Xrep, a plasmid-stimulating X chromosomal sequence bearing similarities to the BK virus replication origin and viral enhancers

Riley, Donald E.; Reeves, Raymond; Gartler, Stanley M.

doi:10.1093/nar/14.23.9407

Cited by 10 publications

(2 citation statements)

References 36 publications

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“…Homopurine-homopyrimidine sequences are likely to play an important biological role in eukaryotes. They are frequently found at interesting locations in the genome: upstream of many eukaryotic genes (Larsen and Weintraub, 1982;Nickol and Felsenfeld, 1983;Schon et al, 1983;Elgin, 1984;Evans et al, 1984;McKeon et al, 1984;Kilpatrick et al, 1986), in the vicinity of replication origins (Soeda et al, 1979;Riley et al, 1986;Mirkin et al, 1987) or in sites involved in genetic recombination (Davis et al, 1980;Hentschel, 1982;Moos and Gallwitz, 1983;Htun et al, 1984;Wohlrab et al, 1987). Moreover, a nuclear protein with nucleolitic activity has been described to interact specifically with d(G.C)Q sequences in eukaryotic chromatin (Ruiz-Carrillo and Renaud, 1987).…”

Section: Discussionmentioning

confidence: 99%

Structural polymorphism of homopurine-homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions.

et al. 1989

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In this paper, we have analysed the conformational behaviour shown by the homopurine–homopyrimidine alternating d(GA.CT)22 sequence cloned into SV40. Our results show that, in the presence of zinc ions, the d(GA.CT)22 sequence adopts an altered secondary DNA structure (*H‐DNA) which differs from either B‐DNA or H‐DNA. Formation of *H‐DNA is facilitated by negative supercoiling and does not appear to require base protonation, since it is induced at neutral pH by approximately 0.4 mM ZnCl2. The patterns of OsO4 and DEPC modification obtained in the presence of zinc are compatible with a homopurine–homopurine–homopyridimine triplex, though other structural models for *H‐DNA are also possible. The hypersensitivity to S1‐cleavage of the d(GA.CT)22 sequence is reinterpreted in terms of the equilibria between the B‐, H‐ and *H‐forms of the sequence. These results reveal the high degree of structural polymorphism shown by homopurine‐homopyrimidine sequences. Its biological relevance is discussed.

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Section: Discussionmentioning

confidence: 99%

Structural polymorphism of homopurine-homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions.

et al. 1989

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“…Restriction enzyme digestions were carried out according to the manufacturer's specifications. Further details of ligation, genomic library construction, bacterial transformation, and plasmid purification have been previously reported (39,41). Nucleotide sequencing was performed by a slight modification of the Sanger method (39).…”

Section: Methodsmentioning

confidence: 99%

Development of a polymerase chain reaction-based diagnosis of Trichomonas vaginalis

et al. 1992

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We developed a polymerase chain reaction (PCR)-based test for detecting the protozoan parasite Trichomonas vaginalis. Genomic libraries were constructed from two independent clinical isolates of T. vaginalis. From these libraries, 12 genomic clones were purified, sequenced, and then screened for uniqueness by computerassisted sequence comparisons. PCR reactions were performed to evaluate eight PCR-primer pairs, including a primer pair that targeted the T. vaginalis ferredoxin gene. All eight primer pairs yielded PCR products of the expected sizes. However, six of the primer pairs amplified their respective target sequences in limited numbers of clinical T. vaginalis isolates, suggesting the presence of significant genomic variability among isolates. An exception was a primer pair, termed TVA5-TVA6, that amplified a 102-bp genomic sequence, termed A6p, in all of 24 clinical isolates. The A6p sequence was not detected by PCR in human DNA or in a wide variety of flagellates, ciliates, or bacteria tested. The A6p sequence appears highly selective for a broad range of T. vaginalis isolates and holds promise for PCR-based diagnosis of the parasite.

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Stochastic models for heterogeneous DNA sequences

Churchill

1989

Bltn Mathcal Biology

294

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The composition of naturally occurring DNA sequences is often strikingly heterogeneous. In this paper, the DNA sequence is viewed as a stochastic process with local compositional properties determined by the states of a hidden Markov chain. The model used is a discrete-state, discrete-outcome version of a general model for non-stationary time series proposed by Kitagawa (1987). A smoothing algorithm is described which can be used to reconstruct the hidden process and produce graphic displays of the compositional structure of a sequence. The problem of parameter estimation is approached using likelihood methods and an EM algorithm for approximating the maximum likelihood estimate is derived. The methods are applied to sequences from yeast mitochondrial DNA, human and mouse mitochondrial DNAs, a human X chromosomal fragment and the complete genome of bacteriophage lambda.

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Xrep, a plasmid-stimulating X chromosomal sequence bearing similarities to the BK virus replication origin and viral enhancers

Abstract: The human X chromosome-linked fragment, "Xrep," was sequenced because it exerts a positive effect on plasmid growth in both E. coli and Saccharomyces cerevisiae.

Cited by 10 publications

References 36 publications

Structural polymorphism of homopurine-homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions.

Structural polymorphism of homopurine-homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions.

Development of a polymerase chain reaction-based diagnosis of Trichomonas vaginalis

Stochastic models for heterogeneous DNA sequences

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