poly(dT) and poly(dA) from a specific site at the 3' end of the RNA template. With this model RNA template-primer, optimal conditions for double-stranded DNA synthesis are described. Analysis of the kinetics of DNA synthesis shows that initially there is rapid synthesis of poly(dT). After a brief time lag, poly(dA) synthesis and the DNA polymerase-associated RNase H activity are initiated. While poly(rA) is directing the synthesis of poly(dT), the requirements for DNA synthesis indicate that the newly synthesized poly(dT) is acting as template for poly(dA) synthesis. Furthermore, selective inhibitor studies using NaF show that activation of RNase H is not just a time-related event, but is required for synthesis of the anti-complementary strand of DNA. To determine the specific role of RNase H in this synthetic sequence, the primer for poly(dA) synthesis was investigated. By use of formamide--poly-acrylamide slab gel electrophoresis, it is shown that poly(dT) is not acting as both template and primer for poly(dA) synthesis since no poly(dT)-poly(dA) covalent linkages are observed in radioactive poly(dA) product. Identification of 2',3'-[32P]AMP on paper chromatograms of alkali-treated poly(dA) product synthesized with [alpha-32P]dATP as substrate demonstrates the presence of rAMP-dAMP phosphodiester linkages in the poly(dA) product. Therefore, a new functional role of RNase H is demonstrated in the RNA-directed synthesis of double-stranded DNA. Not only is RNase H responsible for the degradation of poly(rA) following formation of a poly(rA)-poly(dT) hybrid but also the poly(rA)fragments generated are serving as primers for initiation of synthesis of the second strand of the double-stranded DNA.

Avian Leukosis Virus↗
PubMed1979

BK virus DNA sequence: extent of homology with simian virus 40 DNA.

The primary nucleotide sequence of three regions of BK virus (BKV) variant (MM) DNA has been determined. The region between map positions 0.715 and 0.900 includes the initiation points and partial coding sequences of the putative VP2 and VP3 proteins of BKV(MM), the amino acid sequences of which show over 80% homology with those of VP2 and VP3 of simian virus 40. The sequence of a potential leader protein X, 66 amino acids long for BKV(MM) and 62 long for simian virus 40, is also deduced. The regions between 0.595 and 0.398 and 0.310 and 0.175 include the coding sequence for the entire small t antigen and most of the large T antigen of BKV(MM). The DNA sequence within these regions comprises over 50% of the complete BKV(MM) genome and shows a 70% sequence homology with the corresponding regions of simian virus 40 DNA. This high degree of homology is at variance with the reported homology values of 11--20% estimated by hybridization measurements of heteroduplex analyses. Possible explanations for the discrepancy are discussed.

BK Virus↗
PubMed1979

Cross-links in African swine fever virus DNA.

African swine fever virus DNA sediments in neutral sucrose density gradients as a single component with a sedimentation coefficient of 60S. In alkaline sucrose density gradients, this material shows two components with sedimentation coefficients of 85S and 95S, respectively. The sedimentation rate value of alkali-denatured virus DNA in neutral sucrose density gradients and the renaturation velocity of denatured DNA show that is reassociated much faster than expected from its genetic complexity. This behavior is compatible with the existence of interstrand cross-links in the molecule. We also present results which suggest that there are only a few such cross-links per molecule, that they are sensitive to S1 nuclease digestion, and that they are probably located next to the ends of the DNA.

African Swine Fever Virus↗
PubMed1977

Analysis of the structure of human papilloma virus DNA.

Human papilloma virus DNA has been examined for heterogeneity by electron microscopy, reassociation kinetics, and restriction endonuclease digestion. No heterogeneity in contour length was detected. The reassociation rate of papilloma DNA isolated from pooled warts was consistent with that expected for a homogeneous, unique DNA of molecular weight 5 X 10(6). Restriction endonuclease digestions of five papilloma DNA preparations isolated from pooled warts yielded predominantly fragments of the expected sizes, but significant quantities of fragments atypical in size were also commonly produced.

Base Sequence↗
PubMed1976

Localization of gene functions in polyoma virus DNA.

Polyoma virus mutants of four functionally distinct groups have been mapped by the marker rescue technique using restriction enzyme fragments of wild-type viral DNA. Nontransforming host-range mutants map in the proximal part of the early region of the viral genome. The same DNA fragment that restores a normal host range also restores normal transforming ability to these mutants. ts-25D, a temperature-sensitive (ts)-a class mutant, maps in the distal part of the early region. ts-3 and ts-1260 map in the proximal and distal parts of the late region, respectively.

Chromosome Mapping↗