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B R Shaw

Publications and source records attributed to B R Shaw.

At least 19 recordsLinked to original sources
PubMed1995

Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies.

A set of three 14mer oligodeoxyribonucleotides of sequence d(5'-CTATGGCCTCAG*CT-3'/3'-GATACCGGAGTCGA-5') containing G* variants either as 2'-deoxyguanosine phosphate (unmodified), N7-cyanoborane 2'-deoxyguanosine phosphate (base-modified) or 2'-deoxyguanosine boranophosphate (backbone-modified) were synthesized by template-directed primer extension. Both the N7-cyanoborane 2'-deoxyguanosine triphosphate and 2'-deoxyguanosine alpha-boranotriphosphate nucleotides are good substrates for Sequenase. We infer that a single Sp boranophosphate linkage (which has a stereochemistry equivalent to the corresponding Rp thiophosphate analog) is formed in the backbone-modified 14mer. Thermally induced helix-coil transitions were monitored for the hybridized duplexes using UV and circular dichroism (CD) spectroscopy. The CD spectra of the two types of boron-modified hybrids closely resemble the unmodified parent duplex, forming B-type helices in 150 mM NaCl, 1 mM EDTA, 10 mM phosphate, pH 7.4, buffer. UV melting results indicate that both hybrids have stabilities comparable with the parent duplex as measured by Tm or delta G degree 25. These studies indicate that singly modified base- or backbone-boronated DNA are good analogs of normal DNA.

Base Sequence↗
PubMed1995

N7-cyanoborane-2'-deoxyguanosine 5'-triphosphate is a good substrate for DNA polymerase.

The 5'-triphosphate of the boronated nucleoside analog N7-cyanoborane-2'-deoxyguanosine (7bdGTP) was synthesized, and a series of experiments was initiated to assess the potential of the compound to serve as a substrate for DNA polymerases. We show here that 7bdGTP can be incorporated into DNA by Sequenase. The resulting hemiboronated extension products are resistant to cleavage by treatment with either DMS and heat or a number of restriction enzymes. Further, in the polymerase chain reaction, 7bdGTP can be utilized as a substrate for Taq polymerase. Finally, by kinetic analysis, we have found that 7bdGTP is a more efficient substrate for exonuclease-free Klenow than normal dGTP. Thus, the introduction of a cyanoborane moiety to the N7 position of dGTP results in a nucleotide that is accepted in lieu of normal dGTP by a number of DNA polymerases.

Base Sequence↗
PubMed1993

Echinomycin, a bis-intercalating agent, induces C-->T mutations via cytosine deamination.

Echinomycin, a bis-intercalating, antitumor drug, has been studied for its ability to induce the deamination of cytosine to uracil (C-->U) in double-stranded DNA. We have employed a sensitive lacZ alpha-complementation reversion assay to detect G.C-->A.T mutations at a number of sites in M13mp2 DNA to determine the extent to which distortions of DNA structure induced by echinomycin may affect C-->U rates. When double-stranded M13mp2 DNA with a 12-base target containing a CpG site was incubated at 37 degrees C, the reversion frequency of the echinomycin-treated DNA increased linearly over time, with a rate constant 3-fold greater than DNA incubated without echinomycin. Of the 11 ways that blue pseudo-revertants can occur in the target, 96% of the observed revertants arose from C-->T and tandem CC-->TT transitions, with 78% attributable to single-base C-->T changes at three sites. Transfection into ung+ cells decreased the reversion frequencies by 85% to near background levels, indicating that the increase in C-->T mutations was due to deamination of C to U. The cytosine deamination rate constants for the entire target at pH 6.0 and 37 degrees C were 1.2 x 10(-11) sec-1 for untreated DNA and 3.5 x 10(-11) sec-1 for echinomycin-treated DNA. The increase in C-->T mutation rates occurred at cytosines both proximal and distal to a CpG echinomycin-binding site. We hypothesize that this increase in deamination rate is due to a more open or single-stranded DNA structure caused by the echinomycin: DNA interaction.

Base Sequence↗
PubMed1992

Variable temperature infrared spectroscopy of cytosine-guanine base pairs: tautomerism versus polarization.

This report describes an infrared (IR) spectroscopic study of a model cytosine-guanine base pair. This base pair is part of a self-consistent experimental system based on lipophilic ribose derivatives of cytidine (C), guanosine (G) and O6-methylguanosine (O6MeG) that are soluble in non-aqueous, low dielectric solvents at appreciable concentrations. Previous experiments on this system have revealed different rotation dynamics for the amino bonds within the CG base pair, an observation that could be explained by the presence of rare tautomers (P.O. Lowdin, Reviews of Modern Physics 35,724 (1963)), or by mutual polarization of the base pairs (L.D. Williams, N.G. Williams and B.R. Shaw,J.Am.Chem.Soc. 112,829 (1990)). The IR spectra in the OH and NH stretching region indicate formation of hydrogen-bonded CG base pairs and self associates in 1,2-dichlorobenzene over a temperature range from 10 to 290K. Changes in the lineshapes and intensities of the IR bands with temperature correlate with phase transitions of the solvent, but no evidence is seen for an OH stretching band that would indicate the formation of hydroxyl tautomers within base pairs. Similarly, the relative intensities of the C = O stretching bands of CG in cyclohexane solution remain constant over this same temperature range, confirming that within the base pair, the tautomeric states of the bases remain essentially unperturbed in the 2-amino/6-keto form of G and the 2-keto/4-amino form of C. The spectra of O6-MeG aid in the band assignments, since this molecule is frozen in an equivalent of the 2-amino/6-hydroxyl tautomer, but without the OH group and its associated stretching band. We conclude that the probability of tautomerism does not appear to be sufficient to explain the different rotation dynamics for the two amino bonds of the CG base pair. Rather it is argued that mutual polarization within the base pair, which would increase the bond order of the amino bond of C within the base pair, can explain the results without the formation of unconventional tautomers.

Base Composition↗
PubMed1992

The synthesis and anti-neoplastic activity of N2-isobutyryl-2'-deoxyguanosine-N7-cyanoborane derivatives.

N2-Isobutyryl-2'-deoxyguanosine-N7-cyanoborane derivatives were observed to be potent antineoplastic agents and to be active against a number of human tissue culture tumor cells, e.g. Tmolt3 leukemia, HeLa-S3 uterine carcinoma. Selective agents were active against colon adenocarcinoma, osteosarcoma and glioma growth. These agents preferentially inhibited both DNA and RNA synthesis of L1210 cells. De novo synthesis of purines was significantly inhibited at the regulatory sites of PRPP amido transferase and IMP dehydrogenase. Other sites of inhibition were thymidylate synthetase, OMP decarboxylase and thymidine kinases. The agents also significantly reduced deoxyribonucleotide levels and caused DNA strand scission.

Animals↗
PubMed1990

A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy.

Previously it has not been possible to determine the rate of deamination of cytosine in DNA at 37 degrees C because this reaction occurs so slowly. We describe here a sensitive genetic assay to measure the rate of cytosine deamination in DNA at a single cytosine residue. The assay is based on reversion of a mutant in the lacZ alpha gene coding sequence of bacteriophage M13mp2 and employs ung- bacterial strains lacking the enzyme uracil glycosylase. The assay is sufficiently sensitive to allow us to detect, at a given site, a single deamination event occurring with a background frequency as low as 1 in 200,000. With this assay, we determined cytosine deamination rate constants in single-stranded DNA at temperatures ranging from 30 to 90 degrees C and then calculated that the activation energy for cytosine deamination in single-stranded DNA is 28 +/- 1 kcal/mol. At 80 degrees C, deamination rate constants at six sites varied by less than a factor of 3. At 37 degrees C, the cytosine deamination rate constants for single- and double-stranded DNA at pH 7.4 are 1 x 10(-10) and about 7 x 10(-13) per second, respectively. (In other words, the measured half-life for cytosine in single-stranded DNA at 37 degrees C is ca. 200 years, while in double-stranded DNA it is on the order of 30,000 years.) Thus, cytosine is deaminated approximately 140-fold more slowly when present in the double helix. These and other data indicate that the rate of deamination is strongly dependent upon DNA structure and the degree of protonation of the cytosine. The data suggest that agents which perturb DNA structure or facilitate direct protonation of cytosine may induce deamination at biologically significant rates. The assay provides a means to directly test the hypothesis.

Bacteriophages↗
PubMed1989

Hydrolysis of N3-methyl-2'-deoxycytidine: model compound for reactivity of protonated cytosine residues in DNA.

Protonation of cytosine residues at physiological pH may occur in DNA as a consequence of both alkylation and aberrant base-pair formation. When cytosine derivatives are protonated, they undergo hydrolysis reactions at elevated rates and can either deaminate to form the corresponding uracil derivatives or depyrimidinate generating abasic sites. The kinetic parameters for reaction of protonated cytosine are derived by studying the hydrolysis of N3-methyl-2'-deoxycytidine (m3dC), a cytosine analogue which is predominantly protonated at physiological pH. Both deamination and depyrimidimation reaction rates are shown to be linearly dependent upon the fraction of protonated molecules. We present here thermodynamic parameters which allow determination of hydrolysis rates of m3dC as functions of pH and temperature. Protonation of cytosine residues in DNA, as induced by aberrant base-pair formation or base modification, may accelerate the rate of both deamination and depyrimidation up to several thousand-fold under physiological conditions.

Chemical Phenomena↗
PubMed1987

Base stacking and molecular polarizability: effect of a methyl group in the 5-position of pyrimidines.

Substitution of a methyl group in the 5-position of pyrimidines increases melting temperatures and modifies biological properties of DNA. Increased DNA stability is often attributed to hydrophobic interactions between water and the methyl group. However, we present evidence that the major effect of methyl substitution is to increase the molecular polarizability of the pyrimidine, thereby increasing the base stacking. Experimentally determined base stacking interaction constants for free bases in water are shown to correlate well with calculated molecular polarizability and DNA melting temperatures.

Adenine↗
PubMed1987

Histone modifications accompanying the onset of developmental commitment.

In the sea urchin, Strongylocentrotus purpuratus, three cell types comprise the 16-cell stage embryo: micromeres, macromeres, and mesomeres. We have analyzed these three cell types for nuclear proteins that were synthesized during the earliest stages of embryonic development. The most striking differences in composition of newly synthesized proteins were found between the micromeres, which are the most committed cell type, and the macromeres and mesomeres. First, the micromeres lacked triply modified forms of histone H3; the levels of doubly modified forms of H3 were also greatly reduced. In contrast, micromeres were enriched in a band which migrated at the position of unmodified, unacetylated, histone H3 protein. Second, the overall distribution of H2A histone variants differed among the three cell types. Compared with macromeres and mesomeres, micromeres had a higher ratio of alpha-stage to cleavage-stage (CS) histone H2A; the micromere nuclei were depleted by 50 and 35%, respectively, in embryonically synthesized histone CS-H2A. Third, micromeres displayed different profiles of H1 histones. (a) They contained a cleavage-stage H1 histone which migrated faster than that of macromeres and mesomeres. This protein displays the electrophoretic behavior expected for a protein with reduced levels of posttranslational covalent modification. (b) Micromeres also had reduced levels of an H1 histone (designated H1 alpha a) band found in the alpha-H1 region of macromeres and mesomeres. These changes in chromatin modification correlate with the degree of commitment of cells in the developing embryo; they may reflect differing activities of the chromatin modifying enzymes in the various cell types at the 16-cell stage. Thus, the newly synthesized chromatin proteins of the individual blastomere types already differ in the developing sea urchin by the 16-cell stage. We suggest that variations in histone subtypes and in the levels of activity of chromatin modifying enzymes, e.g., acetylases and phosphorylases, could be involved in commitment and differentiation of different cell types.

Acetylation↗
PubMed1987

DNA base modification: ionized base pairs and mutagenesis.

The nature of hydrogen bonding between normal and modified bases has been re-examined. It is proposed that hydrogen-bonding schemes may involve tautomeric, ionized or conformational forms (syn, anti and wobble). Several important cases are presented or reviewed in which physical evidence indicates the existence of ionized base pairs. When thermodynamic values determined in aqueous solution under physiological conditions are considered, it can be argued that base ionization will contribute substantially to the stability of many biologically relevant base pairs containing modified bases. A significant incidence of ionized bases in DNA may have important kinetic ramifications for the further chemical reactivity of both the modified base and its cross-strand pairing partner. Moreover, DNA structure at and surrounding ionized base pairs may be altered. For this reason, the model presented in this study should be useful as DNA-sequence analysis becomes more commonly applied to the study of mutagenesis.

Base Composition↗
PubMed1987

Protonated base pairs explain the ambiguous pairing properties of O6-methylguanine.

The base-pairing interactions of promutagenic O6-methylguanine (O6-MeGua) with cytosine and thymine in deuterated chloroform were investigated by 1H NMR spectroscopy. Nucleosides were derivatized at hydroxyl positions with triisopropylsilyl groups to obtain solubility in nonaqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. We were able to observe hydrogen-bonding interactions between nucleic acid bases in a solvent of low dielectric constant, a condition that approximates the hydrophobic interior of the DNA helix. O6-MeGua was observed to form a hydrogen-bonded mispair with thymine. Whereas O6-MeGua did not form hydrogen bonds with cytosine (via usual, wobble, or unusual tautomeric structures), it did form a 1:1 hydrogen-bonded complex with protonated cytosine. The pairing of unprotonated cytosine in chloroform is thus consistent with the known preference of O6-MeGua for thymine over cytosine in polymerase reactions. In contrast, the pairing of protonated cytosine is consistent with the greater stability of oligonucleotide duplexes containing cytosine.O6-MeGua as compared with thymine.O6-MeGua base pairs [Gaffney, B. L., Markey, L. A. & Jones, R. A. (1984) Biochemistry 23, 5686-5691]. Our observation that cytosine must be protonated in order to pair with O6-MeGua suggests that the cytosine.O6-MeGua base pair in DNA is stabilized by protonation of cytosine. Through this mechanism, methylation at the O6 position of guanine in double-stranded DNA could promote cross-strand deamination of cytosine (or 5-methylcytosine) to produce uracil (or thymine).

Base Composition↗
PubMed1986

Intraocular pressure elevation after pupillary dilation in open angle glaucoma.

Acute elevation of intraocular pressure frequently follows pupillary dilation in patients with primary open angle glaucoma. A retrospective study of 60 patients (116 eyes) with primary open angle glaucoma was done to assess the frequency and severity of intraocular pressure elevation following dilation with 2.5% phenylephrine hydrochloride (Neo-Synephrine) and 1% tropicamide (Mydriacyl). Significant pressure elevation (greater than 5 mm Hg) occurred in 37 eyes (32%). Marked pressure elevation (greater than 10 mm Hg) occurred in 14 eyes (12%). The only significant risk factor found was treatment with miotics. The change of intraocular pressure one hour after dilation was compared with the one-hour postoperative change in intraocular pressure in those patients (12 patients, 18 eyes) who subsequently underwent argon laser trabeculoplasty. No statistically significant correlation was found. There is a potential hazard of routine dilation of eyes with open angle glaucoma.

Adult↗
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↗