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At least 217 records · Page 12Linked to original sources
PubMed1997

Separation of oligonucleotides of identical size, but different base composition, by free zone capillary electrophoresis in strongly acidic, isoelectric buffers.

A novel method for analyzing oligonucleotides of the same length, but bearing a single base substitution, is reported, based on free zone capillary electrophoresis (CZE) under rather acidic pH values. For this purpose, a set of four 18-mers of fairly random base composition has been synthesized, bearing, in nucleotide 9, the following bases: T, C, G or A. Theoretical predictions, based on titration curves of single free nucleotides, allowed us to predict that the simultaneous separation of a mixture of all four oligonucleotides could be possible in a pH 3-4 window. In fact, electrophoresis at pH 5.7 gave a single, asymmetric peak, whereas CZE at pH 4.8 could resolve three out of four species (the T9 and G9 oligonucleotides co-migrating into a single zone). A unique separation power could be obtained at pH 3.3 in a buffer comprising an amphoteric species (isoelectric iminodiacetic acid, IDA) and 7 M urea. Although IDA exhibited a pI of 2.23 (for a 100 mM solution), the addition of 7 M urea (necessary to denature the oligonucleotides) raised the apparent pH of the solution to 3.3.

Acids↗
PubMed2002

Effect of glass fiber surface treatments on mechanical strength of epoxy based composite materials.

Sizing glass fibers with silane coupling agents enhances the adhesion and the durability of the fiber/polymer matrix interface in composite materials. There are several tests to determine the interfacial strength between a fiber and resin, but all of them present difficulties in interpreting the results and/or sample preparation. In this study, we observed the influence of different aminosilanes fiber coatings on the resistance of epoxy-based composite materials using a very easy fractographic test. In addition, we tried a new fluorescence method to get information on a molecular level precisely at the interface. Strength was taken into account from two standpoints: (i) mechanical strength and (ii) the resistance to hydrolysis of the interface in oriented glass-reinforced epoxy-based composites. Three silanes: gamma-aminopropyltriethoxysilane, gamma-Aminopropylmethyldiethoxysilane, and gamma-Aminopropyldimethylethoxysilane were used to obtain different molecular structures at the interface. It was concluded that: (i) the more accessible amine groups are, the higher the interface rigidity is; (ii) an interpenetrating network mechanism seems to be the most important for adhesion and therefore to the interfacial strength; and (iii) the higher the degree of crosslinking in the silane coupling layer is, the higher the hydrolytic damage rate is.

Journal Article↗
PubMed1969

Deoxyribonucleic acid base composition in the taxonomy of Staphylococcus.

Twenty-four strains of Staphylococcus aureus, including eight known mutants of S. aureus and strains growing under a variety of environmental conditions or exposed to a number of physical and chemical agents, maintained a remarkably narrow range of guanine plus cytosine (GC) content (32.4 to 35.1%). The wide range of GC content (30.7 to 40%) reported in the literature was due to the variety of methods and calculations used rather than to any substantial variation in base composition. The UV-2 "mutant" (ATCC 13680) with a GC content of 67.6% reported to be derived from S. aureus (ATCC 13679) was a species of Corynebacterium. The data presented were consistent with the concept that base composition changes only to a very slight degree by mutation.

Bacteriological Techniques↗
PubMed1984

DNA base composition, DNA-DNA homology and long-chain fatty acid studies on streptococcus thermophilus and Streptococcus salivarius.

DNA base composition, DNA-DNA homology and long-chain fatty acid studies were performed on Streptococcus thermophilus and Streptococcus salivarius. These species possess similar mol % G + C values (about 37 to 41), long-chain fatty acid profiles and belong to a single DNA homology group. On the basis of the present and earlier studies it is proposed that Streptococcus thermophilus (Orla-Jensen) be reclassified as Streptococcus salivarius subsp. thermophilus comb. nov.

Base Composition↗
PubMed1980

Base composition of transfer RNAs from vegetative and developing cells of Dictyostelium discoideum.

In a previous comparison of tRNAs from vegetative and developing cells of Dictyostelium discoideum, displacements of chromatographic peaks were observed for a number of aminoacyl-tRNAs (Palatnik, C.M., Katz, E.R. and Brenner, M. (1977) J. Biol. Chem. 252, 694-703). Since the development peak eluted ahead of the vegetative peak in all but one case, and since levels of amino acid acceptance and tRNA chromatographic profiles were otherwise quite similar, it was suggested that a common change or a very small number of changes in base modification were occurring during development. We have threfore compared tRNAs from both stages with respect particularly to their minor base composition. Of the minor bases which we have analyzed no reproducible differences between the two stages have been detected. Moreover, we have been unable to confirm a recent report (Dingermann, T., Schmidt, W. and Kersten, H. (1977) FEBS Lett. 80, 205-208) that a significant change occurs in the ribothymidine content of tRNA during Dictyostelium discoideum development.

Base Composition↗
PubMed1985

A microanalytical procedure for determination of the base composition of DNA.

A new procedure for the determination of the percentage guanine plus cytosine (% G+C; mol/100 mol) values of microquantities of DNA is described. Its principle is a DNA-polymerase-I-directed nick translation of DNA in the presence of dGTP, dTTP, [3H]dCTP, and [alpha-32P]dATP. Kinetics experiments indicate that the plateau value is reached in about 20 min of incubation under our experimental conditions. Percentage G+C is obtained from the linear relation 1/(% G+C) = 0.01 K [32P]/[3H] + 0.01, where the ratio of trichloroacetic-acid-precipitable radioactivity is taken into account, the K value being determined for each experiment by using a few reference DNAs of known composition. This procedure has proven suitable for analysis of plasmidic, viral and cellular DNAs of different base composition (25-75% G+C), shape (linear and circular double-stranded DNA) and size (100-150 000 base pairs). Usual methods for % G+C analysis (buoyant density and melting temperature determinations) yield unreliable results in the presence of either modified or unusual bases: the double-labeling procedure is still valid under these conditions. The latter is, therefore, the method of choice for analysis or rare DNA species which are available in very small quantities (it requires amounts of DNA as low as 1 ng, i.e. several order of magnitude lower than those used for chromatographic analysis of DNA hydrolysates). Since the obtention of highly purified DNA is an essential prerequisite for the double-labeling procedure, a method for purification of bacterial DNA is detailed in the present work.

Base Composition↗
PubMed2002

Marginal integrity of different resin-based composites for posterior teeth: an in vitro dye-penetration study on eight resin-composite and compomer-/adhesive combinations with a particular look at the additional use of flow-composites.

OBJECTIVE: To determine improvements in marginal adaptation of resin-based composite restorative systems by means of flow-composites (Solitaire 2/Gluma Solid Bond, Solitaire 2/Flow Line/Gluma Solid Bond, Point 4/Optibond Solo Plus, Point 4/Revolution/Optibond Solo Plus) and to determine the equality of simplified bonding systems (Solitaire 2/Gluma Comfort Bond, Tetric Ceram/Tetric Flow/Excite, Dyract AP/Prime & Bond NT/NRC, Pertac II/Prompt-L-Pop) in marginal gap formation. METHODS: The marginal dye penetration (2% methylene-blue) was investigated separately for the approximal boxes of Class II mod-cavities with one cervical margin of the approximal box within enamel, the other within cementum. The surface analysis determined the percentage of dye-penetrated cervical and lateral margins of the approximal boxes, while the in depth investigation reported the mean dye penetration (mm) at both different cervical margins. RESULTS: After thermocycling (5000 x , 5-55 degrees C) the percentage of dye penetration at the cervical cementum margins ranged from 16.5 +/- 5.9% (Solitaire/Flow Line/Gluma Solid Bond) to 82.8 +/- 5.7% (Pertac II/Prompt L-Pop), for the cervical enamel margins from 10.1 +/- 5.2% (Dyract AP/NRC/P & B NT) to 72.7 +/- 7.9% (Pertac II/Prompt L-Pop), and for the lateral enamel margins of the approximal boxes from 4.8 +/- 2.3% (Dyract AP/NRC/P & B NT) to 53.9 +/- 6.8% (Pertac II/Prompt L-Pop). In the in-depth dye penetration investigation the mean dye penetration ranged from 0.2 +/- 0.2 mm (Point 4/Revolution/Optibond Solo Plus) to 1.7 +/- 0.2 mm (Pertac II/Prompt L-Pop) at the cementum margins. At the enamel margins only Pertac II/Prompt L-Pop and Solitaire 2/Gluma Solid Bond showed mean in depth dye-penetrations deeper than 0.1 mm. SIGNIFICANCE: Pertac II/Prompt-L-Pop showed a statistically significant (significance level alpha = 0.05, Wilcoxon test) higher percentage of dye-penetrated margins than most of the other restorative systems.

Compomers↗
PubMed2000

Cavity wall adaptation of resin-based composites lined with flowable composites.

PURPOSE: To compare the adhesion of a flowable resin-based composite (RBC) vs. a condensable RBC to tooth structure using scanning electron microscopy (SEM). MATERIALS AND METHODS: Fifteen recently extracted human teeth were prepared for Class I restorations and equally divided into three groups. Group 1 was filled with Heliomolar bonded with Syntac Single Component. Group 2 was lined with Flow-It in addition to ALERT condensable RBC bonded with Bond-1 Primer/Adhesive. Group 3 was filled with ALERT bonded with Bond-1 Primer/Adhesive. All teeth were thermocycled, sectioned and evaluated for gap formation with the SEM. RESULTS: SEM at x15 demonstrated that restorations with the flowable RBC at the tooth/restoration interface showed no evidence of marginal gaps between the RBC material or at the underlying tooth structure. A significant difference (P < 0.05) in wall adaptation was found between Groups 2 and 3.

Acid Etching, Dental↗
PubMed1999

Nucleic acid duplex stability: influence of base composition on cation effects.

The effects of counter ion on a nucleic acid duplex stability were investigated. Since a linear free energy relationship for the thermostability of oligonucleotide duplexes between those in 1 M and in 100 mM NaCl-phosphate buffer were observed regardless of whether they are DNA-DNA, RNA-RNA or RNA-DNA duplexes, simple prediction systems for [Delta] G degrees 37as well as T mvalues in 100 mM NaCl-phosphate buffer were established. These predictions were successful with an average error of only 2.4 degrees C for T mand 5. 7% for G degrees 37values. The number of Na+newly bound to a duplex when the duplex forms (-[Delta] n) was significantly influenced by the base composition, and -[Delta] n for d(GCCAGTTAA)/d(TTAACTGGC) was different for MgCl2, CaCl2, BaCl2and MnCl2(from 0.70 to 0.76 with the same order of the duplex stability). Almost no additive effects on the duplex stability was observed for NaCl and MgCl2, suggesting a competitive binding for these cations. The sequence-dependent manner of [Delta] n suggests the presence of preferential base pairs or nearest-neighbor base pairs for the cation binding, which would affect nearest-neighbor parameters.

Base Composition↗
PubMed1984

23Na NMR relaxation study of the effects of conformation and base composition on the interactions of counterions with double-helical DNA.

NMR relaxation rates (T1(-1) and T2(-1)) have been determined for 23Na in aqueous salt solutions containing various types of helical double-stranded deoxyribonucleic acids. These measurements were performed on three synthetic polynucleotides having different overall conformations, poly-(dA-dT).poly(dA-dT) (alternating B-DNA), poly(dG-dC).poly(dG-dC) at low salt (B-DNA), and Br-poly(dG-dC).Br-poly(dG-dC) (left-handed Z-DNA), and on four types of natural DNA differing in base composition, Clostridium perfringens (26% GC), calf thymus (40% GC), Escherichia coli (50% GC), and Micrococcus lysodeikticus (72% GC). For all types of DNA investigated, except poly(dA-dT).poly(dA-dT), the 23Na NMR spectra measured at 21 degrees C and an applied field of 4.7 T are non-Lorentzian. These non-Lorentzian spectra were analyzed on the basis of the two-state model and the standard theory of nonexponential quadrupolar relaxation processes in order to obtain estimates of the correlation times (tau c) characteristic of the sodium nuclei associated with the various nucleic acids. All of the correlation times estimated in this way are in the range of nanoseconds. The magnitudes of these correlation times show a significant dependence on the overall conformation of the nucleic acid (B vs. Z) but not on its base composition. To investigate the concentration dependence of tau c, sodium or magnesium salts were added to solutions of Br-poly(dG-dC).Br-poly(dG-dC) (Z-DNA).(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Determination of DNA base composition by small scale acrylamide-CsCl gradient centrifugation.

In this paper we describe a simple and rapid protocol for DNA base composition determination by CsCl gradient in the presence of acrylamide. This method permits the determination of GC content in microgram amounts of DNA, and results are easily documented in photographs or graphs. The protocol was applied to the characterization of nematode DNA, but can be used for other organisms. Analyzing several experiments the mean standard deviation observed in the calculated GC content is near 1.3%.

Acrylamide↗
PubMed1978

Base composition changes in hepatocyte nuclei DNA of rats at different ages.

DNA extracted from isolated hepatic nuclei of rats at different aged (1 h, 6 and 30 days of life) has been characterized by (i) melting temperature, (ii) buoyant density, (iii) thermal denaturation on hydroxyapatite and (iv) nucleoside composition. The melting midpoint (Tm) determined spectrophotometrically in 0.1 X SSC (0.15 M NaCl/0.0015 M sodium citrate) is 71.9 +/- 0.4 for 1-h-old rats and decreases to 70.7 +/- 0.3 in 6-day-old animals. The buoyant densities of DNAs determined by CsCl on both native and alkaline-denaturated and reneutralized DNA were also found to decrease with age. Hydroxyapatite thermal denaturation of sonicated DNA confirmed the significant difference between the Tm values of 1-h-old and 6-day-old rats (86.5 +/- 0.5 and 85.2 +/- 0.1, respectively). The possibility that these differences in Tm values could be due to an increase in methyl bases, has been ruled out by the finding that the amount of [3H]methyl incorporated in relation to the DNA synthesis is constant at these two ages. The alternative possibility of a change in base composition has been tested by the chromatographic analysis of nucleosides. The dG + dC content is 0.433 +/- 0.003 in 1-h-old rats and decreases to 0.411 +/- 0.002 and to 0.403 +/- 0.005 in 6-day- and 30-day-old rats, respectively. The physiological significance of the different base composition is discussed in relation to the possibility that specific DNA sequences are synthesized during the non-premitotic synthesis which has been found to take place during the first 6 days of life.

Aging↗
PubMed1980

Deoxyribonucleic acid base compositions of dermatophytes.

DNA was extracted and purified from 55 dermatophyte isolates representing 34 species of Trichophyton, Microsporum and Epidermophyton. The base compositions of the chromosomal DNA were determined by CsCl density gradient centrifugation and were found to be in the narrow range of 48.7 to 50.3 mol % G + C. A satellite DNA component assumed to be of mitochondrial origin was present in most strains, with a G + C content ranging from 14.7 to 30.8 mol % G + C. Heterogeneity in microscopic and colonial characteristics was not reflected in differences in the mean G + C content of the chromosomal DNAs. Strains varied in the G + C contents of satelite DNA, but these did not correlate with traditional species concepts.

Arthrodermataceae↗
PubMed2005

Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.

Regional biases in substitution pattern are likely to be responsible for the large-scale variation in base composition observed in vertebrate genomes. However, the evolutionary forces responsible for these biases are still not clearly defined. In order to study the processes of mutation and fixation across the entire human genome, we analyzed patterns of substitution in Alu repeats since their insertion. We also studied patterns of human polymorphism within the repeats. There is a highly significant effect of recombination rate on the pattern of substitution, whereas no such effect is seen on the pattern of polymorphism. These results suggest that regional biases in substitution are caused by biased gene conversion, a process that increases the probability of fixation of mutations that increase GC content. Furthermore, the strongest correlate of substitution patterns is found to be male recombination rates rather than female or sex-averaged recombination rates. This indicates that in addition to sexual dimorphism in recombination rates, the sexes also differ in the relative rates of crossover and gene conversion.

Alu Elements↗
PubMed1998

Problems with parsimony in sequences of biased base composition.

Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis demonstrates that parsimony can be misleading even when levels of sequence divergence are as low as 10%; parsimony incorrectly infers an excess of common to rare changes. Caution must therefore be excercised in the use of parsimony.

Base Composition↗
PubMed1983

Effect of diet on plasma acid-base composition in normal humans.

Steady-state plasma and urine acid-base composition was assessed in 19 studies of 16 normal subjects who ingested constant amounts of one of three diets that resulted in different rates of endogenous noncarbonic acid production (EAP) within the normal range. Renal net acid excretion (NAE) was used to quantify EAP since the two variables are positively correlated in normal subjects. A significant positive correlation was observed between plasma [H+] and plasma PCO2, and between plasma [HCO3-] and plasma PCO2, among the subjects. Multiple correlation analysis revealed a significant interrelationship among plasma [H+], plasma PCO2, and NAE (r = 0.71, P less than 0.001), and among plasma [HCO3-], plasma PCO2, and NAE (r = 0.77, P less than 0.001). The partial correlation coefficients indicated a significant positive correlation between plasma [H+] and NAE, and a significant negative correlation between plasma [HCO3-] and NAE, when plasma PCO2 was held constant. These findings indicate that two factors influence the level at which plasma [H+] is maintained in normal subjects: (1) the steady-state rate of endogenous noncarbonic acid production, and (2) the setpoint at which plasma PCO2 is regulated by the respiratory system. Plasma [HCO3-] is also co-determined by these two factors. In disease states, therefore, both factors must be known before a disturbance in acid-base homeostasis can be excluded.

Acid-Base Equilibrium↗
PubMed1973

DNA base composition of rickettsiae.

There is a small but distinct difference in DNA base composition between the typhus and spotted fever groups of rickettsiae. The molar percentages of guanine plus cytosine for Rickettsia prowazeki, R. typhi, and R. canada are approximately 30, for R. rickettsi, R. conori, and R. akari they are about 32.5. The percentage for trench fever rickettsia, Rochalimaea quintana, is 38.6.

Animals↗