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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↗

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↗

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↗

PubMed1989

[The effect of water content on wear of Bis.GMA-Tri.EDMA based composite resins].

The wear properties of Bis.GMA-Tri.EDMA based composite resins to an Ag-Pd-Cu-Au alloy examined, using a trial sliding frictional wear testing machine, and the effects of water in a specimen on wearing characteristics were discussed. The water absorbed into the specimens softened the surface of the material and decreased the wear-resistant properties of them. On the other hand, the increase of Bis.GMA content improved slightly the wear characteristics. In the range of 60-76 wt% filler content, the wear of experimental composite resin decreased according to increase of filler content. In the case of 50 wt% filler content resins, however, the wear of experimental composite resins was significantly less than in the other cases. There was high negative correlation between wear rate and Vicker's hardness of experimental composite resins (r = -0.84). In addition, there was high correlation between wear rate and amount of absorbed water in the specimens of 76 wt% filler (r = 0.92).

Bisphenol A-Glycidyl Methacrylate↗

PubMed1979

DNA base compositions and photoreactivation capabilities of six Hansenula species.

The DNA base compositions and photoreactivable sectors of six species of Hansenula were determined. The G+C ratios revealed two groups; the first had values of 38 to 44% and the second had lower values of 32-36%. Hansenula muscicola could not repair the UV-induced damage; whereas, H. dryadoides, H. lynferdii, H. ofunaensis, H. philodendra, and H. syndowiorum could do so.

Ascomycota↗

PubMed1999

Structural and dynamical properties of two DNA oligomers with the same base composition and different sequence.

We compared the structural and dynamical properties of two DNA fragments, 27 bp long, having the same base composition but a different sequence. This work aims to understand how the base sequence on a purine rich strand in a double helix, which is important for many biological functions, is related to structural features and to measurable physical quantities. Structural characterization of the two samples was performed both by conventional spectroscopic methods (circular dichroism and UV denaturation experiments) and by means of a gamma-ray footprinting technique which gives information on fine conformational differences. Dynamical features of the samples were studied by fluorescence polarization anisotropy (FPA) measurements which allow the evaluation of some hydrodynamic parameters, such as the hydrodynamic radius and the elastic torsion constant of DNA. Using a gamma-ray footprinting technique, we observed that the interruption of the long homopurine-homopyrimidine run in the control sample, due to the 'scrambling' operation, alters the DNA three-dimensional structure, also at nucleotide level. Besides, an increase in thermal stability and in the torsional rigidity of the 'scrambled' sample was observed. A possible association between base-stacking interaction and torsional rigidity was inferred from the comparison of the two samples.

Algorithms↗

PubMedDate not supplied

Dependence of DNA helix flexibility on base composition.

We have used triplet anisotropy decay techniques to study the flexibility of synthetic DNA fragments with different base pair compositions. We have found major differences in the torsional and bending stiffness of poly(dG) . poly(dC), poly(dA) . poly(dT) and poly(dA-dC) . poly(dT-dG). Poly(dG) . poly(dC) has a torsional modulus more than 40 times larger than poly(dA-dC) . poly(dT-dG), and approximately 20 times larger than poly(dA) . poly(dT). These differences imply that the torsional stiffness of DNA can vary greatly with base composition. The Young's modulus (bending stiffness) we have measured for poly(dG) . poly(dC) is at least twice that of poly(dA-dC) . poly(dT-dG) or random sequence DNA, and is at least threefold greater than that of poly(dA) . poly(dT). This implies that the bending stiffness of DNA is also strongly dependent on base composition. In light of this dramatic base composition dependence, we suggest here that such stiffness variation may lead to local variations in the stability of chromatin or other protein complexes that require bending or twisting of the DNA helix.

Animals↗

PubMed1973

Minor base composition of "70S-associated" 4S RNA from avian myeloblastosis virus.

Using a chemical isotope derivative method, we have determined the minor base composition of the "70S-associated" 4S RNA isolated from avian myeloblastosis virus. The minor base composition of this "70S-associated" 4S RNA is strikingly similar to that of the corresponding "free" 4S RNA of the virion. This minor base content, plus the capacity to esterify amino acids, establishes that both of these virion 4S RNA fractions contain transfer RNA. The percentage of minor bases in virion "70S-associated" 4S RNA is, however, much lower than in "free" 4S virion RNA and in myeloblast 4S RNA. The implication is that the "70S-associated" 4S RNA fraction as isolated herein also contains RNA that is not transfer RNA. This latter RNA may represent either degradation products of high molecular weight RNA or indigenous 4S RNA of undetermined function.

Animals↗

PubMed1998

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes.

Variation in GC content, GC skew and AT skew along genomic regions was examined at third codon positions in completely sequenced prokaryotes. Eight out of nine eubacteria studied show GC and AT skews that change sign at the origin of replication. The leading strand in DNA replication is G-T rich at codon position 3 in six eubacteria, but C-T rich in two Mycoplasma species. In M. genitalium the AT and GC skews are symmetrical around the origin and terminus of replication, whereas its GC content variation has been shown to have a centre of symmetry elsewhere in the genome. Borrelia burgdorferi and Treponema pallidum show extraordinary extents of base composition skew correlated with direction of DNA replication. Base composition skews measured at third codon positions probably reflect mutational biases, whereas those measured over all bases in a sequence (or at codon positions 1 and 2) can be strongly affected by protein considerations due to the tendency in some bacteria for genes to be transcribed in the same direction that they are replicated. Consequently in some species the direction of skew for total genomic DNA is opposite to that for codon position 3.

Archaea↗

PubMed1990

Chloroplast genes transferred to the nuclear plant genome have adjusted to nuclear base composition and codon usage.

During plant evolution, some plastid genes have been moved to the nuclear genome. These transferred genes are now correctly expressed in the nucleus, their products being transported into the chloroplast. We compared the base compositions, the distributions of some dinucleotides and codon usages of transferred, nuclear and chloroplast genes in two dicots and two monocots plant species. Our results indicate that transferred genes have adjusted to nuclear base composition and codon usage, being now more similar to the nuclear genes than to the chloroplast ones in every species analyzed.

Base Composition↗

PubMed1966

Deoxyribonucleic acid base composition of some members of the Micrococcaceae.

Auletta, Angela E. (Catholic University, Washington, D.C.), and E. R. Kennedy. Deoxyribonucleic acid base composition of some members of the Micrococcaceae. J. Bacteriol. 92:28-34. 1966.-Thirty-seven strains from the genera Micrococcus, Staphylococcus, Gaffkya, and Sarcina were examined for deoxyribonucleic acid base composition and biochemical activity. Organisms were tested for production of catalase, coagulase, deoxyribonuclease, oxidase, phosphatase, hydrogen sulfide, indole, and acetoin; nitrate reduction; gelatin, starch, and urea hydrolysis; citrate and ammonium phosphate utilization; NaCl tolerance; growth at 10 and 45 C, and growth in litmus milk. They were tested for production of acid from dextrose and mannitol under anaerobic conditions, and for aerobic production of acid from dextrose, mannitol, lactose, sucrose, raffinose, maltose, xylose, and glycerol. Organisms could be divided into two groups on the basis of guanine-cytosine (GC) content. Group I had an average GC content of 32%, and included all organisms which produced acid from dextrose. Group II had an average GC content of 62%, and included those organisms incapable of producing acid from dextrose under anaerobic conditions. Sarcina ureae had a GC content of 43%.

Carbohydrate Metabolism↗

PubMed1988

Effect of base composition at the center of inverted repeated DNA sequences on cruciform transitions in DNA.

We have analyzed the effect of base composition at the center of symmetry of inverted repeated DNA sequences on cruciform transitions in supercoiled DNA. For this we have constructed two series of palindromic DNA sequences: one set with differing center and one set with differing center and arm sequences. The F series consists of two 96-base pair perfect inverted repeats which are identical except for the central 10 base pairs which consist of pure AT or GC base pairs. The S series was constructed such that the overall base composition of the inverted repeats was identical but in which the positioning of blocks of AT- and GC-rich sequences varied. The rate of cruciform formation for the inverted repeats in plasmid pUC8 was dramatically influenced by the 8-10 base pairs at the center of the inverted repeat. Inverted repeats with 8-10 AT base pairs in the center were kinetically much more active in cruciform formation than inverted repeats with 8-10 GC base pairs in the center. These experiments show a dominant influence of the center sequences of inverted repeats on the rate of cruciform formation.

Base Sequence↗

PubMed1996

Thermodynamics of the interactions of sanguinarine with DNA: influence of ionic strength and base composition.

Using a combination of spectrophotometric and spectrofluorimetric techniques, we report the first thermodynamic characterization of sanguinarine binding to a series of natural and synthetic host DNA duplexes over a wide range of temperature and sodium concentration. The binding isotherms fit reasonably well to the neighbour exclusion model. The salt and temperature dependence of the binding constants is used to estimate the thermodynamic parameters involved in the interaction of the alkaloid with DNA. The resulting binding data are found to be sensitive to the ionic strength of the medium, base composition and sequence of base pairs. When the sodium ion concentration is increased from 0.005 M to 0.5 M, the binding free energy changes vary in a range from -8.47 to -7.1 kcal mol-1, which corresponds to a binding constant range from 1.85 x 10(6) to 1.8 x 10(5) M-1 at 20 degrees C. More distinct is the spread in the binding enthalpy changes which range from -6.35 to -2.62 kcal mol-1 corresponding to binding entropy changes from +7.22 to +15.3 cal K-1 mol-1 at 20 degrees C. On the other hand when the GC content of the host DNA duplexes is increased, the binding free energy varies in a range from -7.28 to -8.58 kcal mol-1 with the binding enthalpy changes ranging from -0.46 to -14.31 kcal mol-1, while corresponding binding entropy changes range from +23.3 to -19.56 cal K-1 mol-1 at 20 degrees C. Sanguinarine binding to natural DNAs and homo- and heteropolymers of AT is characterized by negative enthalpy changes and positive entropy changes, while binding to homo- and heteropolymers of GC is reflected by both negative enthalpy changes and entropy changes. Possible molecular contributions towards sign and magnitude of the thermodynamic parameters and their dependence on ionic strength, base composition and sequences, are discussed.

Alkaloids↗

PubMed1977

Base composition of DNA from some reptiles.

The DNA base composition was studied in 9 reptilian species (4 chelonians, 3 saurians, and 2 ophidians) by the thermal denaturation method. This preliminary investigation has brought to light differences in GC percentages and in the shape of melting curves between chelonian DNA and that from saurians and ophidians.

Animals↗

PubMed1968

Deoxyribonucleic acid base composition of the genus Lactobacillus.

Deoxyribonucleic acids of 45 strains of Lactobacillus and 5 strains of Bifidobacterium which had been analyzed for base composition by chromatographic means were examined at equilibrium in a CsCl density gradient. Regression analysis showed that there have been systematic errors involved in the estimation of guanine plus cytosine (GC) content by the chemical method, and that the relation between buoyant density and base composition is indeed linear and best fitted by the equation GC = 10.309 (rho-1.662), which compares well in slope with the equation of Schildkraut, Marmur, and Doty. With the improved data obtained in this study, the specific groupings of the species of both genera were reevaluated.

Centrifugation, Density Gradient↗

PubMed1994

Influence of nucleic acid base composition on radiation-induced strand breakage in single stranded DNA: a time resolved study.

The following study investigates the pathways involved in the induction of single strand breaks (ssb) in various samples of single stranded (ss) DNA (calf thymus, Micrococcus lysodeikticus, Clostridium perfringens) with differing nucleic acid base composition. The time scale for the induction of ssb was determined from changes in the light scattering intensity following pulse irradiation of aqueous solutions containing these ssDNA samples at pH7.8 under either aerated or deaerated conditions. The induction of ssb under these conditions is predominantly by the hydroxyl radical and shows various kinetically distinct components. The immediate ssb (t < 0.02 s) account for approximately 40-60% of the total yield of ssb. The majority of these ssb are suggested to arise from the 'common' initial attack of the hydroxyl radicals at the sugar phosphate backbone for each of the three DNA samples. Furthermore, slower components for ssb formation (t > 0.02 s) were observed and are suggested to occur through base radical mediated H-atom abstraction from the sugar moiety. The half lives for formation of the majority of ssb, formed through this base radical-mediated H-atom abstraction(s), are in the range of 20-43 ms. The yields of these 'base-mediated' ssb vary markedly (under both aerobic and anaerobic conditions) and reflect the base composition of the DNA sample. It is suggested from these studies that the OH-induced base radicals of guanine/cytosine are more effective precursors for strand breakage than those from adenine/thymine in ssDNA.

Base Composition↗

PubMed1996

Cytophotometric determination of heterochromatin base composition in interphase nuclei of plant cells.

The use of DNA base-specific fluorochromes and static cytophotometry at different thresholds of fluorescence intensity is proposed for studying the base composition of differently condensed chromatin fractions in plant interphase nuclei. Results are reported of such analyses on nuclei from leaflets of Posidonia oceanica and Helianthus annuus, which confirm other findings obtained on the same materials by biochemical and molecular methods.

Base Composition↗