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:3.1.31.1 (micrococcal nuclease)
2,818 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The assembly of chromatin from newly synthesized nucleosomal histones (labeled with [3H]arginine) and new DNA (density-labeled with [125I]iododeoxyuridine)was studied in growing cultured mouse cells. The nucleosomal histones were specifically examined by dissociating histone H1 and nonhistone proteins from unsheared chromatin either by incubation in 0.6 M NaCl or by digestion with micrococcal nuclease to release nucleosomes. In both cases, the four nucleosomal histones (H2A, H2B, H3, and H4) are essentially the only proteins that remain bound to DNA and that are labeled by [3H]arginine. After formaldehyde fixation, H1-depleted chromatin containing dense DNA can be completely resolved in CsCl buoyant density gradients from that containing unreplicated DNA; separation of nucleosomes is satisfactory although less complete. New DNA and new histones are already assembled into chromatin possessing characteristic nucleosomal structure after 3 min of synthesis (the shortest time studied), as shown by the kinetics of digestion of new DNA by micrococcal nuclease, by the distribution of new DNA and new histones in nucleosomes. However, after 3-30 min of synthesis most new nucleosomal histones are associated with unreplicated DNA rather than with new DNA. It is concluded that new nucleosomes are assembled on DNA at some distance from DNA replication sites, with concomitant migration of preexisting nucleosomes onto new DNA.
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PMID:Assembly of new nucleosomal histones and new DNA into chromatin. 27 57

It is shown by enzymatic digestion of chromatin from rat liver or Guerin ascites tumour (GAT) that treatments, which abolish the 180 base pair repeat, as revealed by digestion with micrococcal nuclease (shearing in salt solutions of medium ionic strength, sonication, fixation with formaldehyde in the presence of 5 M urea), have little effect on the 10 nucleotide repeat, observed in deoxyribonuclease I digests.
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PMID:Persistence of the ten-nucleotide repeat in chromatin unfolded in urea, as revealed by digestion with deoxyribonuclease i. 96 74

We describe a method of isolating a homogeneous population of "trimmed" monomeric nucleosomes from Hela cells. These nucleoprotein particles contain a 140 +/- 5 base pair length of DNA and have a histone/DNA ratio of 1.2. They lack H1 and contain equal amounts of the four smaller histones. The DNA contains no single strand nicks. The particles sediment with an S20,w of 11S in D2O density gradients. After formaldehyde fixation, they band at a density of 1.4370 in neutral CsCl. Digestion of nucleosomes with either micrococcal nuclease or DNase I generates the same pattern of DNA fragments observed when intact nuclei are digested. Circular dichroism spectra indicate that the 280 nm positive ellipticity maximum of nucleosomes is about one-half that of chromatin. In the presence of 6 M urea, nucleosomes sediment with an S20,w of 6S, have a multiphasic thermal denaturation profile, and exhibit a circular dichroic spectrum nearly identical to that of B-form DNA. Our yield of purified nucleosomes (10-15% of the input DNA) is similar to the yields of other methods; our nucleosome population is substantially more homogeneous than those previously reported.
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PMID:Preparation and physical characterization of a homogeneous population of monomeric nucleosomes from HeLa cells. 96 93

Nucleolar organizer region (NOR) silver staining was applied to sections of fixed material. A positive reaction on cryo-ultrathin sections was found as well as on semithin and ultrathin Lowicryl sections. Repeatable staining that was easy to control was obtained by a one-step procedure after aldehyde-Carnoy fixation. Fixation of the material by formaldehyde and glutaraldehyde alone in cacodylate buffer also maintained reaction selectivity when ammonium chloride was used after fixation. Enzymatic digestion by pronase, RNase A, DNase I, or micrococcal nuclease was applied to ultrathin Lowicryl sections. Pronase digestion removed the silver-stained proteins, whereas digestion by the nucleases did not. A routine procedure is proposed for easy NOR silver staining of sections that preserves a good tissue ultrastructure and is also compatible with cytochemical and immunological investigations.
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PMID:Silver staining of the nucleolar organizer regions (NORs) on Lowicryl and cryo-ultrathin sections. 258 Aug 79

Androgen receptors were attached covalently in situ to their nuclear acceptor sites with the contact site cross-linker, formaldehyde. Chromatin, prepared from sonicated nuclei of rat prostate, was labeled by isotope exchange with [3H]dihydrotestosterone and found to contain 19,000 +/- 900 (mean +/- S.E.) salt-extractable androgen receptors/nucleus which sedimented in the 3-4 S region of 7.6-76% (v/v) glycerol gradients and at a density of approximately 1.28-1.35 g/ml in CsCl gradients. After incubation of the chromatin with 0.5% (w/v) formaldehyde for 1 h at 4 degrees C, there was a 90% reduction in the concentration of free androgen receptors and an increase in the density of the androgen binding sites recovered from CsCl gradients. Extensive digestion of the cross-linked chromatin with micrococcal nuclease liberated 18% of the androgen receptors as 3-4 S entities and caused an overall decrease in the density of the receptor-acceptor complexes. Ribonuclease digestions had no effect on the androgen receptors cross-linked to chromatin. Mild digestion of the cross-linked preparations with trypsin, alone or in combination with micrococcal nuclease, resulted in the release of 74% and 97% of the androgen receptors, respectively. Together, these findings imply that two classes of receptor-acceptor complexes are present in prostatic chromatin--one, containing about 20% of the androgen receptors in which the receptors are in direct contact with DNA but not with proteins and the other, containing most of the androgen receptors in which the receptors are adjacent to acceptor proteins but not to DNA.
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PMID:In situ cross-linking of androgen receptors to nuclear acceptor sites of rat prostate with formaldehyde. 401 1

Replicating simian virus 40 (SV40) chromosomes were found to be similar to other eukaryotic chromosomes in that the rate and extent of micrococcal nuclease (MNase) digestion were greater with replicating than with nonreplicating mature SV40 chromatin. MNase digestion of replicating SV40 chromosomes, pulse labeled in either intact cells or nuclear extracts, resulted in the rapid release of nascent DNA as essentially bare fragments of duplex DNA (3-7S) that had an average length of 120 base pairs and were degraded during the course of the reaction. In addition, nucleosomal monomers, equivalent in size to those from mature chromosomes, were released. On the other hand, MNase digestion of uniformly labeled mature SV40 chromosomes resulted in the release of only nucleosomal monomers and oligomers. The small nascent DNA fragments released from replicating chromosomes represented prenucleosomal DNA (PN-DNA) from the region of replication forks that encompasses the actual sites of DNA synthesis and includes Okazaki fragments. Predigestion of replicating SV40 chromosomes with both Escherichia coli exonuclease III (3'-5') and bacteriophage T7 gene 6 exonuclease (5'-3') resulted in complete degradation of PN-DNA. This result, together with the observation that isolated PN-DNA annealed equally well to both strands of SV40 restriction fragments, demonstrated that PN-DNA originates from both sides of replication forks. Over 90% of isolated Okazaki fragments annealed only to the retrograde DNA template. The characteristics of isolated PN-DNA were assessed by examining its sensitivity to MNase and single strand specific S1 endonuclease, sedimentation behavior before and after deproteinization, buoyant density in CsCl after formaldehyde treatment, and size on agarose gels. In addition, it was observed that MNase digestion of purified SV40 DNA also resulted in the release of a transient intermediate similar in size to PN-DNA, indicating that a DNA-protein complex is not required to account for the appearance of PN-DNA. These and other data provide a model of replicating chromosomes in which DNA synthesis occurs on a region of replication forks that is free of nucleosomes and is designated as prenucleosomal DNA.
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PMID:Structure of chromatin at deoxyribonucleic acid replication forks: prenucleosomal deoxyribonucleic acid is rapidly excised from replicating simian virus 40 chromosomes by micrococcal nuclease. 627 44

Micrococcal nuclease digestion of nuclei from sea urchin embryos revealed transient changes in chromatin structure which resulted in a reduction in the repeat length of nascent chromatin DNA as compared with bulk DNA. This was considered to be entirely the consequence of in vivo events at the replication fork (Cell 14, 259, 1978). However, a micrococcal nuclease-generated sliding of nucleosome cores relative to nascent DNA, which might account for the smaller DNA fragments, was not excluded. In vivo [3H]thymidine pulse-labeled nuclei were fixed with a formaldehyde prior to micrococcal nuclease digestion. This linked chromatin proteins to DNA and thus prevented any in vitro sliding of histone cores. All the nascent DNAs exhibiting shorter repeat lengths after micrococcal nuclease digestion, were resolved at identical mobilities in polyacrylamide gels of DNA from fixed and unfixed nuclei. We conclude that these differences in repeat lengths between nascent and bulk DNA was generated in vivo by changes in chromatin structure during replication, rather than by micrococcal nuclease-induced sliding of histone cores in vitro.
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PMID:Reduced repeat length of nascent nucleosomal DNA is generated by replicating chromatin in vivo. 673 96

Covalent adducts formed by the reaction of DNA with chemical carcinogens and mutagens may be detected by a 32P-labeling test. DNA preparations exposed to chemicals known to bind covalently to DNA [N-methyl-N-nitrosourea, dimethyl sulfate, formaldehyde, beta-propiolactone, propylene oxide, streptozotocin, nitrogen mustard, and 1,3-bis(2-chloroethyl)-1-nitrosourea] were digested to a mixture of deoxynucleoside 3'-monophosphates by incubation with micrococcal endonuclease (EC 3.1.31.1) and spleen exonuclease (EC 3.1.16.1). The digests were treated with [gamma-32P]ATP and T4 polynucleotide kinase (ATP:5'-dephosphopolynucleotide 5'-phosphotransferase, EC 2.7.1.78) to convert the monophosphates to 5'-32P-labeled deoxynucleoside 3',5'-bis-phosphates. These compounds were then separated on polyethyleneimine-cellulose thin layers in ammonium formate and ammonium sulfate solutions. Autoradiograms of the chromatograms obtained by this high-resolution procedure showed the presence of nucleotides derived from chemically altered, as well as normal, DNA constituents. Maps from DNA exposed to any of the chemicals used exhibited a spot pattern typical for the particular chemical. This method detected a single adduct in 10(5) DNA nucleotides without requiring that the compound under investigation be radioactive and thus provides a useful test to screen chemicals for their capacity to damage DNA by covalent binding.
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PMID:32P-labeling test for DNA damage. 703 43

Ethidium bromide and polylysine interact with nucleosomal DNA and lead to change of biochemical properties and to morphological changes as to the distance between the two core particles of a nucleosome dimer. With increasing polylysine concentration, the buoyant density of nucleosomes decrease and the accessibility of the nucleosomal DNA to micrococcal nuclease is lowered. Electron microscopy of polylysine treated nucleosome dimers reveals a shortening of the internucleosomal distance as compared with controls. Treatment of nucleosomes with ethidium bromide leads to an enhanced accessibility of the nucleosomal DNA to micrococcal nuclease. Electron microscopy reveals an increase in length of the DNA connecting the two nucleosome cores in the presence of the dye. Both the binding of polylysine and the treatment with ethidium bromide apparently do not affect the histone arrangement within the nucleosome core as suggested by chemical cross-linking of histones and DNA with formaldehyde, and no obvious morphological change of the nucleosome cores can be observed.
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PMID:Binding of polylysine and ethidium bromide to nucleosomal DNA: comparison of biochemical and electron microscopical results. 721 Aug 13

It is shown that whole cells can be effectively fixed in the presence of formaldehyde at -12 degrees C. This reaction is used for the study of the native structure of chromatin. In the nuclei isolated from fixed cells the chromatin has the nucleosomal structure. The size of nucleosomal DNA in these nuclei estimated by hydrolysis with staphylococcal nuclease does not differ significantly from repeat length in the nuclei fixed after isolation or in non-fixed nuclei. However it is shown that mono- and oligonucleosomes in the nuclei from fixed whole cells are significantly more stable to the exonucleolytic degradation than in either nuclei fixed after isolation or non-fixed nuclei. The results suggest that the nuclei isolation does not appreciably affect the chromatin structure. The fixation of whole cells by formaldehyde in frozen suspension can be used also to study the structure of other cellular components and macromolecular complexes directly in the whole cell.
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PMID:[Length of nucleosomal DNA repeat in whole cells, fixed by freezing in the presence of formaldehyde]. 740


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