Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.30.1 (S1 nuclease)
3,660 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We examined structural properties of poly d(C4A2).d(T2G4), the telomeric DNA sequence of the ciliated protozoan Tetrahymena. Under conditions of high negative supercoiling, poly d(C4A2).d(T2G4) inserted in a circular plasmid vector was preferentially sensitive to digestion with S1 nuclease. Only the C4A2 strand was sensitive to first-strand S1 cutting, with a markedly skewed pattern of hypersensitive sites in tracts of either 46 or 7 tandem repeats. Linear poly d(C4A2).(T2G4) showed no preferential S1 sensitivity, no circular dichroism spectra indicative of a Z-DNA conformation, no unusual Tm, and no unusual migration in polyacrylamide gel electrophoresis. The S1 nuclease sensitivity properties are consistent with a model proposed previously for supercoiled poly d(CT).d(AG) (Pulleyblank et al., Cell 42:271-280, 1985), consisting of a double-stranded, protonated, right-handed underwound helix. We propose that this structure is shared by related telomeric sequences and may play a role in their biological recognition.
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PMID:S1 nuclease sensitivity of a double-stranded telomeric DNA sequence. 281 22

The transition from lineform DNA to cruciform DNA (cruciformation) within the cloned telomere sequences of the Leporipoxvirus Shope fibroma virus (SFV) has been studied. The viral telomere sequences have been cloned in recombination-deficient Escherichia coli as a 322 base-pair, imperfect palindromic insert in pUC13. The inverted repeat configuration is equivalent to the arrangement of the telomere structures observed within viral DNA replicative intermediates. A major cruciform structure in the purified recombinant plasmid has been identified and mapped using, as probes, the enzymes AflII, nuclease S1 and bacteriophage T7 endonuclease I. It was extruded from the central axis of the cloned viral inverted repeat and, by unrestricted branch migration, attained a size commensurate with the superhelical density of the plasmid molecule at native superhelical densities. This major cruciform extrusion event was the only detectable duplex DNA perturbation, induced by negative superhelical torsion, in the insert viral sequences. No significant steady-state pool of extruded cruciform was identified in E. coli. However, the identification of a major deletion variant generated even in the recombination-deficient E. coli strain DB1256 (recA recBC sbcB) suggested that the cruciform may be extruded transiently in vivo. The lineform to cruciform transition has been further characterized in vitro using two-dimensional agarose gel electrophoresis. The transition was marked by a high energy of formation (delta Gf = 44 kcal/mol), and an apparently low activation energy that enabled facile transitions at physiological temperatures provided there was sufficient torsional energy. By comparing cruciformation in a series of related bidirectional central axis deletions of the telomeric insert, it has been concluded that the presence of extrahelical bases in the terminal hairpin structures contributes substantially to the high delta Gf value. Also, viral sequences flanking the extruded cruciform were shown to influence the measured delta Gf value. Several general features of poxvirus telomere structure that would be expected to influence the facility of cruciform extrusion are discussed along with the implications of the observed cruciform transition event on the replicative process of poxviruses in vivo.
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PMID:Cruciform extrusion in plasmids bearing the replicative intermediate configuration of a poxvirus telomere. 282 85

The non-telomeric variant surface glycoprotein (VSG) genes in Trypanosoma brucei are activated by a duplicative transposition to a telomeric expression site. We have determined the 5' end of the transposed segment of the gene for VSG 117 and infer from comparison with similar data obtained by others that the crossover can occur at variable positions within short repeats present upstream of this gene and in the expression site. We have analysed nascent and steady state transcripts of the transposed gene and its neighbouring expression site DNA. The results indicate that transcription starts upstream of the transposed gene segment in the expression site and that transcripts are rapidly processed at specific points identified by protection of DNA-RNA hybrids against digestion by nuclease S1 or Exo VII. Hence, this gene appears to be activated by a process akin to promoter addition.
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PMID:Transcription of a transposed trypanosome surface antigen gene starts upstream of the transposed segment. 300 50

We determined the complete nucleotide sequence of the RAD3 gene of Saccharomyces cerevisiae. The coding region of the gene contained 2,334 base pairs that could encode a protein with a calculated molecular weight of 89,796. Analysis of RAD3 mRNA by Northern blots and by S1 nuclease mapping indicated that the transcript was approximately 2.5 kilobases and did not contain intervening sequences. Fusions between the RAD3 gene and the lac'Z gene of Escherichia coli were constructed and used to demonstrate that the RAD3 gene was not inducible by DNA damage caused by UV radiation or 4-nitroquinoline-1-oxide. Two UV-sensitive chromosomal mutant alleles of RAD3, rad3-1 and rad3-2, were rescued by gap repair of a centromeric plasmid, and their sequences were determined. The rad3-1 mutation changed a glutamic acid to lysine, and the rad3-2 mutation changed a glycine to arginine. Previous studies have shown that disruption of the RAD3 gene results in loss of an essential function and is associated with inviability of haploid cells. In the present experiments, plasmids carrying the rad3-1 and rad3-2 mutations were introduced into haploid cells containing a disrupted RAD3 gene. These plasmids expressed the essential function of RAD3 but not its DNA repair function. A 74-base-pair deletion at the 3' end of the RAD3 coding region or a fusion of this deletion to the E. coli lac'Z gene did not affect either function of RAD3.
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PMID:RAD3 gene of Saccharomyces cerevisiae: nucleotide sequence of wild-type and mutant alleles, transcript mapping, and aspects of gene regulation. 388 9

Previous studies with MCF-7 cells demonstrated that several agents induce greater strand breakage in active genes than in nontranscribed centromeric regions. To better assess the effects of gene activity and inactivity, an allele-specific DNA strand break assay was developed, which allowed direct comparison of damage at a specific genetic locus on the active and inactive X chromosomes. The ZP lymphoblastoid cell line is heterozygous at the glucose-6-phosphate dehydrogenase (G6PD) locus, and the unexpressed (A) allele on the inactive X chromosome contains a FokI restriction site that is lacking in the expressed (B) allele on the active X. ZP cells were treated with camptothecin or amsacrine, and subjected to alkaline-induced DNA unwinding. Following detergent lysis and digestion of single-stranded DNA with S1 nuclease, the remaining double-stranded DNA was isolated and subjected to polymerase chain reaction (PCR) with primers that flank the polymorphic FokI site, with [alpha-32P]dCTP being added in the last PCR cycle. The resulting labeled PCR product was cleaved with FokI to assess the A/B allele ratio in the double-stranded DNA fraction. Treatment with camptothecin and amsacrine increased the apparent A/B ratio by factors of 2-3 and 1.5-2 respectively, indicating that the active B allele is preferentially damaged by these agents.
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PMID:Selective damage to the active X chromosome by camptothecin and amsacrine as determined by an allele-specific alkaline unwinding assay. 748 52

We have applied the method of two-dimensional gel electrophoresis to study a pH-dependent structural transition in plasmid carrying the Tetrahymena telomeric sequence, (G4T2)n. A study of the two-dimensional patterns makes it possible to obtain energetic characteristics of the transition. We have obtained the nucleation energy of the structure. It proved to be two times lower than the nucleation energy of H-DNA determined before for a d(AG)n insert. The finding partly explains the formation of an eclectic structure in telomeric sequences. We also studied the effect of Zn++ ions on the two-dimensional patterns of gel electrophoresis. Our data show that Zn++ ions can significantly affect the transitions themselves. This finding leads to reinterpretation of numerous data on probing of structural transitions in DNA by the S1 nuclease.
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PMID:Study of pH-dependent structural transition in telomeric sequences by two-dimensional gel electrophoresis. 850 Apr 56

Sequences present at the genomic termini of herpesviruses become linked during lytic-phase replication and provide the substrate for cleavage and packaging of unit length viral genomes. We have previously shown that homologs of the consensus herpesvirus cleavage-packaging signals, pac1 and pac2, are located at the left and right genomic termini of human herpesvirus 6 (HHV-6), respectively. Immediately adjacent to these elements are two distinct arrays of human telomeric repeat sequences (TRS). We now show that the unique sequence element formed at the junction of HHV-6B genome concatemers (pac2-pac1) is necessary and sufficient for virally mediated cleavage of plasmid DNAs containing the HHV-6B lytic-phase origin of DNA replication (oriLyt). The concatemeric junction sequence also allowed for the packaging of these plasmid molecules into intracellular nucleocapsids as well as mature, infectious viral particles. In addition, this element significantly enhanced the replication efficiency of oriLyt-containing plasmids in virally infected cells. Experiments revealed that the concatemeric junction sequence possesses an unusual, S1 nuclease-sensitive conformation (anisomorphic DNA), which might play a role in this apparent enhancement of DNA replication--although additional studies will be required to test this hypothesis. Finally, we also analyzed whether the presence of flanking viral TRS had any effect on the functional activity of the minimal concatemeric junction (pac2-pac1). These experiments revealed that the TRS motifs, either alone or in combination, had no effect on the efficiency of virally mediated DNA replication or DNA cleavage. Taken together, these data show that the cleavage and packaging of HHV-6 DNA are mediated by cis-acting consensus sequences similar to those found in other herpesviruses, and that these sequences also influence the efficiency of HHV-6 DNA replication. Since the adjacent TRS do not influence either viral cleavage and packaging or viral DNA replication, their function remains uncertain.
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PMID:Functional identification and analysis of cis-acting sequences which mediate genome cleavage and packaging in human herpesvirus 6. 942 Feb 30

We have demonstrated recently that chronic hyperoxic treatment accelerates the rate of aging of fibroblasts and the rate of telomere shortening in parallel. It was hypothesized that accelerated telomere shortening is due to preferential accumulation of oxidative damage in telomeres. To test this hypothesis, we measured the accumulation of sites sensitive to S1 nuclease treatment in telomeres, in minisatellites, and in the bulk of the genome of fibroblasts under different models of oxidative stress as well as after treatment with the alkylating agent, N-methyl-N'-nitro-N-nitrosoguanidine. A comparison with qualitative data obtained by alkaline electrophoresis reveals that the sites transferred to double-strand breaks by treatment with low concentrations of S1 nuclease are, in fact, single-stranded regions in the DNA. These regions may resemble single-stranded overhangs, gaps, or conventional single-strand breaks. The frequency of single-stranded regions is significantly higher in telomeres than in minisatellites or in the bulk of the genome under all conditions tested. Those regions induced in minisatellites or in the overall genome by a bolus dose of hydrogen peroxide are completely repaired within 24 h. On the other hand, 50 +/- 12% of H2O2-induced single-stranded regions remain unrepaired for at least 19 days in telomeres of human fibroblasts, leading to a significant increase of the telomeric steady-state level of these lesions. This preferential accumulation might significantly contribute to telomere shortening.
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PMID:Preferential accumulation of single-stranded regions in telomeres of human fibroblasts. 951 33

Telomere length in MRC-5 fibroblasts remains constant if the cells are proliferation-inhibited for up to 3 months by confluency. However, the apparent frequency of single-stranded sites in telomeres, measured as sensitivity to degradation by S1 nuclease, increases about fourfold during this extended inhibition of proliferation. After release of the cells, the frequency of telomeric single-stranded sites decreases to control values, and the telomere shortening rate increases about threefold as compared to controls proliferating without inhibition. This acceleration is transitory, the telomere shortening rate decreases to control values after about two population doublings after release. Finally, temporarily arrested fibroblast populations senesce at a lower cumulative population doubling level, but at about the same telomere length, as continuously proliferating controls. The data suggest that metabolic time-dependent single-strand degradation is a major cause of telomere shortening. They support the idea that telomere shortening plays an important role in triggering cellular senescence.
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PMID:Accelerated telomere shortening in fibroblasts after extended periods of confluency. 960 97

Telomere shortening triggers replicative senescence in human fibroblasts. The inability of DNA polymerases to replicate a linear DNA molecule completely (the end replication problem) is one cause of telomere shortening. Other possible causes are the formation of single-stranded overhangs at the end of telomeres and the preferential vulnerability of telomeres to oxidative stress. To elucidate the relative importance of these possibilities, amount and distribution of telomeric single-strand breaks, length of the G-rich overhang, and telomere shortening rate in human MRC-5 fibroblasts were measured. Treatment of nonproliferating cells with hydrogen peroxide increases the sensitivity to S1 nuclease in telomeres preferentially and accelerates their shortening by a corresponding amount as soon as the cells proliferate. A reduction of the activity of intracellular peroxides using the spin trap alpha-phenyl-t-butyl-nitrone reduces the telomere shortening rate and increases the replicative life span. The length of the telomeric single-stranded overhang is independent of DNA damaging stresses, but single-strand breaks accumulate randomly all along the telomere after alkylation. The telomere shortening rate and the rate of replicative aging can be either accelerated or decelerated by a modification of the amount of oxidative stress. Quantitatively, stress-mediated telomere damage contributes most to telomere shortening under standard conditions.
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PMID:Accumulation of single-strand breaks is the major cause of telomere shortening in human fibroblasts. 1065 92


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