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PubMed1985

Binding of sanguinarine to deoxyribonucleic acids of differing base composition.

The binding of the alkaloid sanguinarine to natural DNAs of differing GC content has been studied by spectrophotometry and viscometry techniques. Binding parameters determined from spectrophotometric measurements by Scatchard analysis, according to an excluded-site model, indicate a very high specificity of sanguinarine binding to GC rich DNA. In the strong binding region, the increase of contour length of DNA depends strongly on its base composition, being larger with GC rich DNA than with AT rich DNA. It is concluded that the alkaloid binds preferentially to the GC pairs in DNA template.

Alkaloids↗
PubMed1993

Codon usage bias and base composition of nuclear genes in Drosophila.

The nuclear genes of Drosophila evolve at various rates. This variation seems to correlate with codon-usage bias. In order to elucidate the determining factors of the various evolutionary rates and codon-usage bias in the Drosophila nuclear genome, we compared patterns of codon-usage bias with base compositions of exons and introns. Our results clearly show the existence of selective constraints at the translational level for synonymous (silent) sites and, on the other hand, the neutrality or near neutrality of long stretches of nucleotide sequence within noncoding regions. These features were found for comparisons among nuclear genes in a particular species (Drosophila melanogaster, Drosophila pseudoobscura and Drosophila virilis) as well as in a particular gene (alcohol dehydrogenase) among different species in the genus Drosophila. The patterns of evolution of synonymous sites in Drosophila are more similar to those in the prokaryotes than they are to those in mammals. If a difference in the level of expression of each gene is a main reason for the difference in the degree of selective constraint, the evolution of synonymous sites of Drosophila genes would be sensitive to the level of expression among genes and would change as the level of expression becomes altered in different species. Our analysis verifies these predictions and also identifies additional selective constraints at the translational level in Drosophila.

Animals↗
PubMed1972

Deoxyribonucleic acid base composition of species in the yeast genus Kluyveromyces van der Walt emend. van der Walt.

The deoxyribonucleic acid base composition (percent guanine + cytosine [GC]) was determined for 29 strains, representing 18 species of the genus Kluyveromyces. It was concluded that on the basis of GC content (47.4%) and other properties K. veronae occupies an uncertain position in the genus Kluyveromyces. The GC content of the remaining 17 species ranged from 35.3 to 43.4%, and three groups of species were recognized. The GC content of the first ranged from 35.3 to 38.0%; that of the second group from 39.5 to 41.7%; that of the third group from 42.4 to 43.4%. Several species revealed a nearly identical GC content. The GC contents do not correspond in all instances with the five groups of species proposed by van der Walt.

Acetone↗
PubMedDate not supplied

Guidance of shrinkage vectors vs irradiation at reduced intensity for improving marginal seal of class V resin-based composite restorations in vitro.

This study evaluated the influence of radiation intensity on polymerization of a resin-based composite (RBC) and compared the influence of guidance of shrinkage vectors vs irradiation at reduced light intensity on the marginal seal of Class V RBC restorations in vitro. The degree of cure was studied indirectly by measuring the Vickers hardness (1.96 N, 30 seconds) at the bottom of disc-shaped specimens 2 mm in height at different periods of time after light irradiation. After one hour, irradiation using a high-intensity curing light (Heliolux GTE, Vivadent, 600 mW/cm2) [HICL] from close distance for 20 seconds, 40 seconds or 60 seconds or a low-intensity curing light (Vivalux, 250 mW/cm2) [LICL] from close distance for 60 seconds produced higher hardness values compared to 20 seconds or 40 seconds using the LICL or using the HICL from a distance of 10 mm. After three and 24 hours, higher hardness was observed for all irradiation protocols. After 24 hours, only specimens irradiated by the HICL for 20 seconds or 40 seconds from 10 mm distance featured significantly lower hardness compared to the remaining curing modes. The influence of different irradiation strategies on marginal seal of Class V RBC restorations was evaluated in vitro using dye penetration after water storage (60 days, 37 degrees C) and thermocycling (2500 cycles 5 degrees-55 degrees C). The HICL produced more dye penetration than the LICL. Placing the light tip directly over or 10 mm above the center of the cavity ("standard irradiation, ["distance irradiation"]") resulted in similar penetration values. In contrast, positioning the light tip apical to the cervical margin and moving it slowly to the center of the cavity ("cervical start irradiation") compromised the marginal seal.

Analysis of Variance↗
PubMed2004

Fracture resistance of resin-based composite and ceramic inlays luted to sound human teeth.

PURPOSE: To assess the fracture resistance of resin-based composites (Zeta, Targis, Solidex,) and ceramic (Vitadur Alpha) inlays luted to extracted sound human premolars and classify their fracture modes. METHODS: 40 extracted sound human premolars were prepared to receive an indirect inlay restoration. They were divided into four different restorative materials groups as follows: Group A, Vitadur Alpha; Group B, Zeta; Group C, Targis; and Group D, Solidex. All restorations were luted with a resin luting cement (Opal). Specimens were loaded to failure in compression, and statistically analyzed (ANOVA). Fracture modes were recorded. RESULTS: There were no statistical differences among the four groups (A, 1,070 +/- 313.8 N; B, 942.4 +/- 172.4 N; C, 1,039 +/- 271.9 N; D, 1,022 +/- 186.3 N). The predominant failure mode was a severe fracture of tooth and/or restoration.

Aluminum Oxide↗
PubMed1993

Heterochromatin study demonstrating the non-linearity of fluorometry useful for calculating genomic base composition.

A novel procedure for calculating base-pair frequencies in whole genomes is reported. This has been developed during a study of the role of heterochromatin in microevolution. Closely related species of the Crepis praemorsa complex have similar karyotypes but for their heterochromatin. The changes in relative AT frequency between species have been attributed to heterochromatin sequences by in situ banding of chromosomes with two base-specific fluorochromes. The absolute genome size of species, measured by cytofluorometry, correlated positively with increased karyotypic heterochromatin, as did the proportion of AT bases in the DNA. However, the determination of base content has called for a curvilinear interpretation of data obtained with two base-specific fluorochromes (bisbenzimide Hoechst 33342 and mithramycin), in contrast to the commonly assumed but erroneous direct relationship between fluorescence intensity and base content. Essentially, the fluorochromes' requirements for a sequence of certain base-pairs lead to the notion of Coefficients of Overspecificity: the result is a simple formula for calculating the AT proportion in a genome relative to a reference species from cytometric data, taking account of ligand binding statistics. These statistics and probabilities of oligonucleotide binding are essentially the same.

Adenine↗
PubMed1994

Influence of base composition on membrane binding and cellular uptake of 10-mer phosphorothioate oligonucleotides in Chinese hamster ovary (CHRC5) cells.

A key problem in antisense therapeutics is the relatively poor cell uptake of oligonucleotides and subsequent transport to the cytoplasm and nucleus. Although the chemical characteristics of oligonucleotides seem likely to affect their uptake by cells, little is known about this issue. In this article we explore the effect of base composition on oligonucleotide uptake. We show that phosphorothioate homo-G oligomers have a distinctly greater cellular uptake than other phosphorothioate homooligomers. This is probably due to a greater initial association with the plasma membrane, because homo-G oligomers show the greatest binding to liposome membranes, when tested at physiological ionic strength. Under different buffer conditions appreciable differences in membrane binding to liposomes were detected for the various homooligonucleotides.

Animals↗
PubMed1994

Inclusion of synthetic DNA templates of similar length and base composition to PCR-amplified products in restriction enzyme digestions: an efficient aid in characterization of point mutations.

Because of a subtle anomaly we encountered upon an analytical gel while characterizing a point mutation in an exon of a patient, we decided to perform expensive and time-consuming procedures to characterize the anomaly. Although initial and subsequent Southern blots and PCR analyses of this patient's mutation suggested that his mutation lay directly within a TaqI recognition site, further characterization revealed that the mutation actually lay in a base immediately outside the recognition site. Had we included an appropriate double-stranded DNA control in the restriction enzyme digestion of this patient's PCR-amplified exon, we could have arrived at the correct conclusion as to the location of the mutation without incurring high costs and time loss. This brief report depicts the use of DNA controls of appropriate length and base composition as a means of avoiding erroneous conclusions and expense in routine mutational analyses in the clinical setting.

Alleles↗
PubMed1998

Modified base compositions at degenerate positions of a mutagenic oligonucleotide enhance randomness in site-saturation mutagenesis.

Site-saturation mutagenesis, using degenerate oligonucleotide primers, is a frequently used method in introducing various mutations in a selected target codon. Oligonucleotides that are synthesized using equimolar concentrations of nucleoside phosphoramidites (dA, dC, dG, dT) in the positions to be saturated, result in a mutant population that is biased towards the original nucleotides. We found that this bias could be eliminated by modifying the concentrations of nucleoside phosphoramidites during the oligonucleotide synthesis. We synthesized eight degenerate oligonucleotides to saturate eight different codons, and sequenced a total of 344 mutagenized codons. In six of these eight oligonucleotides, we reduced to varying extents the concentrations of those nucleotides in the target positions that would form base pairs with the template. From the data, we analyzed the effects of different base compositions in the oligonucleotides when mutagenizing different codons, the influence of the positions of mismatches, and the significance of different non-Watson-Crick base pairs. Based on these results, we suggest levels to which different phosphoramidites should be reduced when synthesizing oligonucleotides for site-saturation mutagenesis.

Base Composition↗
PubMed1963

HETEROGENEITY OF DNA IN DENSITY AND BASE COMPOSITION.

Chromatography, on methylated-albumin columns, of DNA from calf thymus, mouse testis, and Bacillus subtilis, yielded, on elution by a sodium chloride gradient, fractions differing in density. The fractions eluted by higher sodium chloride concentrations had lower densities in a CsCl density gradient. Since DNA with higher guaninecytosine content is eluted from the column with lower concentration of sodium chloride and has higher density, the density heterogeneity of DNA is best interpreted as a result of heterogeneity of base composition. An extra band observed in calf-thymus DNA had a higher density than that of the main DNA; it was eluted at a lower concentration of NaCl, indicating a higher content of guanine and cytosine. On the other hand, an additional DNA component in the mouse-testis DNA had a lower density and also it was eluted at a lower salt concentration, possibly an indication of an unusual base component in its structure.

Animals↗
PubMed1967

Determination of the base composition of deoxyribonucleic acid by measurement of the adenine-granine ratio.

A method is described for determination of the base composition (as guanine+cytosine or adenine+thymine content) of DNA by accurate measurement of the adenine/guanine ratio. The DNA is hydrolysed with 0.03n-hydrochloric acid for 40min. to release the purines. The hydrolysate is subjected to ion-exchange chromatography on Zeo-Karb 225. Apurinic acids are eluted with 0.03n-hydrochloric acid and then guanine and adenine are eluted separately with 2n-hydrochloric acid. Guanine and adenine are each collected as a single fraction, and the amount of base in each case is determined by measuring the volume and the extinction at suitable wavelengths. For use in the calculations, millimolar extinction coefficients in 2n-hydrochloric acid of 12.09 for adenine at 262mmu, and 10.77 for guanine at 248mmu, were determined with authentic samples of bases. The method gives extremely reproducible results: from 12 determinations with calf thymus DNA the adenine/guanine molar ratio had a standard deviation of 0.011; this corresponds to a standard deviation in guanine+cytosine content of 0.2% guanine+cytosine.

Adenine↗
PubMed1996

DNA binding mechanism of O6-alkylguanine-DNA alkyltransferase: stoichiometry and effects of DNA base composition and secondary structure on complex stability.

O6-Alkylguanine-DNA alkyltransferase (AGT) is an important cellular defense against the mutagenic effects of DNA alkylating agents. In humans this defense can contribute to the ability of some tumors to resist the effects of chemotherapeutic agents that act through DNA alkylation. We report here studies that characterize the interaction of AGT with DNA. We show that although AGT sediments as a monomer in the absence of DNA, it binds cooperatively to single stranded deoxyribonucleotides. The stoichiometries of complexes formed with 16-, 30-, and 80-base oligodeoxyribonucleotides are 3.8 +/- 0.3, 5.3 +/- 0.2, and 8.9 +/- 0.2, respectively; the binding density decreasing from approximately 4 nt/monomer to approximately 9 nt/monomer as DNA length increases over this range. Binding competition assays show that DNA affinities depend only weakly on base composition or secondary structure, although in general G + C-rich sequences are bound with greater affinity than are A + T-rich ones and single-stranded DNA is bound with greater affinity than duplex forms. These results suggest mechanisms by which AGT may search for alkylated sites and interact with them to effect DNA repair.

Base Composition↗
PubMed1980

Physicochemical measurement of the base composition of mRNA-related sequences of the human alpha and beta globin genes.

Hybrids formed between human alpha and beta globin cDNA and total human cellular DNA have been studied by thermal denaturation and cesium chloride density gradient centrifugation. From these studies, the weight average G + C content of human alpha globin cDNA has been determined to be 62% +/- 2% and that of human beta globin cDNA 51% +/- 2%. These values correlate well with the results of G + C content of the human alpha and beta globin cDNAs as determined by direct nucleotide sequence analysis of the cDNAs. Thermal denaturation and cesium chloride density gradient centrifugation of DNA-cDNA hybrids can therefore provide accurate information on the base composition of mRNA related sequences of any single copy gene for which a relatively pure cDNA can be obtained, without the necessity for direct nucleotide sequence analysis.

Base Composition↗
PubMed1999

Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure.

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be alpha-helix, beta-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.

Animals↗
PubMed2003

The effect of filler and silane content on conversion of resin-based composite.

OBJECTIVE: This study examines the influence of filler loading and silane content on the conversion of photoactivated, resin-based composites as determined using Fourier transform infrared spectroscopy (FTIR). METHOD: Zirconia/silica filler was processed with a silane coupling agent (gamma-methacryloxypropyltrimethoxysilane) to achieve a range of silane-to-filler compositions. Treated fillers were compounded with a photoactivated BisGMA/TEGDMA resin to yield a series of pastes all containing 72 wt% total solids. Diffuse reflectance FTIR was used to characterize methacrylate unsaturation of the silane on the filler particles while paste conversion was determined using transmission FTIR. A resin matrix conversion was determined by adjusting the paste conversion for silane unsaturation. Two additional series of pastes were compounded to achieve variable filler-to-resin ratios using non-treated filler and filler processed with 8 wt% silane. Paste conversion was determined using transmission FTIR. RESULTS: Pastes compounded from fillers containing variable percent silane demonstrated linearly decreasing conversion (R(2)=0.986) with increasing silane content and ranged from 52.7 to 62.8%. Adjusting paste conversion for silane unsaturation yielded similar resin matrix conversion for all cured pastes (65.1+/-0.8%). Pastes compounded with increasing filler-to-resin ratios had progressively decreasing conversion. Correcting for silane unsaturation suggests this effect was independent of whether the filler was silane-treated or not. SIGNIFICANCE: Composite resin matrix conversion as determined via FTIR can be underestimated by the presence of unreacted methacrylate from silane on the filler. A corrected resin matrix conversion can be estimated by adjusting for silane unsaturation. Additionally, increasing filler-to-resin ratio progressively decreases conversion independent of the presence of silane on the filler.

Composite Resins↗
PubMed1978

Sensitivity to lytic agents and DNA base composition of several aerobic spore-bearing bacilli.

The authors studied the possible relationship between a genetic characteristic, like DNA base composition, and certain phenotypic characteristics, i.e., sensitivity to lytic agents, morphology of colonies, and biochemical reactions in 34 strains of spore-bearing bacilli. From the results obtained two groups of bacilli have been identified. The first group includes the species B. subtilis, B. pumilus, B. licheniformis, and B. firmus and one strain of B. megaterium. The mean value of the GC% of the DNA is 44.22 +/- 1.76. All the strains examined are highly sensitive to lysozyme and resistant to sodium lauryl sulphate (S.L.S.); the surface colonies have a "rhizoid" appearance and the microcolonies on slide microculture are star-shaped. The second group includes the species B. cereus, B. cereus var. mycoides, B. anthracis, and B. thuringiensis. The mean value of the GC% of the DNA is 33.65 +/- 0.59. All the strains belonging to this group are resistant to both lysozyme and S.L.S., and the surface macro-colonies and the microcolonies have a "medusae head" appearance. The two groups also have certain different biochemical reactions; e.g., anaerobic growth and the egg yolk reaction, with few exception, are negative for the first group and positive for the second; furthermore, the strains in the first group (with rare exceptions) cause fermentation in the three carbohydrates, glucose, arabinose, and xylose, while glucose only is fermented by all strains with one exception in the second group. The position of B. megaterium is not yet clear, although one strain may certainly be included in the first group. Lysis by lipase is extremely variable and does not correlate with any of the other characteristics studied. The other species studied in relation to the characteristics, considered in our research (B. coagulans, B. macerans, B. polymyxa, B. laterosporus, B. alvei, B. circulans, B. stearothermophilus, and B. brevis), are not susceptible to grouping, either in the first, or in the second or even in a separate group.

Bacillus↗
PubMed1999

Effects of handpiece lubrication on resin-based composite bond strength to enamel.

PURPOSE: To evaluate the effects of handpiece lubrication on the bond strengths of resin-based composite (RBC) to enamel using two different bonding systems. MATERIALS AND METHODS: Sixty extracted noncarious human maxillary incisors were imbedded in acrylic resin tray material with the facial surfaces exposed. 320 grit sandpaper was used to create a flat surface of enamel. The embedded teeth were randomly divided into two bonding systems groups: half used All-Bond 2 and half used OpiBond FL. Within these two groups the teeth were again randomly divided into three subgroups: Dry: 10 teeth prepared with a sterilized unlubricated handpiece; Lube & Run: 10 teeth prepared with a handpiece that was lubricated and run for 30 seconds prior to use; Lube: 10 teeth prepared with a handpiece that was lubricated and not run prior to its use. The enamel was prepared by lightly roughening with a medium grit diamond in the respective handpieces. The preparations were etched for 15 s with 32% phosphoric acid, rinsed with water for 5 s, and dried with compressed air for 5 s. Either bond system was applied and light-cured. A hybrid RBC was placed and light-cured for 60 s. The teeth were stored in water at 37 degrees C 1 week. Shear bond strengths were measured and the collected data subjected to an ANOVA followed by a Tukey's and Bonferroni t-test were performed. RESULTS: The Dry group and the Lube & Run group had stronger mean shear strengths than did the Lube group. The difference between the mean shear strengths for the Dry group and the Lube & Run group was not statistically significant (P < 0.05). A significant difference was found between the Dry group and the Lube group and between the Lube & Run group and the Lube group (P < 0.05). The mean shear strength for All-Bond 2 was higher than for OptiBond FL (P = 0.0054).

Analysis of Variance↗