Deoxyribonucleic Acid Base Research Articles

Streptococcus downei sp. nov. for Strains Previously Described as Streptococcus mutans Serotype h

Strains of streptococci originally isolated from the dental plaque of monkeys (Macaca fascicularis) and designated as Streptococcus mutans serotype h were compared with the other species of the mutans streptococcus group. Despite the close resemblance noted previously between these strains and Streptococcus sobrinus, closer examination revealed several important differences. Strains of serotype h ferment mannitol but not sorbitol, melibiose, inulin, or raffinose, do not produce hydrogen peroxide, and are unable to grow in the presence of bacitracin at 2 units per ml. They exhibit a distinct polypeptide pattern by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and possess several antigens absent from S. sobrinus as revealed by Western blotting (immunoblotting). Virtually identical polar lipid patterns were observed by two-dimensional thin-layer chromatography for both serotype h strains and S. sobrinus, although on the basis of long-chain fatty acid analysis by capillary gas-liquid chromatography, the former could be distinguished by the presence of a peak tentatively identified as cyclopropane acid (cis-9, 10-methyleneoctadecanoate (ΔC 19:0). Deoxyribonucleic acid (DNA)-DNA hybridization studies by both the S1 nuclease and renaturation rate methods showed that serotype h strains differ from S. mutans, S. sobrinus, Streptococcus cricetus, Streptococcus rattus, Streptococcus ferus, and Streptococcus macacae. On the basis of these data, we believe that S. mutans serotype h strains represent a distinct species for which the name Streptococcus downei is proposed. The DNA base composition is 41 to 42 moles percent guanine plus cytosine. The type strain is strain MFe28 (NCTC 11391T), which is cariogenic in monoassociated germfree rats.

Deoxyribonucleic Acid Base Sequence Relatedness among Members of the Yeast Genus Kluyveromyces

Deoxyribonucleic acid (DNA) base composition and DNA base sequence relatedness comparisons were used for species delineation in the genus Kluyveromyces. Base composition values separated the members of the genus into three groups. The groups were further subdivided by comparing base sequences by using DNA/DNA renaturation experiments. Two DNA homology groups were identified. The first group included Kluyveromyces marxianus, Kluyveromyces fragilis, Kluyveromyces bulgaricus, Kluyveromyces cicerisporus, Kluyveromyces wikenii, and three anamorphs (Candida kefyr, Candida pseudotropicalis, and Torula cremoris); the members of this group exhibited ≥90% DNA base sequence complementarity. The second group consisted of Kluyveromyces lactis, Kluyveromyces vanudenii, Kluyveromyces drosophilarum, and Kluyveromyces phaseolosporus; various pairs of these yeasts shared 64 to 98% of their DNA sequences. The two groups were only distantly related to each other (≤15% DNA base sequence complementarity). The other Kluyveromyces species appear to be unique, not being closely related to either of the two homology groups or to one another. Relationships deduced from comparisons of DNAs agreed well with those deduced by other workers from immunological comparisons of exo-β-glucanases and from isoenzyme analysis but were only in partial agreement with a taxonomic arrangement made on the basis of mating studies. We propose recognition of the following species: Kluyveromyces aestuarii, Kluyveromyces africanus, Kluyveromyces blattae, Kluyveromyces delphensis, Kluyveromyces dobzhanskii, K. lactis (syn. K. drosophilarum, K. phaseolosporus, and K. vanudenii), Kluyveromyces lodderi, K. marxianus (syn. K. bulgaricus, K. cicerisporus, K. fragilis, and K. wikenii), Kluyveromyces phaffii, Kluyveromyces polysporus, Kluyveromyces thermotolerans, Kluyveromyces waltii, and Kluyveromyces wickerhamii.

Reclassification of Pseudomonas acidovorans den Dooren de Jong 1926 and Pseudomonas testosteroni Marcus and Talalay 1956 as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb. nov., with an Emended Description of the Genus Comamonas

We examined 36 strains of Pseudomonas acidovorans, Pseudomonas testosteroni, and Comamonas terrigena on the basis of phenotypic characters, chemotaxonomic characters, and deoxyribonucleic acid (DNA)-DNA homology. Strains of these three species share many phenotypic characteristics; these organisms exhibit higher levels of DNA-DNA homology and higher levels of electrophoretic enzyme pattern similarity within the three species than with Pseudomonas aeruginosa. The strains in the three species could be differentiated on the basis of carbon compound assimilation patterns, cellular fatty acid composition, and DNA base composition. We propose that Pseudomonas acidovorans and Pseudomonas testosteroni be transferred to the genus Comamonas, as Comamonas acidovorans comb. nov. and Comamonas testosteroni comb, nov., respectively.

Deoxyribonucleic Acid Homologies of Hyphomicrobium spp., Hyphomonas spp., and Other Hyphal, Budding Bacteria

The levels of genetic relatedness of 19 Hyphomicrobium strains which utilize one-carbon compounds were determined by deoxyribonucleic acid (DNA)-DNA hybridization in solution under optimal conditions (S1 nuclease technique). Most of these hyphomicrobia fell into four groups with high levels of relatedness (level of homology within each group, 86 to 110%). These groups were only distantly related to each other (levels of homology between groups, 1 to 9%). Three additional groups of C1-utilizing hyphomicrobia were represented by only one strain each. In addition, the levels of DNA-DNA homology of four Hyphomonas species and 11 Hyphomicrobium-Hyphomonas-like isolates were determined. Seven of these isolates formed three groups containing two or three strains each; the level of homology within each group was 94 to 120%. These groups of peptide-utilizing strains were related to Hyphomonas spp. at a DNA-DNA homology level of 13 to 43%; thus, they represented new species of Hyphomonas. Four of the isolates had less than 10% DNA homology with either Hyphomicrobium reference strains or Hyphomonas spp. Strain B-1408 was distinguished by its DNA base composition of 46.19 mol% guanine plus cytosine, which is 14 mol% below the average base composition of Hyphomicrobium spp. or Hyphomonas spp. The levels of genetic relatedness of other hyphal, budding bacteria, such as Pedomicrobium spp., genus F, Rhodomicrobium vannielii, and genus T, to Hyphomicrobium sp. strain MC-750 were too low to be evaluated by DNA-DNA hybridization techniques.

Proton NMR investigation of the nucleosome core particle: evidence for regions of altered hydrogen bonding.

Novel 1H nuclear magnetic resonance (NMR) resonances, arising from exchangeable protons and centered at approximately 11.2 and 10.1 parts per million (ppm), have been observed in the low-field spectrum (10-15 ppm) of the chicken erythrocyte core particle [145 +/- 2 base pairs (bp)]. These peaks are located upfield from the normal adenine-thymine (A-T) and guanine-cytosine (G-C) imino peaks characteristic of B-form deoxyribonucleic acid (DNA) and are not observed in free DNA under identical conditions. The appearance of the new peaks is ionic strength dependent and temperature-reversible below 75 degrees C. At 25 degrees C, the upfield peak area represents 5% of the DNA base pairs (7 bp), while between 45 and 55 degrees C, the area increases to 18%, affecting approximately 25 bp. Area increases in the upfield resonances result in a complementary decrease in the A-T and G-C imino peaks found between 12 and 14 ppm. We believe these novel proton signals represent a histone-induced DNA conformational change which involves localized alteration of base pairing in the core particle.

Interactions of several polycyclic aromatic hydrocarbons with DNA base molecules studied by absorption spectroscopy and fluorescence quenching

The interactions of several polycyclic aromatic hydrocarbons (PAHs) including benzo[ a]pyrene, benzo[ e]pyrene, benz[ a]anthracene, 7,12-dimethylbenz[ a]anthracene, 3-methylcholanthrene, dibenz[ a, c]anthracene and dibenz[ a, h]anthracene with selected deoxyribonucleic acid (DNA) bases, i.e. adenine, thymine, cytosine and 5-methylcytosine, and a nucleoside, guanosine, have been studied employing UV-visible absorption spectroscopy, fluorescence quenching and electrochemical measurements. The results indicate that PAHs interact with DNA bases by forming modernately strong 1:1 charge transfer (CT) complexes in their ground state. The fluorescence of PAHs was only quenched by 5-methylcytosine, quanosine and cytosine, and this was at lower than diffusion controlled rates in dimethyl sulfoxide. The fluorescence quenching rate constants showed a better inverse correlation with the solvent reorganization energies than with the free energies of activation calculated using the Marcus model of electron transfer.

Deoxyribonucleic Acid Base Compositions and Nucleotide Distributions of 65 Strains of Budding Bacteria

A total of 65 strains of appendaged or prosthecate, budding bacteria from our culture collection were selected for a study of deoxyribonucleic acid (DNA) base composition and nucleotide distribution. These strains represented 11 genera, including 4 genera of hyphal, budding bacteria which have not been formally described yet. The DNA species were thermally denatured, and absorbance-temperature profiles were recorded. The midpoints, widths, and asymmetries of the melting transitions were determined. When the DNA base compositions and nucleotide distributions were plotted on a dissimilarity map, it became evident that the strains of each genus occupied a distinct area. The distribution of strains within such an area indicated the degree of heterogeneity of a genus. When 16 Hyphomicrobium strains were analyzed, they formed five clusters within their generic area. These clusters correlated well with groups which had been previously established by DNA base composition analyses, by DNA-DNA homology studies, and by numerical taxonomy. Nine of the strains investigated were distinguished by melting profiles which were skewed uniquely to the left.

Paramagnetic intermediates in the photolysis of purine free base in frozen aqueous glasses

UV irradiation of purine free base used as a model for the purine bases in deoxyribonucleic acid, in aqueous glassy solutions, produces stable photo-products, as well as reactive paramagnetic intermediates such as triplet states, trapped electrons, purine radical cations and anions and solvent radicals. Electron spin resonance techniques and parameters were used to characterize the intermediates produced during the UV irradiation of purine in aqueous glasses at 77 K at different pH values (8 M NaClO 4, 12 M LiCl, 5 M H 2SO 4, 6 M H 3PO 4 and 8 M NaOH). Biphotonic ionization of the base through a triplet intermediate is one of the principal photodestruction paths in basic and neutral glasses. The quantum yields for the production of trapped electrons in 8 M NaOH and 8 M NaClO 4 glasses are 0.02 and 0.0023 respectively. In 12 M LiCl, 5 M H 2SO 4 and 6 M H 3PO 4 glasses, energy transfer from the purine molecules to the surrounding solvent molecules is observed. This transfer of energy produces Cl − 2, SO − 4, SO − 3 and HPO − 4 radical ions.

Synthetic models related to deoxyribonucleic acid base–psoralen interactions. Syntheses and studies of bichromophore systems containing psoralen moieties

The syntheses of new bispsoralen derivatives (IIn) and (IIIm) are reported. The photophysical properties of these potential deoxyribonucleic acid (DNA) bisintercalating drugs are studied and compared with compounds (I) and (IV) where the psoralen moiety is linked with a DNA base. The singlet and triplet deactivation processes underline the role of intercalation in the photobiological activity of psoralen with DNA. Some attempts at complexation of compounds (IIn) and (IIIm) with DNA are also reported.

Polyacrylamide gel analysis of spiroplasmas proteins and its contribution to the taxonomy of spiroplasmas.

Representative strains of the known groups and serogroups of spiroplasmas have been compared on the basis of the results of one- and two-dimensional protein analysis on polyacrylamide gels. Each of the four subgroups of the Spiroplasma citri complex (S. citri and honeybee, corn stunt, and 277F spiroplasmas) has characteristic protein profiles and maps. Spiroplasma G1 isolated from flowers has a protein profile closely related to that of the honeybee spiroplasmas (KC3, BC3, AS576, B1707, B88, and B63). The flower spiroplasmas fall into two groups on the basis of the mole percentage (mol%) of guanine plus cytosine (G + C) of their deoxyribonucleic acid (DNA) 26 and 30 mol %, respectively) and their serologic properties. The three flower spiroplasmas (OBMG, BNR1, and 23-6) with 26 mol % of G + C have the same basic protein pattern. Although some of the flower spiroplasmas with 30 mol % of G + C have closely related protein patterns, others have more distant profiles. Spiroplasmas B13 and L89, isolated from honeybees and froghoppers, respectively, had DNA with 30 mol % of G + C and could be included with other flower spiroplasmas with similar DNA base composition on the basis of their protein profiles and maps. Individual proteins separated by two-dimensional analysis on polyacrylamide gels have been used for the production of monospecific immunoglobulins, which are useful in taxonomic studies.

Taxonomy of the Neisseriae: Deoxyribonucleic Acid Base Composition, Interspecific Transformation, and Deoxyribonucleic Acid Hybridization

Deoxyribonucleic acid (DNA) base composition, intergenic transformation efficiency, and DNA hybridization were used to determine the relatedness of a variety of established or proposed species of Neisseria and Branhamella. These studies indicated that these bacteria form three genetic groupings. Group I, comprised of N. meningitidis, N. gonorrhoeae, N. subflava, N. flava, N. perflava, N. sicca, N. mucosa, N. cinerea, N. flavescens, N. lactamica, N. elongata, N. canis, and N. denitrificans, was characterized by DNA base compositions ranging between 49.3 and 55.6 mol% guanine plus cytosine. Group II, comprised of N. cuniculi, N. caviae, and N. ovis, was characterized by DNA base compositions ranging between 45.3 and 47.3 mol% guanine plus cytosine. Group III, comprised of one species, B. catarrhalis, was characterized by DNA base compositions between 41 and 42 mol% guanine plus cytosine. Transformation and DNA hybridization results revealed that members of each group, with few exceptions, exhibited high DNA homology with other members of the same group but most often distinctly lower levels of homology with members of a different group. These data suggest that N. ovis, N. caviae, and N. cuniculi may be significantly different from other neisseriae and from branhamellae to warrant their separation in a distinct genus.

Interaction between 9-substituted benzo[alpha]phenoxazine derivatives and DNA and relationships to their antibacterial activities

Studies were made on the intermolecular interaction of ten 9-diethylaminobenzo [α]-phenoxazonium salts (BPZ) and calf-thymus deoxyribonucleic acid (DNA) and antibacterial activities for Staphylococcus aureus 209P of BPZ. (1) The interaction system of BPZ and DNA was found to show a flow dichroism in the visible region. A value of the ΔE in the equation ΔE=E11-E⊥ is found to be negative, and flow dichroism studies indicate that BPZ intercalates in the same plane as DNA base pairs. (2) The flow dichroism's ratio in the visible region produced by the interaction of BPZ with DNA paralleled in minimum inhibitory concentration (MIC) of BPZ for Staphylococcus aureus 209P.

Confirmation of Bacteroides gingivalis as a Species Distinct from Bacteroides asaccharolyticus

We divided the asaccharolytic, black-pigmented Bacteroides strains into two groups on the basis of deoxyribonucleic acid (DNA) base ratios, DNA hybridization (S1 nuclease method) results, and direct hemagglutination. One homologous group of strains, which included the type strain of Bacteroides asaccharolyticus and had guanine-plus-cytosine contents of 52 to 54 mol%, contained only nonoral isolates. Another DNA homology group contained all of the strains from periodontal pockets and some nonoral isolates. These strains appeared to belong to the recently described new species Bacteroides gingivalis Coykendall et al. B. gingivalis strains had guanine-plus-cytosine contents of 48 to 50 mol%, showed high DNA homology values, and shared hemagglutinating activity. No DNA homology was observed between the two groups. Using a different method of analysis for DNA homology (S1 nuclease method), we confirmed the conclusion of Coykendall et al., who separated these two groups into different species, B. asaccharolyticus and B. gingivalis. Two strains from infected root canals could not be placed in either of these two species. On the basis of the DNA homology results, all asaccharolytic strains were distinguished clearly from the saccharolytic, black-pigmented Bacteroides strains, which at present are classified in the species Bacteroides melaninogenicus.

Pyrolysis of deoxyribonucleic acid: Isolation and mass spectrometry of individual pyrolysis products

Calf thymus deoxyribonucleic acid (DNA) was subjected to pyrolysis as 1 × 10 −7 atm and 220–250°C. The sublimate was collected and its composition was examined by thin-layer chromatography and mass spectrometry. It contained, inter alia, three of the four major DNA bases, a bis-methylfuranyladenine, two mono-methylfuranyladenines and a methylfuranyleytosine. The recovery of the sublimate, as a percentage of the total of each present in the DNA, was: adenine, 27%; cytosine, 40%; thymine, 60%. The mass spectrum of the sublimate was compared with that obtained directly from DNA.

Dependence of mononucleosome deoxyribonucleic acid conformation on the deoxyribonucleic acid length and H1/H5 content. Circular dichroism and thermal denaturation studies.

Four mononucleosome preparations were isolated from micrococcal nuclease digests of chicken erythrocyte nuclei which differed in average deoxyribonucleic acid (DNA) length and in H1 and H5 content. The circular dichroism properties of the unperturbed mononucleosome preparations and the corresponding H1- and H5-depleted species demonstrate that the nucleoprotein spectra above 250 nm are all altered relative to protein-free DNA by the addition of a single negative band at 275 nm, similar to the band observed for psi-DNA. The quantitative analysis of the psi-type band intensity for any of the higher molecular weight unperturbed samples relative to core particle mononucleosomes yielded a constant number of DNA base pairs (approximately 140) contributing to this new band. Upon removal of H1 and H5 from the mononucleosome preparations which have sufficiently long linker DNA, the psi-type band intensity indicates an approximately 30 base pair reduction in the number of core DNA base pairs contributing to the altered circular dichroism properties. The psi-type band is proposed to be due to the compact DNA tertiary structure, i.e., the manner in which the DNA is wound around the histone core allowing interactions between adjacent turns of the superhelix. This interpretation implies that approximately 30 base pairs of core DNA are removed from the unique core tertiary structure when the linker DNA is not bound by H1 or H5. The circular dichroism analysis correlates well with the thermal denaturation properties of mononucleosomes. Removal of H1 and H5 causes an overall reduction in the thermal stability of both core and linker DNA. The degree of destabilization is greatest when the average DNA length is maximum. Some core DNA is lost from the highest temperature melting bands when histone-free DNA is present. These results indicate two regions of different conformational and thermodynamic stability in core DNA. The length of attached linker DNA and its histone content influence the two regions of the core to differing extents.

Deoxyribonucleic Acid Homologies of Lactobacillus jensenii, Lactobacillus leichmannii, and Lactobacillus acidophilus

Labeled [3H]deoxyribonucleic acid (DNA) from Lactobacillus jensenii ATCC 25258 yielded a substantial amount of heteroduplexes only with DNA molecules from other strains of L. jensenii. A low yield of heteroduplexing was obtained between DNAs of L. jensenii and L. acidophilus, although both species had the same guanine plus cytosine content (36 mol%). The striking phenotypic similarity between L. jensenii and L. leichmannii was not reflected in their DNA base composition (36 and 50 mol% guanine plus cytosine, respectively), and, as expected, they produced a very low yield of hybridized DNAs. Although the phylogenic relationship between these different species of Lactobacillus cannot be deduced from their DNA relatedness, it can nevertheless be established from the structural similarity of their D-lactic dehydrogenases.

Catalytic release of deoxyribonucleic acid bases by oxidation and reduction of an iron.bleomycin complex.

Catalytic release of deoxyribonucleic acid bases by oxidation and reduction of an iron.bleomycin complex.

Contribution to the Characterization of Bacillus megaterium

A study of the cellular and colonial morphologies, the deoxyribonucleic acid (DNA) base composition, the degree of lysis by lysozyme, and some fundamental biochemical reactions was carried out on 23 strains previously identified as members of Bacillus megaterium. Included among these was NCTC 10342, the neotype strain of B. megaterium. The results showed that, primarily on the basis of their biochemical reactions, two of the strains belong to B. cereus, two belong to B. subtilis, and 19 belong to B. megaterium. The first two strains mentioned above clearly differed from B. megaterium strains with respect to their DNA base composition (33.2 and 34.3 mol% guanine plus cytosine [G+C]), their lysis by lysozyme (5.6 and 6.6%), and the morphology of their macro-and microcolonies. These properties were not helpful in differentiating the other two strains from the B. megaterium strains, for the two strains showed high G+C values (45.9 and 47.4 mol%) and high values of lysis by lysozyme, (92.9 and 96.7%). The 19 remaining strains, confirmed as members of B. megaterium, had G+C contents which varied from 37.3 to 43.0 mol% and lysis percentages which varied from 67.0 to 94.9. For these strains, a significant (P < 0.05) correlation was found between the DNA base composition and lysis by lysozyme. Three biogroups were established on the basis of the biochemical reactions of the 19 strains. These biogroups are similar to the “aggregate” and the “intermediate” strains of B. megaterium established by Gordon et al.

Pathogenic Vibrio isolated from cultured eels. IV. Deoxyribonucleic acid studies.

The molecular taxonomic position of a new pathogenic vibrio isolated from cultured eels has been studied. The bacterium had been classified as V. anguillarum Type B, V. anguillarum f. anguillicida, on the basis of phenotypic properties. The percent guanine plus cytosine content of deoxyribonucleic acid (DNA) was 46.3%, which is within or appreciably close to the DNA base composition ranges of the existing Vibrio species. Polynucleotide sequence analysis by means of optical measurement of renatured DNA, however, provided proof that the present vibrio was distinct from the existing species of the genus Vibrio. The isolates from diseased eels represented a homologous group (96-97% homology for reference ET-7617 strain DNA) with the genome size of 2, 000 to 2, 500×106 daltons. On the other hand the reference strain was very distantly related to other Vibrio species: 12-23% related to V. anguillarum; 2-17% to V. fischeri; 14% to V. parahaemolyticus; 12% to V. alginolyticus; 9% to V. cholerae. Therefore the present organism was considered as a new member of the genus Vibrio.

Antitumor Agents XXIX: Effects of Eupahyssopin on Nucleic Acid, Protein, Anaerobic, and Aerobic Metabolism of Ehrlich Ascites Tumor Cells

Evidence is presented that the antitumor agent eupahyssopin, a germacranolide, inhibits deoxyribonucleic acid, ribonucleic acid, protein, and cholesterol synthesis of Ehrlich ascites tumor cells in CF1 male mice. Eupahyssopin appears to bind to nucleotide bases of deoxyribonucleic acid. The drug also inhibits deoxyribonucleic acid and messenger ribonucleic acid polymerase activities and, marginally, thymidylate synthetase activity. Template activity, as regulated by phosphorylation of histones and nonhistones, and cyclic 3ʹ,5ʹ-adenosine monophosphate levels also were affected by drug therapy. Lysosomal enzymes, e.g., deoxyribonuclease and ribonuclease, and cathepsin activities were inhibited by eupahyssopin administration. A number of sulfhydryl-bearing enzymes of the glycolytic and Krebs cycles were inhibited by drug treatment, as were enzymes required for glycogen synthesis and breakdown and for phosphatase hydrolysis. Eupahyssopin also inhibited both basal respiration and coupled oxidative phosphorylation processes of the tumor cell. It was proposed that eupahyssopin, which contains the O=CC=CH2 as an α-methylene γ-lactone moiety within its allylic ester side chain, has the ability to undergo a rapid Michael-type addition with sulfhydryl groups of these enzymes and thus to inhibit their activities in a manner analogous to that described for other sesquiterpene antitumor agents containing the O=CC=CH2 moiety.