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)

The frequencies of chromosomal aberrations induced by the restriction endonuclease Alu I (recognition site AG/CT) can be elevated to a similar extent by additional treatments with a single-strand-specific endonuclease from Neurospora crassa (EC 3.1.30.1), or with ammonium sulfate in which the Neurospora endonuclease is suspended. These data indicate that Alu I does not produce DNA single-strand breaks in the chromatin of living cells, which can be recognized by the Neurospora endonuclease. The salt may induce conformational changes in the chromatin which make more recognition sites available for Alu I. Experiments with recovery times between the treatments with Alu I and the salt indicate that Alu I can act in the nucleus for at least 40 min.
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PMID:Elevation of Alu I-induced frequencies of chromosomal aberrations in Chinese hamster ovary cells by Neurospora crassa endonuclease and by ammonium sulfate. 301 98

Using S1 nuclease protection assays, we have examined the representation of cell cycle-dependent H4 histone RNAs in the nuclear matrix and nonmatrix nuclear fractions of human cells. Cytoplasmic and nuclear fractions were prepared from exponentially growing HeLa S3 cells by double detergent (sodium deoxycholate and NP40) lysis. The nuclear matrix and nonmatrix nuclear fractions were then prepared by digestion of nuclei with RNase-free DNase I and subsequent high-salt [0.4 M (NH4)2SO4] extraction. Subcellular fractions were characterized by 1) DNA, RNA, and protein composition; 2) electrophoretic analysis of the proteins in each fraction; 3) the representation of 45S ribosomal RNA precursors and processed 18S and 28S ribosomal RNAs; and 4) the presence of mitochondrial RNAs. In contrast to ribosomal and messenger RNA precursors, which are largely associated with the nuclear matrix, the human H4 histone RNAs in the nucleus were found predominantly in the nonmatrix nuclear fraction. The presence of H4 histone RNA in the nonmatrix nuclear fraction appeared to be coupled to DNA replication, since inhibition of DNA synthesis by hydroxyurea resulted in a loss of histone RNA from the nucleus. Our results suggest either that the association of histone RNAs with the nuclear matrix is very transient or that posttranscriptional modifications of the rapidly processed histone gene transcripts do not involve the nuclear matrix.
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PMID:Localization of human histone gene transcripts predominantly in the nonmatrix nuclear fraction. 301 90

The nuclear non-polyadenylated RNA from HeLa cells infected with adenovirus-2 was examined for the presence of molecules containing the first intervening sequence (IVS1) of the major late premessenger RNA. Four molecules with the approximate size of free IVS1 in sucrose gradients (1021 nucleotides) were separated by polyacrylamide gel electrophoresis and characterized by complementary methods: S1 nuclease mapping, susceptibility to debranching enzyme, RNAase-H-directed cleavage. The results indicate that the most abundant RNA form is the excised lariat IVS1. We also find linear IVS1 and a randomly nicked lariat, the latter probably being made during RNA isolation. The fourth RNA is a leader 1-IVS1 molecule. No truncated IVS1 which might indicate that IVS1 is excised by several cycle of cleavage-ligation was detected. A study of the distribution of the four RNAs in hnRNP shows that they are part of RNPs of about 70 S. However, each RNP has distinct sedimentation characteristics and sensitivity to salt dissociation. Together, the results suggest that the excised lariat IVS1 is released from the large late premRNP under the form of a 70 S RNP, where it is linearized.
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PMID:Nuclear non-polyadenylated RNAs containing the first intervening sequence of the major late premessenger RNA from adenovirus-2: characterization and distribution in ribonucleoproteins. 303 61

The initial stages of transcription have been characterized using a template containing the gene II promoter region of M13 phage. Initiation of transcription in the presence of all four nucleotides gives rise to the 140-residue run-off transcript, with a minor pause at the RNA hexamer stage. Cycling, leading to the accumulation of significant amounts of short oligonucleotides [1], was not observed. An RNA hexamer GUUUUU was the sole product when GpU and UTP were used and the ternary complex with the hexamer was stable and resistant to high salt (0.4 M) and S1 nuclease attack. After direct ultraviolet photocrosslinking of the RNA hexamer to RNA polymerase in the ternary complex, the radioactive label incorporation into various subunits was determined by autoradiography after sodium tetradecyl sulfate gel electrophoresis to be as follows: sigma, 86%; beta, 14%; beta' and alpha, negligible. Both electrophoresis and sucrose gradient centrifugation experiments indicate that the sigma subunit is not released from the ternary complex when either the RNA hexamer or the 140-residue RNA is synthesized on this template, even though the complexes are stable.
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PMID:Transcription initiation by Escherichia coli RNA polymerase at the gene II promoter of M13 phage: stability of ternary complex, direct photocrosslinking to nascent RNA, and retention of sigma subunit. 331 3

The interaction of poly-N6-methyladenylic acid (poly(m6A) with poly-5-bromouridylic acid (poly(BU) was studied by the mixing curve method. A.1 m6A: 2 BU stoichiometry was clearly indicated over a wide range of ionic strengths at neutral pH, while the binding of poly(m6A) to poly(U) is known to occur with 1 m6A:1 U. Digestion by nuclease S1 confirmed this stoichiometry, indicating the absence of single strands in a 1:2 mixture. Heating profile analysis and hydroxyapatite column chromatography provided further confirmation of this finding. To determine whether 1:2 stoichiometry holds in a monomer-polymer system, the interaction of N6-methyl-9-methyladenine (m6m9A), a corresponding monomer of poly(m6A), with poly(BU) was investigated. Equilibrium dialysis experiments showed the stoichiometry of the interaction to be 1 m6A:2 BU. Thus, we would describe some structural studies of the above complexes using c.d. and i.r. spectroscopy. Poly (m6A).2poly(BU) and m6m9A.2poly(BU) are helical and analogous to each other in structure, and the bases in the complexes are all bound by hydrogen-bonding. N6-(delta 2-isopentenyl)- and N6-allyl-9-methyladenine were also found to form complexes with poly(BU), giving similar c.d. spectra with that of m6m9A.2poly(BU). The melting experiments indicated the Tms to be substantially decreased, compared to the parent unmodified complexes, even though the Tm dependence of the polymer complex on salt concentration conforms to the typical triple strand. In the following, the biological significance of this novel pairing will be discussed.
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PMID:Interactions of poly-N6-methyladenylic acid and N6-substituted-9-methyladenines with poly-5-bromouridylic acid: a novel base-pairing. 391 14

A crude in vitro transcription system which selectively transcribes DNA fragments containing the promoter region of the Tetrahymena pyriformis rRNA gene has been prepared from T. pyriformis. The system requires both an S100 fraction of lysed isolated macronuclei and an S100 extract of whole cells. When a HhaI-HindIII fragment of the promoter containing plasmid pEN 19-1 is employed as a template, transcription yields two major products of about 560 (A) and 510 (B) bases in length. The analysis of the transcription products of truncated templates showed that RNA A is a runoff transcript and RNA B is produced by nucleolytic cleavage of RNA A at a site about 50 nucleotides to the left of the HindIII cleavage site. S1 nuclease mapping was used to demonstrate that the 5' end of RNA A is identical with that predicted for a transcript which was initiated at the same site on the gene as the in vivo 35S rRNA precursor. Transcription is dependent upon the addition of promoter containing DNA, is inhibited by 1 microgram/mL actinomycin D, and is insensitive to 200 micrograms/mL alpha-amanitin. Transcription is dependent upon the salt levels in the assay exhibiting activity peaks at 58 mM KCl, 28 mM (NH4)2SO4, and 3 mM MgCl2. Several minor transcription start sites to the left of the major initiation site become active at high salt, yielding several minor longer transcripts. High salt also inhibits the RNA cleavage activity, reducing the levels of RNA B produced.
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PMID:Characterization of a crude selective PolI transcription system from Tetrahymena pyriformis. 608 6

Single-stranded DNA is not transcribed randomly by yeast RNA polymerase B. A denatured yeast DNA fragment, containing the gene for yeast alcohol dehydrogenase I, directs the transcription of defined RNA products visualized as discrete RNA . DNA hybrid bands following S1 nuclease treatment and agarose gel electrophoresis. Blocking the 3' end of the template by 3' deoxyadenosine did not change the band pattern but reduced the proportion of RNA covalently bound to the DNA from 20 to 4%. On the other hand, the band pattern was affected by the salt concentration, the nature of the divalent cation and the nucleoside triphosphate concentration. The four major RNA bands, found at low substrate concentration, hybridized to the same region of the template. This observation suggests the potential requirement for DNA destabilization in gene activation.
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PMID:Single-stranded DNA transcription by yeast RNA polymerase B. 617 53

We find that the cloned DNAs of human U1 small nuclear RNA genes contain two nuclease S1-sensitive sites, one about 1.8 kilobases downstream of the U1 RNA coding region and the other around 0.3 kilobase upstream. The downstream site is unusually sensitive to the nuclease, being cleaved in both linear and negatively supercoiled DNAs. The extent of cleavage at this site is enhanced at lower pH and reduced concentrations of NaCl; the effects of salt are more apparent on linear than supercoiled DNAs. The nuclease S1 sensitivity of this downstream site is dependent on the presence of the sequence (dC-dT)n X (dA-dG)n, where n = 15-25. (One gene with n = 5 is resistant to nuclease S1 cleavage in this region.) In contrast, the nuclease S1 site upstream of the coding region is cleaved only when the DNA is supercoiled. This site also has a homopyrimidine X homopurine bias in the DNA strands, but the sequence is less regular. In the course of these studies, we detected several discrepancies between our restriction maps of some U1 RNA genes and those published by others. Our maps demonstrate that all seven cloned human U1 RNA genes are very similar in sequence for as much as 2.3 kilobases downstream of the U1 RNA coding region.
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PMID:Human U1 RNA genes contain an unusually sensitive nuclease S1 cleavage site within the conserved 3' flanking region. 620 12

Bacteriophage T7 DNA reacts uniformly with trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene(anti-BPDE). The reaction product retains the native configuration so that only one site sensitive to S1 nuclease is produced for every 70 anti-BPDE adducts. DNA treated with anti-BPDE is retained on benzoylated naphthoylated DEAE-cellulose even after washing with 1.0 M salt solutions. About 100 adducts per T7 molecule are required for adherence which is not due to breaks or single-stranded regions since adherence is not affected by S1 nuclease treatment. The binding of anti-BPDE reacted DNA to benzoylated naphthoylated DEAE-cellulose is cooperative and requires many residues per bound fragment. Treatment of T7 DNA treated with anti-BPDE with restriction endonuclease yields smaller molecules, still containing adducts, which do not adhere. We interpret these results to mean that reaction with BPDE does not involve deformation of the DNA structure and that the adducts lie in a position which they are readily accessible for interaction with aromatic groups on the column resin.
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PMID:Reaction of T7 DNA with a polycyclic aromatic hydrocarbon. Lack of structural perturbation. 624 97

Poly(dG-dC).poly(dG-dC) and poly(dG).poly(dC) were modified by treatment with N-acetoxy-N-2-acetylaminofluorene, and their conformations were examined by circular dichroism and susceptibility to nuclease S1 digestion. A sample of poly(dG-dC).poly(dG-dC) modified to an extent of 28% with acetylaminofluorene (AAF) at the C(8) position of the deoxyguanosine residues showed a circular dichroism spectrum that had the characteristics of the Z conformation seen in unmodified poly(dG-dC).poly(dG-dC) at high ethanol or salt concentrations. A sample of poly(dG-dC).poly(dG-dC) modified only 3% by AAF showed a spectrum characteristic of the B form of DNA. However, it was converted to the Z form at ethanol concentrations lower than required to convert unmodified poly(dG-dC).poly(dG-dC) from the B to the Z form. Poly(dG).poly(dC), which does not undergo the B-to-Z transition at high ethanol concentrations, did not show any large conformational changes with high AAF modification. Susceptibility to digestion with nuclease S1 also suggested differences in the conformations of the two modified polynucleotides. Poly(dG-dC).poly(dG-dC) modified by AAF to an extent of 28% was almost completely resistant to nuclease S1 digestion. However, both poly(dG).poly(dC) and DNA modified to similar levels by AAF were highly susceptible to nuclease S1 digestion. Two different conformations for AAF-modified deoxyguanosine are proposed, depending on whether its position is in alternating purine-pyrimidine sequences or in random-sequence DNA.
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PMID:Induction of the Z conformation in poly(dG-dC).poly(dG-dC) by binding of N-2-acetylaminofluorene to guanine residues. 626 1


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