SEARCH · PubMed Health

Results for “Base Composition”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

PubMed1989

Spectrofluorometry of dyes with DNAs of different base composition and conformation.

The increase in fluorescence, upon interaction with several fluorescent dyes was found to depend on the base composition of DNA. 4',6-Diamidino-2-phenylindole-2 HCl and Hoechst 33258 which bind to AT base pairs show a logarithmic relation. This relation is linear when DNAs interact with mithramycin, chromomycin A3, and olivomycin, which bind to GC base pairs. Deviations from these relationships were observed for T2 DNA, containing hydroxymethylcytosine, and for 2C DNA, containing hydroxymethyluracil. On the basis of these data, a simple technique is proposed for determination of base composition. The presence of abnormal bases can be monitored by the use of given fluorophores. Fluorescence intensities were not modified upon linearization of covalently closed circular plasmid pBR322. Denaturation of lambda DNA was accompanied by a decrease of fluorescence, when complexed with the five dyes tested.

Base Sequence↗

PubMed1978

Ribosomal genes in Physarum polycephalum: transcribed and non-transcribed sequences have similar base compositions.

The transcribed and non-transcribed sequences in Physarum polycephalum ribosomal DNA (rDNA) were separated by restriction nuclease digestion of pure rDNA and the products fractionated by zone sedimentation in sucrose gradients. The base compositions of the fragments were determined by analytical centrifugation in CsCl or in CsCl with netropsin. All the fragments had dA + dT contents in the range 44-48%. From the known sequence arrangement and transcription pattern of Physarum rDNA it was concluded that coding sequences, transcribed but non-coding sequences, and non-transcribed sequences all possess similar base compositions, contrary to the situation in many other systems. The thermal denaturation profile of Physarum rDNA is reported. It suggests the rDNA sequence is complex and supports the above conclusion of limited heterogeneity of base composition.

DNA↗

PubMed2005

Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition.

We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A + T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias, and GC --> AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A + T content, ranging from a 1.7-fold increase in transition rate in relatively G + C-rich regions to a 2.6-fold increase in A + T-rich regions. We also observe a relationship between locus A + T content and GC --> AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors in that GC --> AT pressure increases with increasing locus A + T content but decreases with increasing flanking base A + T content and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome.

AT Rich Sequence↗

PubMed1987

Circular dichroism of sanguinarine-DNA complexes: effect of base composition, pH and ionic strength.

The interaction of sanguinarine with various naturally occurring and synthetic deoxyribonucleic acids of different base composition and sequence has been studied from the measurement of circular dichroism spectroscopy in buffer of various ionic strengths and pH values where physico-chemical properties of DNA remain unchanged. Binding of sanguinarine to DNA causes a change in the circular dichroism spectrum of DNA itself by showing the increase of both positive and negative bands and appearance of a broad positive band with peak at 340 nm. All systems studied exhibit extrinsic positive band that is independent of DNA base composition and sequence. Calf thymus DNA-sanguinarine complexes in different salt concentrations show that, at saturation, the magnitude of molar ellipticity at 340 nm increases with decreasing sodium ions concentration. Sanguinarine-DNA complexes in buffer of various pH values also show that the molar ellipticity at 340 nm is greater in acidic pH and lower in alkaline pH. It is concluded that the alterations of secondary structure of DNA upon binding of sanguinarine is maximum in buffer of low ionic strength and acidic pH and the number of bound alkaloid molecules per base pair, at saturation, is more in G-C rich DNA than in A-T rich DNA.

Alkaloids↗

PubMed1984

The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences.

Bacterial genes that code for proteins appear to possess a codon usage characteristic of their overall base composition. This results in different but predictable non-random distributions of nucleotides within codons, permitting the recognition of protein-coding sequences in a wide range of bacterial species. The nature of this distribution depends on the base composition of the coding sequence. The position-specific differences are especially conspicuous in genes of extreme G + C content, allowing the particularly reliable prediction of the reading frame and coding strand of experimentally determined DNA sequences. This finding has been exploited to identify the coding sequence of the viomycin phosphotransferase (vph) gene of Streptomyces vinaceus. An easily applied computer program ("Frame") has been written to carry out and display such analyses.

Bacterial Proteins↗

PubMed2002

Replacement of resin-based composite: evaluation of cavity design, cavity depth, and shade matching.

OBJECTIVE: The aim of this study was to evaluate the effect of different cavity designs, cavity depths, and shade matching on the dimensions of Class I resin-based composite preparations during replacement of the restoration. METHOD AND MATERIALS: Forty Class I cavity preparations were prepared in extracted premolars. The occlusal depths varied from 1.5 to 2.5 mm. In 20 teeth, the buccal and lingual walls were perpendicular to the pulpal floor; in another 20, they were divergent to the pulpal floor. Impressions were made of all preparations. The cavities were restored with resin-based composite. All subgroups were further divided into another two subgroups (n = 5), in which half of the teeth were restored with shade that matched the tooth and the other half were restored with a resin composite that was three shades different from the tooth. After 168 hours in distilled water, the restorations were removed. New impressions were made, and a total of 80 stone casts were fabricated. The perimeter and area of the restorations were recorded with a video-based imaging system. The dimensions of the postoperative cavity preparations were compared to the initial cavity sizes. RESULTS: The depth of the original cavity preparation had a statistically significant effect on the change in cavity dimension, as measured by area and perimeter. The 2.5-mm-deep cavities showed greater loss of tooth structure. No statistically significant difference was found for different cavity designs or shade matching. CONCLUSION: Replacement of Class I resin-based composite restorations results in loss of tooth structure. The deeper the original cavity preparation, the greater the loss of tooth structure at the occlusal cavosurface margin during replacement.

Analysis of Variance↗

PubMed1978

Spectral analysis of high resolution direct-derivative melting curves of DNA for instantaneous and total base composition.

Derivative melting profiles of DNA have been obtained directly by recording the difference in absorbance between two identical solutions maintained at a small constant temperature differential. This deltaA is monitored continuously with increasing temperature in a ratio recording spectrophotometer. Resolution of complex hyperfine structure in the profiles of small homogeneous viral DNAs appears to be significantly better than has been produced by various numerical methods of differentiation. In addition, a spectral method has been modified that permits easy analysis for DNA base composition from the ratio of derivative melting curves obtained at 282 and 260 nm. Eight bacterial and three vertebrate DNAs have been analyzed for total base composition from the product of the instantaneous base composition at small temperature intervals (0.05 degrees C) throughout the entire melting region and the integrated area of the 282 nm profile. The results are in excellent agreement with values determined by traditional methods.

Bacillus subtilis↗

PubMed1984

Deoxyribonucleic acid base composition and taxonomy of Moniliella and allied genera.

DNA base compositions of representative (type) strains of Moniliella, Trichosporonoides and Hyalodendron were determined. Within Trichosporonoides over 16% variance was found. Most species separated well, but M. suaveolens showed considerable heterogeneity. The standard 2% G + C differences for species distinction is probably not applicable to these yeasts. The new combination M. pollinis is proposed for M. tomentosa var. pollinis on the basis of slight ecological, morphological and physiological differences, supported by a marked difference in % G + C.

Base Composition↗

PubMed1997

Base composition of DNA from glomalean fungi: high amounts of methylated cytosine.

Glomales (Zygomycetes) are obligate fungal symbionts of roots of land plants and form arbuscular mycorrhiza. Sporal DNA of 10 isolates belonging to nine species was purified and the base composition was determined by RP-HPLC. Base composition fell in a narrow range between 30 and 35% G + C. A high amount of methylated cytosine (mC) accounting for 2-4% of the total nucleotides was found in all taxa. The DNA melting profile was defined for Scutellospora castanea. It corresponded to 32% G + C, and the shape of the denaturation curve suggested a heterogeneity in the GC content within the fungal genome. Knowledge of GC contents and variations between taxa are essential for evaluating nuclear DNA content using fluorimetric methods, and high proportions of mC/C + mC in the genomes of glomalean fungi could reflect the existence of repeated DNA families. Results are discussed in relation to data for other fungi and eukaryotes.

5-Methylcytosine↗

PubMed1990

DNA base composition determines the specificity of UvrABC endonuclease incision of a psoralen cross-link.

The sequences flanking a psoralen interstrand cross-link may determine how it is repaired. Our comparison of the Escherichia coli UvrABC endonuclease incision of a variety of specific cross-link sequences in a single natural DNA fragment showed that DNA base composition determines which of two cross-linked DNA strands will be incised. G/C enrichment of the region 6-12 bases 5' of the modified T on the furan-side strand results in preferential incision of the furan-side strand. When the G/C-rich region is on the 3' side, or on neither side, incisions occur on either strand. These effects of DNA base composition suggest that UvrAB can bind in two ways to a psoralen cross-link.

Base Composition↗

PubMed2003

Fatigue behavior of the resin-resin bond of partially replaced resin-based composite restorations.

PURPOSES: (1) To evaluate different pre-treatment modes for partial resin-based composite repair using a shear bond strength fatigue design on aged specimens, and (2) to investigate the effect of these pre-treatments on aged and partially replaced Class II resin-based composite restorations. MATERIALS AND METHODS: (Study 1) 150 composite discs (Tetric Ceram) were light-cured, secondary cured, and stored in water for 365 days. The specimens were randomly assigned to five pretreatment groups (n=30): (1) Roughening with a finishing diamond bur + dentin bonding system (DBS, Syntac Classic), (2) Roughening with a silicon carbide bur + DBS, (3) Roughening with a silicon carbide bur + DBS + Tetric Flow, (4) silica-coating (CoJet) + DBS, and (5) silica-coating + dentin bonding agent + Tetric Flow. The disks were restored with fresh repair composite cylinders and after 24-hour water storage, initial bond strengths (n=10) and fatigue bond strengths (n=20; 5,000 cycles in shear mode) were evaluated and fracture modes determined under a SEM. (Study 2): 40 Class II restorations (EBS Multi/Pertac II) were placed in extracted human third molars. The specimens were stored for 365 days and then replaced partially by removing the proximal box and leaving the occlusal part. The partial repairs (Pertac II) were placed after identical pre-treatment modes A-E (n=8). After thermomechanical loading (100,000 x 50 N, simultaneously x2,500 at 5 degrees C/55 degrees C), marginal quality between old and fresh composite was evaluated by SEM at x200 magnification and dye penetration was observed by light microscopy under x50 magnification. RESULTS: Initial repair bond strengths were significantly higher for the groups with additional application of flowable composite compared to composite only (P<0.05; Mann Whitney U test). Diamond finishing revealed the lowest bond strengths. Fatigue bond strengths exhibited the worst results for Group 1 as well, but were similar for Groups 2-5. In the Class II partial repair simulation, Groups 3 and 5 with additional flowable lining exhibited significantly better marginal quality and significantly lower leakage, whereas the other groups revealed up to 100% separation between aged and freshly applied composite.

Composite Resins↗

PubMed2003

Neutral effect of recombination on base composition in Drosophila.

Recombination is thought to have various evolutionary effects on genome evolution. In this study, we investigated the relationship between the base composition and recombination rate in the Drosophila melanogaster genome. Because of a current debate about the accuracy of the estimates of recombination rate in Drosophila, we used eight different measures of recombination rate from recent work. We confirmed that the G + C content of large introns and flanking regions is positively correlated with recombination rate, suggesting that recombination has a neutral effect on base composition in Drosophila. We also confirmed that this neutral effect of recombination is the main determinant of the correlation between synonymous codon usage bias and recombination rate in Drosophila.

Animals↗

PubMed2004

A two-year comparison of resin-based composite tunnel and Class II restorations in a randomized controlled trial.

PURPOSE: To evaluate the performance of total tunnel restoration with resin-based composites compared to Class II resin-based composite restorations in a randomized controlled clinical study. METHODS: 63 approximal carious lesions were restored in 38 patients by two experienced operators. The carious dentin and approximal demineralized enamel were completely removed for the tunnel restoration leaving the marginal ridge intact. The occlusal opening was enlarged to the center of the tooth to make access easy. Conservative cavity preparation was performed for the Class II restorations. All cavities were restored with Scotchbond Multipurpose Plus and Z250. At baseline, 1- and 2-year recalls, the restorations were evaluated clinically by two examiners using a modified USPHS rating system and radiographically for recurrent, caries. RESULTS: Both types of restorations performed well clinically, and there was no significant difference (P> 0.05) by the chi square test in any category. Recurrent caries was not detected. Only one tunnel restoration had to be replaced with a Class II restoration because of falling of the restoration with the marginal ridge after 2 years. However, no significant difference in the survival rates (P> 0.05) could be demonstrated between the restorations by the log-rank test.

Adult↗

PubMed1973

Variation of type-B DNA x-ray fiber diagrams with base composition.

Eight natural DNAs of widely differing base composition have been studied by x-ray diffraction in fibers at high relative humidity. The resulting type B diffraction diagrams showed that all of the DNAs had a 34-A pitch and 3.4-A interbase pair separation. However, the intensity distribution on the inner three layer lines was a strong function of the base content. In diffraction diagrams of very AT-rich DNA, the intensity of the first and third layer line was 2- or 3-times stronger than in the patterns of GC-rich DNA. These high humidity diffraction patterns agree with x-ray scattering from solutions of DNA. The results are interpreted to imply that each AT base pair may have a different cross section than a GC pair. If this is so, it would appreciably alter the currently held ideas concerning DNA recognition.

Animals↗

PubMedDate not supplied

An energy conversion relationship predictive of conversion profiles and depth of cure for resin-based composite.

Predicting the polymerization throughout resin-based composite (RBC) has been reduced to a set of variables involving irradiance of the light source, exposure duration and RBC transmission properties, together with an energy-conversion relationship (ECR) derived from Fourier Transform Infrared Spectroscopic analysis (FTIR) of a single shade of photo-polymerized RBC. The ECR describes the localized energy density required to achieve a desired conversion independent of shade. Using this ECR, conversion was predicted and experimentally verified throughout different opacities of RBC based on knowledge of their transmission properties and the incident radiant energy density (irradiance times exposure time). Also, using RBC transmission properties, a critical scrape-back energy of approximately 32 mJcm(-2) was determined from cylindrical samples of photo-polymerized RBC in which the poorly polymerized material was removed. This value correlates to approximately 22% conversion. The critical scrape-back energy was then used to predict scrape-back lengths obtained from samples polymerized at various energy densities. These results confirm the logarithmic relationship between depth of cure and energy of exposure and the reciprocal relationship between irradiance and time of exposure.

Color↗

PubMed2004

DNA base composition, susceptibility to bacteriophages and interspecific transformation as criteria for classification in the genus Bacillus.

With 25 strains belonging to 12 species of the genus Bacillus, the base composition of DNA, the susceptibility to bacteriophages, and the ability to transform Bacillus subtilis strain Marburg were studied. Analyses of phage DNAs were also performed. The results were as follows: (1) The DNA base compositions were not uniform even among strains belonging to one taxonomic species. (2) The DNAs extracted from B. natto, B. megaterium and B. polymyxa could transform genetic traits of B. subtilis Marburg although the frequencies were not equal. (3) The host ranges of some temperate bacteriophages were correlated with the taxonomical data. On these bases, the phylogenetic relatedness of B. subtilis to B. megaterium was discussed.

Bacillus↗

PubMed2000

In vitro evaluation of margins of replaced resin-based composite restorations.

PURPOSE: To evaluate in vitro any increase in size of Class V resin-based composite (RBC) restorations as a result of replacement. MATERIALS AND METHODS: For group 1, 20 Class V cavity preparations were prepared in extracted incisor and canine teeth. The cavosurface margin was prepared as a butt joint 90-degree angle toward the occlusal wall. Impressions were made of all preparations with a polyvinyl siloxane material. The cavities then received a 1.5-mm 45-degree bevel at the cavosurface margin of the occlusal wall. Impressions were again made of the preparations. The cavities were then restored with a conventional multistep bonding system (Scotchbond Multi-Purpose, 3M Dental Products, St. Paul, Minnesota) and a microfilled RBC (Silux Plus, 3M Dental Products). As a second part of the study (group 2), another 20 Class V cavity preparations were prepared. Half of the cavities received a bevel at the cavosurface margin of the occlusal wall, and half were finished with a butt joint. Impressions were made from all 20 specimens followed by resin-based composite restoration in the same manner as previously described. All the restorations from both group 1 and group 2 were then removed with carbide burs. New impressions were made, and 100 stone models were fabricated. The perimeter and area of the cavity preparations, including the beveled area, were recorded using a video-based imaging system equipped with macro lens, at 10 to 15 times magnification. Both perimeter and area of the postoperative cavity preparation were compared to the initial cavity size for both butt joint and bevel finishing. RESULTS: Intraclass correlation coefficient and paired t-test showed no significant difference between the preoperative bevel type of cavity preparation and its postoperative counterparts for both group 1 and group 2 (p > .05). However, a significant increase in the size of the cavity preparation was found preoperatively when a bevel was placed at the cavosurface margin. Postoperatively, a significant increase in size of the cavities was found for butt joint type finishing for both area (p = .0001) and perimeter (p = .0001), compared to initial cavity size.

Composite Resins↗

PubMed2004

Effect of high intensity vs. soft-start halogen irradiation on light-cured resin-based composites. Part II: Hardness and solubility.

PURPOSE: To determine hardness and solubility of light-cured resin-based composites after high intensity vs. soft-start quartz tungsten halogen irradiation. METHODS: Knoop hardness of resin-based composite specimens was measured at 1.5 mm depth after dry storage for 24 hours at 37 degrees C so as to indirectly evaluate degree of cure. Solubility was determined gravimetrically by extraction of post-cured (24 hours, 37 degrees C) specimens in 50 wt% methanol for 72 hours. Four hybrid (Filtek Z250, Herculite, Solitaire 2, Tetric Ceram), an inhomogeneously filled hybrid (InTen-S) and a microfilled (Filtek A110, formerly Silux Plus) composite were cured using the quartz tungsten halogen units Astralis 10 and Optilux 501 in the high intensity (Astralis 10 High Power: 10 seconds @ 1300 mW/cm2; Optilux Boost: 10 seconds @ 1140 mW/cm2) or soft-start modes (Astralis 10 Pulse: increase to 700 mW/cm2 within 10 seconds, three periods of 2 seconds @ 1300 mW/cm2 alternating with two periods of 2 seconds @ 700 mW/cm2; Optilux Ramp: exponential increase within 10 seconds, followed by 10 seconds @ 1140mW/cm2). RESULTS: For the fast curing composites Z250, Tetric Ceram and InTen-S, equivalent hardness was observed after 10 seconds of high intensity and 20 seconds of soft-start irradiation. For the slower curing composites Herculite, Solitaire 2 and A110, the soft-start protocols produced higher hardness values. Regarding solubility however, the superiority of soft-start irradiation was also seen for Tetric Ceram and InTen-S. The lowest solubility was observed for InTen-S, followed by Z250, whereas Herculite and Solitaire 2 scored highest for this parameter.

Analysis of Variance↗