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B R Shaw

Publications and source records attributed to B R Shaw.

At least 55 records · Page 3Linked to original sources
PubMed1984

Levels of histone H4 diacetylation decrease dramatically during sea urchin embryonic development and correlate with cell doubling rate.

Basic proteins in nuclei and nucleosomes at different stages of development in Arbacia punctulata sea urchins were analyzed directly by in situ protamine release of chromosomal proteins into Triton/acid/urea-polyacrylamide gels. The predominant protein band in the H4 region of 2-cell through 64-cell stage embryos migrates with the mobility expected for diacetylated histone H4 (i.e. H4aa), whereas after blastulation (approximately 300 cells) the predominant H4 species is the unmodified form, H4O. In early embryos this H4aa band is highly labeled in vivo with [3H]acetic acid. The ratio of H4aa:H4O is more than 20-fold greater at the rapidly dividing 2-cell stage than at pluteus stage. This is true for both newly synthesized H4 labeled with [3H]lysine and total H4 (stained). Enhanced acetylation is also found in nucleosomes. The relative amount of this acetylated H4 species correlates roughly with the rate of cell doubling during early embryogenesis, and decreases as the average nucleosomal repeat increases. The results are indicative of a dynamically changing chromatin structure through development, as well as an intimate role of diacetylated histone H4 in the maturation of newly replicated chromatin.

Acetylation↗
PubMed1984

Diffusible factors are responsible for differences in nuclease sensitivity among chromatins originating from different cell types.

We have examined the kinetics of nuclease digestion of chromatin from committed and uncommitted cells in experiments where the nuclei are mixed and co-digested. Cultures of the sea urchin, Arbacia punctulata, were grown to the 16-cell stage in either [3H]thymidine or [14C]thymidine and the macromere, mesomere, and micromere cell types separated. After isolation, sets of nuclei with two different blastomere types (each having different radionucleotide tagging) were mixed and co-digested with micrococcal nuclease or DNase. I. The extent of digestion was monitored by solubility in 5% perchloric acid (PCA). We find no significant differences in initial digestion rates or limit digests among the different cell types when co-digested with either nuclease. Differences in nuclease sensitivity observed when nuclei are digested separately are abolished when nuclei are probed in a mixing experiment. The results support the hypothesis that phenotypic differences in digestibility among different cell types in vitro reflect differences in chromatin-condensing factors which can diffuse between nuclei.

Animals↗
PubMed1983

Shortest nucleosomal repeat lengths during sea urchin development are found in two-cell embryos.

Prior to fertilization, sperm possess one of the longest nucleosome repeat lengths yet determined [approximately 250 base pairs (bp) for the sea urchin Strongylocentrotus purpuratus]. We show here that the two-cell embryo has an average repeat size of 189 +/- 2 bp as probed by micrococcal nuclease; this is the shortest average nucleosomal subunit reported for S. purpuratus. By the eight-cell stage, the average nucleosome repeat increases to 201 +/- 2 bp, and it subsequently increases further during development. These results indicate that a dramatic rearrangement of chromatin occurs upon fertilization and that this chromatin remodeling continues through early development. When two-cell embryos are labeled for 30 min with [3H]thymidine and digested briefly, they exhibit nuclease-hypersensitive fragments averaging 308 bp in size, which are consistent with the size of protected DNA units in replication intermediate complexes at blastula stage (as described by Levy and Jacob [Levy, A., & Jacob, K. M. (1978) Cell (Cambridge, Mass.) 14, 259]). Our results are consistent with two general propositions: (1) long repeat lengths are found in highly differentiated cells, and (2) short repeat lengths are characteristic of cells more active in cell division. Our data would also imply that a rapid increase in the DNA complement, e.g., in the transition from haploid to diploid state following fertilization, is accompanied by a shortening of the average size of DNA in a nucleosome after replication.

Animals↗
PubMed1983

Silver staining of histones in Triton-acid-urea gels.

A reliable method for silver staining histones in Triton-acid-urea gels was developed. Optimum staining is achieved by treating the gels either with amido black or a colorless, water-soluble analog of amido black, 2,7-naphthalenedisulfonic acid, prior to staining with ammoniacal silver. Staining of purified calf thymus histones H2A, H2B, H3, and H4 by this method is 30 times more sensitive than staining with amido black alone, allowing the detection of each histone and its modified forms down to the nanogram level. The use of 2,7-naphthalenedisulfonic acid dramatically shortens the procedure permitting histone patterns to be visualized within 5 h.

Acetates↗
PubMed1981

Structural differences in the chromatin from compartmentalized cells of the sea urchin embryo: differential nuclease accessibility of micromere chromatin.

The chromatin structure of three cell types isolated from the 16-cell stage sea urchin embryo has been probed with micrococcal nuclease. In micromeres, the four small cells at the vegetal pole, the chromatin is found to be considerably more resistant to degradation by micrococcal nuclease than chromatin in the larger mesomere and macromere cells which undergo more cellular divisions and are committed to different developmental fates. The micromeres show an order of magnitude decrease in the initial digestion rate and a limit digest value which is one third that of the larger blastomeres; both observations are suggestive of the formation of a more condensed chromatin structure during the process of commitment, or as the rate of cell division decreases. The decreased sensitivity to nuclease for micromeres is similar to results reported for sperm and larval stages of development.

Animals↗
PubMed1977

Hydrodynamic evidence in support of spacer regions in chromatin.

Quasi-elastic light scattering and sedimentation velocity methods were used to study the hydrodynamic properties of purified dimer subunits obtained from partial digestion of chicken erythrocyte chromatin with staphylococcal nuclease. The experimental value of 1.87 +/- 0.08 X 10(-7) gram per second for the friction factor of these dimer subunits in low ionic strength buffer cannot be reasonably interpreted in terms of a contiguous sphere model. Analysis by means of an equivalent dimer method suggests that the spacer region accounts for a maximum of 19 percent of the friction properties of the dimer.

Animals↗
PubMed1976

Analysis of subunit organization in chicken erythrocyte chromatin.

Micrococcal nuclease digestion of intact chicken erythrocyte nuclei is shown to result in the formation of core nucleoprotein particles containing about 140 base pairs of DNA. These core particles, which are almost entirely devoid of histones f1 and f2c, are derived from transient nucleoprotein particles containing an average of approximately 180 base pairs of DNA. Oligomers of these latter particles may be isolated after brief nuclease digestion. The time course of digestion of these oligomers demonstrates the existence of "spacer" regions of more accessible DNA between core particles. Redigestion of purified monomer core nucleoprotein particles gives rise to both single-strand and double-strand DNA fragment patterns similar to those resulting from digestions of chromatin in situ. This observation indicates that the core particles we isolate are representative of nucleoprotein structures existing within the nucleus.

Animals↗
PubMed1974

A model for particulate structure in chromatin.

A model is proposed for the structure of nuclease-resistant chromatin particles. The model is novel in that it proposes that the DNA in such a particle is wound about a protein core, made up of the hydrophobic regions of histone molecules.

Animals↗
PubMedDate not supplied

Studies on base-boronated oligonucleotides. 2 (1). Incompatibility of DMT and cyanoborane groups during oligonucleotide synthesis.

The cyanoborane (-BH2CN) nucleosides and nucleotides are a new class of compounds that mimic natural and synthetic congeners in many ways and exhibit interesting biochemical and biophysical properties. The B-N bond is isoelectronic with the C-N+ bond of N7-alkylated 2'-nucleosides, as well as the C-C bond of naturally occurring 7-alkyl-7-deazanucleosides. These compounds differ from normal guanosine in that they are incapable of hydrogen bonding at the 7-position. The syntheses of N7-cyanoborane 2'-deoxyguanosine, N2-(dimethylaminomethylene)-N7-cyanoborane 5'-(dimethoxytrityl)-2'-deoxyguanosine (3), and N2-isobutyryl-N7-cyanoborane 5'-(dimethoxytrityl)-2'-deoxyguanosine (9) are described. Removal of the dimethoxytrityl (DMT) group from 3 or 9 is accompanied by significant loss of the cyanoborane moiety. Additionally, dimethoxytritylation of a cyanoboronated nucleoside leads to partial deboronation, thus limiting use of the commercially available 5'-DMT nucleosides as viable precursors in base-boronated oligonucleotide synthesis. The incompatibility of the cyanoborane moiety under DMT removal/addition conditions necessitated the search for an alternative method of protecting the 5'-hydroxyl of the nucleoside. This paper addresses the possible cause of deboronation and describes the synthesis of N7-cyanoboronated nucleosides by a method that avoids transient protection of the sugar hydroxyls.

Boron Compounds↗
PubMedDate not supplied

Deamination of single-stranded DNA cytosine residues in aerobic nitric oxide solution at micromolar total NO exposures.

Deamination of cytosine to uracil is a potential source of mutations in DNA. Here we examine the deaminating ability of aerobic nitric oxide (NO) toward single-stranded DNA at very low (micromolar and below) total exposures, using a sensitive genetic method that allows us to study a single deamination event at a specific site in a 7200-nucleotide DNA molecule within a pool of ca. 100,000 other identical DNA molecules. We incubated gapped C141 M13mp2 DNA with the NO-generating compound, Et2N[N(O)NO]Na (DEA/NO), in aerobic buffer for 16 h to ensure complete autoxidation at pH 7.4 and 37 degrees C. After ultrafiltration to remove small molecules, the DNA was transformed into isogenic Escherichia coli cultures that were either deficient (NR9404, ung-) or proficient (MC1061, ung+) in uracil-DNA glycosylase activity. The gapped DNA was constructed such that the target (CCC) codon was contained in a short single-stranded segment of otherwise double-stranded circular DNA, and the incubation was performed in a closed system to prevent loss of NO to the atmosphere before the reaction was complete. An increase in the reversion frequency in the ung- strain was noted between 0 and 1 microM DEA/NO, and the reversion frequency leveled out between 3 and 30 microM. However, 30 microM "spent" DEA/NO (i.e., that which was similarly incubated for 4 h to complete the autoxidation of NO before the DNA was added) did not increase reversion frequency relative to control. Nearly all (42/43) of the mutations identified after 1 microM DEA/NO treatment were C-->T transitions, and reversion frequency in the isogenic ung+ strain was lower than in the ung- strain. The data are consistent with the hypothesis that total NO exposures in the mumol/L range can lead to C-->T mutations via a mechanism most probably involving deamination of DNA cytosine residues.

Aerobiosis↗
PubMedDate not supplied

Boranophosphate nucleic acids--a versatile DNA backbone.

Important chemical and biochemical properties of boranophosphate DNA and RNA oligonucleotides are reviewed. Stereoregular boranophosphate oligomers can be synthesized enzymatically and form stable duplexes with DNA. Fully boronated, non-stereoregular oligothymidylates, synthesized chemically, form hybrids with poly(A) that have lower melting points than oligothymidylate:poly(A), yet they nevertheless can support the RNase H mediated cleavage of RNA.

Boron Compounds↗