Cloning full-length dengue type 4 viral DNA sequences: Analysis of genes coding for structural proteins

We have cloned and propagated in prokaryotic vectors the viral DNA sequences that are integrated in a variety of cells transformed by adenovirus 2 or SV40. Analysis of the clones reveals that the viral DNA sequences sometimes are arranged in a simple fashion, collinear with the viral genome; in other cell lines there are complex arrangements of viral sequences in which tracts of the viral genome are inverted with respect to each other. In several cases the nucleotide sequences at the joints between cell and viral sequences have been determined: usually there is a sharp transition between cellular and viral DNAs. The viral sequences are integrated at different locations within the genomes of different cell lines; likewise there is no specific site on the viral genomes at which integration occurs. Sometimes the viral sequences are integrated within repetitive cellular DNA, and sometimes within unique sequences. In some cases there is evidence that the viral sequences along with the flanking cell DNA have been amplified after integration. The sequences that flank the viral insertion in the line of SV40-transformed rat cells known as 14B have been used as probes to isolate, from untransformed rat cells, clones that carry the region of the chromosome in which integration occurred. Analysis of the structure of these clones by restriction endonuclease digestion and heteroduplex formation shows that a rearrangement of cellular sequences has occurred, presumably as a consequence of integration.

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Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-005-0365-5 ◽

2004 ◽

Vol 18 (12) ◽

pp. 739-760 ◽

Cited By ~ 48

Author(s):

Rajeshri G. Karki ◽

Yun Tang ◽

Terrence R. Burke ◽

Marc C. Nicklaus

Keyword(s):

Drug Design ◽

Full Length ◽

Viral Dna ◽

Anti Hiv ◽

Hiv 1

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Fast solid support detection of PCR amplified viral DNA sequences using radioiodinated or hapten labelled primers

Nucleic Acids Research ◽

10.1093/nar/18.11.3175 ◽

1990 ◽

Vol 18 (11) ◽

pp. 3175-3183 ◽

Cited By ~ 19

Author(s):

S. Sauvaigo ◽

B. Fouquè ◽

A. Roget ◽

T. Livache ◽

H. Bazin ◽

...

Keyword(s):

Dna Sequences ◽

Solid Support ◽

Viral Dna

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Recombination in SV40-infected cells: Viral DNA sequences at sites of circularization of transfecting linear DNA

Virology ◽

10.1016/0042-6822(81)90506-7 ◽

1981 ◽

Vol 109 (2) ◽

pp. 353-365 ◽

Cited By ~ 8

Author(s):

Mary Woodworth-Gutai

Keyword(s):

Dna Sequences ◽

Viral Dna ◽

Linear Dna ◽

Infected Cells

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Transcriptional control signals of a herpes simplex virus type 1 late (gamma 2) gene lie within bases -34 to +124 relative to the 5' terminus of the mRNA

Molecular and Cellular Biology ◽

10.1128/mcb.6.11.3652-3666.1986 ◽

1986 ◽

Vol 6 (11) ◽

pp. 3652-3666

Author(s):

F L Homa ◽

T M Otal ◽

J C Glorioso ◽

M Levine

Keyword(s):

Herpes Simplex ◽

Dna Sequences ◽

Viral Dna ◽

Regulated Expression ◽

Base Pair Fragment ◽

Simplex Virus ◽

Pair Fragment ◽

Gc Gene ◽

Hsv 1

The cis-acting DNA sequences required for regulated expression of a herpes simplex virus type 1 (HSV-1) late (gamma 2) gene were studied by using viruses containing specific deletions in the 5' transcribed noncoding and upstream regions of the HSV-1 glycoprotein C (gC) gene, a model gamma 2 gene. Nine mutant viruses which had variable 5' and 3' deletions within bases -569 to +124 relative to the 5' terminus of the gC mRNA were isolated. The mutants were isolated by a simple in situ hybridization screening procedure not requiring any prior selective pressure for or against expression of the gC gene. Analysis of RNA extracted from cells infected with individual mutants showed that the DNA sequences required for regulated expression of this gamma 2 gene lay within bases -34 to +124. This 158-base-pair fragment was sufficient to confer accurate and quantitative expression of gC mRNA and to maintain the stringent requirement on viral DNA replication for expression of this gene. Moreover, it was found that sequences located between -34 and +14 contained signals essential for expression of gC. To determine whether the -34 to +124 sequences would function as a gamma 2 promoter when moved to another region of the HSV-1 genome, the 158-base-pair fragment was substituted for the normal thymidine kinase promoter-regulatory sequences in the thymidine-kinase gene locus. Transcription of this chimeric gene was regulated as a gamma 2 gene in that its expression in infected cells was dependent on viral DNA synthesis. The only recognizable consensus sequence upstream of the transcription initiation site for this gene was the TATAAA sequence at -30.

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BK virus-transformed inbred hamster brain cells: status of viral DNA in subclones

Molecular and Cellular Biology ◽

10.1128/mcb.2.7.837-844.1982 ◽

1982 ◽

Vol 2 (7) ◽

pp. 837-844

Author(s):

M M Pater ◽

A Pater ◽

G di Mayorca ◽

E Beth ◽

G Giraldo

Keyword(s):

Cell Line ◽

Dna Sequences ◽

Copy Number ◽

Tumor Antigens ◽

Blot Hybridization ◽

Virus Production ◽

Bk Virus ◽

Free Form ◽

Brain Cells ◽

Viral Dna

We have recently reported that viral DNA sequences in inbred LSH hamster brain cells transformed by the GS variant of BK virus (LSH-BR-BK) are present predominantly in a free form (Beth et al., J. Virol. 40:276-284, 1981). In this report, we confirm that the presence of viral DNA sequences in these cells is not due to virus production, since viral capsid proteins were not detected by immunoprecipitation. Furthermore, we examined the status of viral DNA in 15 subclones of this cell line and detected free and integrated viral DNA sequences in only 5 of the subclones. The other 10 subclones contained exclusively integrated viral DNA sequences, as shown by the blot hybridization of high-molecular-weight cell DNA which was uncleaved or digested with HincII, for which there are no sites in viral DNA. The arrangement of viral DNA in these clones was further analyzed by cleavage of cellular DNA with HpaII and HindIII. Mitomycin (0.03 microgram/ml) treatment of subclones containing only integrated sequences resulted in the appearance of free viral DNA sequences in some of these cells. This result supports the postulation that free viral DNA in LSH-BR-BK cells is made up of excision products of observed tandemly repeated integrated sequences. In addition to the large T- and small t-antigens, LSH-BR-BK and all of its 15 subclones contained two antigen species which were larger than large T and one species which was smaller than small t. The number of tumor antigens in the LSH- BR-BK cell line and its subclones with a large copy number in a free form was not more than in the subclones with low copy number and integrated DNA. This suggests that free viral DNA is not a template for tumor antigen production in transformed cells.

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