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PubMed2005

The regional rule for bacterial base composition.

If one looks at the composition of coding DNA and of three types of intergenic regions--those between convergent, parallel and divergent genes--a striking pattern is seen in a wide range of bacteria. The AT-content of coding sequence is lowest, and the AT-contents of the intergenic regions increase in the order: convergent, parallel and divergent. Why does this pattern occur? In this article, I suggest an explanation based on the structural requirements for the binding of transcription factors.

Bacteria↗
PubMed2004

Selecting nanotechnology-based composites using colorimetric and visual analysis for the restoration of anterior dentition: a case report.

Currently it is possible to use direct composites and layering techniques to replicate the complex internal structures, visible shape, color, and surface anatomy of natural teeth. To do so, however, requires dentists to understand the principles of nature and the science of dental materials to determine the most suitable restorative material for a specific indication. By incorporating relatively new technologies--colorimetric analysis, which provides computerized shade guide definitions of a tooth and essential information to verify shade mapping, and a new nanotechnology-based direct composite--into composite layering techniques, dentists can more predictably replicate the esthetics of natural teeth. This article presents a case in which both technologies, used in combination with a composite layering technique, contributed to the esthetic and functional restoration of the maxillary central incisors.

Adult↗
PubMed2003

Optimum growth temperature and the base composition of open reading frames in prokaryotes.

The purine-loading index (PLI) is the difference between the numbers of purines (A+G) and pyrimidines (T+C) per kilobase of single-stranded nucleic acid. By purine-loading their mRNAs organisms may minimize unnecessary RNA-RNA interactions and prevent inadvertent formation of "self" double-stranded RNA. Since RNA-RNA interactions have a strong entropy-driven component, this need to minimize should increase as temperature increases. Consistent with this, we report for 550 prokaryotic species that optimum growth temperature is related to the average PLI of open reading frames. With increasing temperature prokaryotes tend to acquire base A and lose base C, while keeping bases T and G relatively constant. Accordingly, while the PLI increases, the (G+C)% decreases. The previously observed positive correlation between (G+C)% and optimum growth temperature, which applies to RNA species whose structure is of major importance for their function (ribosomal and transfer RNAs) does not apply to mRNAs, and hence is unlikely to apply generally to genomic DNA.

Bacteria↗
PubMed2006

Contrasting patterns of sequence divergence and base composition between Drosophila introns and intergenic regions.

Two non-coding DNA classes, introns and intergenic regions, of Drosophila melanogaster exhibit contrasting evolutionary patterns. GC content is significantly higher in intergenic regions and affects their degree of nucleotide variability. Divergence is positively correlated with recombination rate in intergenic regions, but not in introns. We argue that these differences are due to different selective constraints rather than mutational or recombinational mechanisms.

Animals↗
PubMed1992

DNA base composition, aerotolerance and enzyme patterns of Leptotrichia buccalis.

The guanine plus cytosine content of the DNA of Leptotrichia buccalis varied from 28.4 to 29.5 mol% (three strains). Eleven strains examined grew well under anaerobic and microaerobic conditions, but slowly in air in the presence of CO2. When examined for preformed enzymes in the APIZYM Complete Research Kit, positive reactions were obtained for several glucosidases and carboxylic ester hydrolases, and for a few peptidases.

Air↗
PubMed1998

Effect of base composition on DNA bending by phosphate neutralization.

Of the many forces involved in DNA bending by proteins, we have focused on the possible role of asymmetric phosphate neutralization due to interactions between the negatively charged phosphate backbone of duplex DNA and cationic amino acids of an approaching protein. The resulting unbalanced charge distribution along the duplex DNA is thought to induce the double helix to collapse toward the neutralized surface. Previous work has confirmed that DNA bending (approximately 20.7 +/- 4 degrees) is induced by asymmetric incorporation of six uncharged racemic methylphosphonate analogs partially neutralizing one face of GC-rich duplex DNA. We have now analyzed DNA duplexes with similar patches of methylphosphonate linkages in an AT-rich sequence context and again observe bending toward the neutralized face, to an extent (20 +/- 0.6 degrees) comparable to that observed for neutral patches in GC-rich DNA. The similar induced bend angles in AT-rich and GC-rich contexts does not reveal increased flexibility in AT-rich sequences, or a particular propensity of A-T base pairs to roll toward the minor groove in the tested sequences.

Base Composition↗
PubMed2002

Base composition bias might result from competition for metabolic resources.

The GC content of bacterial genomes varies from 25 to 75%, but the reason for this variation is unclear. Here, we show that genomes of bacteria that rely on their host for survival (obligatory pathogens or symbionts) tend to be AT rich. Furthermore, we have analysed bacterial phages, plasmids and insertion sequences, which might also be regarded as 'intracellular pathogens', and show that they too are significantly richer in AT than their hosts. We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences.

AT Rich Sequence↗
PubMed1982

Relative base composition of initiation sites for transcription in developing frog embryos.

The use of an inhibitor (0.4 N (NH4)2SO4) and an activator (sodium polydextran sulfate) of initiation of transcription in nuclei of frog embryos in vitro indicated that initiation sites for transcription are relatively A--T-rich. Comparison of incorporation of labeled ATP, UTP, and GTP, when initiation of transcription is prevented, indicates that initiation sites become relatively less A--T-rich as development proceeds. Inhibition of initiation of transcription in isolated nuclei blocks the normal increase in rate of transcription that occurs when cells enter the S phase, showing that an increased level of transcription depends upon a greater number of initiation sites.

Adenosine Triphosphate↗
PubMed2002

Molecular population genetics of Xdh and the evolution of base composition in Drosophila.

Few loci have been measured for DNA polymorphism and divergence in several species. Here we report such data from the protein-coding region of xanthine dehydrogenase (Xdh) in 22 species of Drosophila. Many of our samples were from closely related species, allowing us to confidently assign substitutions to individual lineages. Surprisingly, Xdh appears to be fixing more A/T mutations than G/C mutations in most lineages, leading to evolution of higher A/T content in the recent past. We found no compelling evidence for selection on protein variation, though some aspects of the data support the notion that a significant fraction of amino acid polymorphisms are slightly deleterious. Finally, we found no convincing evidence that levels of silent heterozygosity are associated with rates of protein evolution.

Amino Acid Substitution↗
PubMed1988

DNA base composition and homology values in the classification of some Rhodococcus species.

Similar DNA homology values were recorded when a modified S1 nuclease technique and a standard nitrocellulose membrane filter method were applied to representative strains of Rhodococcus. The DNA homology data showed that R. globerulus, R. luteus and R. sputi form distinct genomic species. The congruence between the DNA homology and earlier numerical phenetic data was good, but there was evidence that some strains had been misclassified in the previous studies. In particular, the type strains of R. obuensis and R. sputi belong to a single genomic species. The former name is thus a later, subjective synonym of the latter. The guanine plus cytosine content of the DNA of the rhodococci fell within the range 61 to 72 mol%.

Base Composition↗
PubMedDate not supplied

Taxonomy of pasteurella anatipestifer. 1. DNA base composition and DNA-DNA hybridization analysis.

DNA was isolated from 15 strains of Pasteurella anatipestifer and from one strain each of Moraxella nonliquefaciens, M. bovis, Pasteurella multocida, P. haemolytica, P. gallinarum, P. pneumotropica, and P. ureae. The guanine-plus-cytosine contents of P. anatipestifer ranged from 32 to 35 mole %, whereas those of Moraxella and Pasteurella spp. were much higher, ranging from 40 to 45 mole %. DNA-DNA hybridization analysis revealed that homology of nine P. anatipestifer strains to strains ATCC 11845 and PA 15 was 52 to 100%, whereas homology of Moraxella and Pasteurella strains to these strains was only 3 to 17%. Similarly, homology of P. anatipestifer strains, Moraxella, and Pasteurella species other than P. multocida to P. multocida reference strain P-2192 was low. These results strongly suggest that P. anatipestifer is genetically unrelated to either Pasteurella or Moraxella.

Base Composition↗
PubMed1984

DNA base composition and DNA relatedness among species of Trichosporon Behrend.

The nuclear DNA of 28 species (30 strains investigated) of yeasts classified currently or previously in the genus Trichosporon. was analysed for its molar percentage of guanine + cytosine (mol% G + C). This criterion, together with biochemical characteristics, suggested the separation of the organisms studied into two groups. The first group, which appears related to the Ascomycetes, includes thirteen species with a G + C content lower than 50 mol% (34.7-48.8), and lacks urease (except T. margaritiferum). The second group appears related to the Basidiomycetes and includes fifteen species with a G + C content higher than 50 mol% (57-64) and has the ability to hydrolyse urea. A DNA homology experiment with T. beigelii and twelve other species of the second group showed very low values of complementarity with T. beigelii-labeled DNA. All these species must be considered as taxa other than T. beigelii.

Ascomycota↗
PubMed2004

Base composition and expression level of human genes.

It is well known that the gene distribution is non-uniform in the human genome, reaching the highest concentration in the GC-rich isochores. Also the amino acid frequencies, and the hydrophobicity, of the corresponding encoded proteins are affected by the high GC level of the genes localized in the GC-rich isochores. It was hypothesized that the gene expression level as well is higher in GC-rich compared to GC-poor isochores [Mol. Biol. Evol. 10 (1993) 186]. Several features of human genes and proteins, namely expression level, coding and non-coding lengths, and hydrophobicity were investigated in the present paper. The results support the hypothesis reported above, since all the parameters so far studied converge to the same conclusion, that the average expression level of the GC-rich genes is significantly higher than that of the GC-poor genes.

Base Composition↗
PubMed1989

Thermodynamics of the interactions of m-AMSA and o-AMSA with nucleic acids: influence of ionic strength and DNA base composition.

The equilibrium binding of the antitumor agent m-AMSA and its biologically inactive analog o-AMSA to native and synthetic DNAs are compared over a wide range of ionic strengths and temperatures. Although o-AMSA binds DNA with a higher affinity than m-AMSA it is not effective as an antitumor agent. Both m-AMSA and o-AMSA bind DNA in an intercalative manner. Indepth investigations into the thermodynamic parameters of these interactions reveal the interaction of m-AMSA with DNA to be an enthalpy driven process. In contrast, the structurally similar but biologically inactive o-AMSA binds DNA through an entropy driven process. The differences in thermodynamic mechanisms of binding between the two isomers reveal that the electronic and/or steric factors resulting from the position of the methoxy substituent group on the anilino ring directs the DNA binding properties of these compounds and ultimately the biological effectiveness as an antitumor agent.

Amsacrine↗
PubMed1991

[Determination of DNA base composition and levels of DNA-DNA hybridization of Actinobacillus actinomycetemcomitans].

Using the strains of Actinobacillus actinomycetemcomitans (Aa) and Haemophilus aphrophilus (Haph) in experiments, the mole percent quanine plus cytosine content (mol% G + C) and level of DNA-DNA hybridization (DNA homology) were determined for the first time in oral microbiologic study in China. DNA was extracted by Marmur's method. The mol% G + C of DNA was determined by thermal denaturation method (Tm). DNA-DNA hybridization was carried out by De Ley's optical procedure (initial renaturation rate). The results are as follows: 1. The mol% G + C of DNA of Aa is different from that of Haph. 2. 2 strains of Aa had high DNA homology (73.8%) and the DNA homology between Aa and Haph was low (33.9%). It was confirmed that Aa and Haph are different species. In order to identify the bacteria in periodontal pockets accurately, it is necessary to carry out the nucleic acid study in bacterial classification.

Actinobacillus↗