Deoxyribonucleic Acid Base Research Articles

Electrical Transport Properties of Au-Doped Deoxyribonucleic Acid Molecules

Deoxyribonucleic acid (DNA) molecules were doped with Au atoms and their electrical transport properties were measured. The Au doping was carried out by incubating a mixture of HAuCl4·3H2O and DNA solutions. The binding of Au atoms to DNA bases was identified using Fourier transform infrared spectroscopy and X-ray photoemission spectroscopy. The Au-doped DNA molecules were deposited on nanoelectrodes and the presence of the molecules between the electrodes was determined by both scanning electron microscopy and atomic force microscopy. Measurement of the current-voltage characteristics showed that the Au-doped DNA molecules exhibited a higher conductivity than undoped DNA molecules. Detailed analysis of the chemical composition shows that there is a strong possibility of reliably controlling the conductivity of DNA molecules using this method.

Mathematical Model for Polaronic Effects of Charge Transport in DNA

In this work, the charge transport in deoxyribonucleic acid (DNA) is theoretically analyzed. We develop an novel mathematical model based on the polaron model by Komineas et al. We improve the model for considering the effect of bulk temperature. In order to conserve the norm of the wavefunction, the numerical code based on implicit Successive Over Relaxation (SOR) scheme is developed for solving time-dependent Schrödinger equation. The equations of motions of DNA base pairs and the bulk molecules are also efficiently solved simultaneously. It is found that the mean velocity of the polaron in DNA becomes faster as bulk temperature. Futhermore, detailed systematical study for various parameters in the model is made by the use of the code developed here. Consequently, we can accumulate the basic understanding of charge transport phenomena in DNA.

Voltammetric determination of all DNA nucleotides

The voltammetric oxidation of all deoxyribonucleic acid (DNA) monophosphate nucleotides is investigated for the first time over a wide pH range by differential pulse voltammetry with a glassy carbon electrode. Experimental conditions such as the electrode size, supporting electrolyte composition, and pH were optimized to obtain the best peak potential separation and higher currents. This enabled the simultaneous voltammetric determination of all four DNA bases in equimolar mixtures and detection limits in the nanomolar range at physiological pH. It was also possible to detect for the first time the oxidation of each of the purine and pyrimidine nucleotides free in solution or as monomers in single-stranded DNA.

Ion conductive characteristics of DNA containing PEO chains covalently bound on nucleic acid bases

AbstractIn order to prepare flexible and ion conductive deoxyribonucleic acid (DNA) films without phase separation, DNA was modified with poly(ethylene oxide) (PEO). PEOs with molecular weight of 150 to 2000 were fixed to the amino groups of nucleic acid bases in DNA (PEO‐DNA). Brittle DNA films turned flexible after PEO modification, and the highest ionic conductivity was obtained when PEO with molecular weight of 1000 was modified. Though Na+, counter cation of phosphate group, was expected to migrate in these PEOx‐DNA hybrids as a carrier ion, ionic conductivity was only 1.3 × 10−6 S cm−1. Addition of salts to PEO1000‐DNA considerably improved the ionic conductivity, and sodium bis(trifluoromethanesulfonyl)imide (NaTFSI) was the best salt for this purpose. When NaTFSI, 5 mol% to the oxyethylene (OE) unit, was mixed with PEO1000‐DNA, the highest ionic conductivity of 1.77 × 10−5 S cm−1 was observed at 30°C. Copyright © 2004 John Wiley & Sons, Ltd.

Transgene methylation in mice reflects copy number but not expression level.

In mammals, CpG methylation is one of the mechanisms of epigenetic control over the linear sequence of bases of deoxyribonucleic acid (DNA); about 70% of CpG dinucleotides are methylated. The actual signal that triggers DNA methylation is not known, although repetitive DNA has been shown to be an attractive template for DNA methylases. To address methylation events associated with transgenic copy number, we have analyzed transgenes that are actively transcribed in a tissue-specific manner. We have compared gross transgene methylation by restriction-enzyme digestion in expressing and nonexpressing tissues. The observed pattern suggests that the DNA methylation machinery can recognize repeated genomic sequences independently of their transcriptional activity.

Proposal on personal identifiers generated from the STR information of DNA

The individual differences in the repeat count of several bases, short tandem repeat (STR), among all of the deoxyribonucleic acid (DNA) base sequences, can be used as unique DNA information for a personal identification (ID). We propose a method to generate a personal identifier (hereafter referred to as a “DNA personal ID”) by specifying multiple STR locations (called “loci”) and then sequencing the repeat count information. We also conducted a validation experiment to verify the proposed principle based on actual DNA data. We verified that the matching probability of DNA personal IDs becomes exponentially smaller, to about 10-n, as n stages of loci are used and that no correlation exists among the loci. Next, we considered the various issues that will be encountered when applying DNA personal IDs to information security systems, such as biometric personal authentication systems.

On the reaction of mutagenic aflatoxin B 1 oxide and benz[ a]pyrene diol oxide with guanine residue in DNA double helix

Theoretical calculation was performed to study the binding mechanism of intercalators to deoxyribonucleic acid (DNA) base pairs. The structures of intercalating complexes and ligand–DNA adducts of mutagenic aflatoxin B 1 8,9-oxide ( 1) and benz[ a]pyrene diol oxide ( 2) and the reactivity for S N2 type nucleophilic oxirane ring opening for 2 were investigated. Calculation clarified the following points: 1. The atomic contacts between two reaction sites (nucleophilic N2 or N7 nitrogen lone pair of guanine residue in DNA base pairs and electrophilic carbon of three-membered oxirane ring in mutagenic 1 and 2) are considerably short, suggesting that intercalation makes two reaction sites closer and consequently promotes the covalent binding of mutagens to guanine base. 2. In the adducts of 1 and 2 with DNA double helix, large planar coumarin ring of 1 exists in the major groove of double helix and planar aromatic ring system of 2 in minor groove of it. The regularly layered structure of B type DNA double helix is not distorted in the adduct of 1, however, the double helix is considerably distorted in the adduct of 2. 3. Two mutagens probably intercalate into DNA base pairs and make stable complexes which are followed by transition structures (TSs) for covalent binding. Judging from the activation energy (Δ E ≠) estimated to be 47.7 kcal/mol, the reactivity for covalent binding is considerably low, implying that intercalation must play an important role as precedent phenomena to covalent binding between bases and intercalators. Calculation suggests that the reactivity for S N2 type nucleophilic reaction itself (the stability of TS for covalent binding) is not so high, and therefore, the potency for mutagenesis might be attributing to the formation of stable (and consequently) long standing intercalating complex and stable ligand–DNA adduct.

Session 6 structural implications of BER enzymes: Dragons dancing—The structural biology of DNA base excision repair

The chapter discusses the structural visions and insights into base excision repair (BER) systems. These structures are at the heart of an emerging view of a coherent, but fluid mosaic of deoxyribonucleic acid (DNA) repair networks within the cell. The structural biology of the macromolecular complexes, acting in DNA BER, is consequently pointing toward an emerging understanding of the spatial geometry, linking individual repair steps and also of a structurally encoded regulation of enzyme partnerships that ensure efficient repair of DNA damage. In general, the emerging understanding of DNA and the BER enzyme structures and complexes, as described in the following papers, is taking our understanding of BER to a higher level that may prove relevant to many cellular processes, requiring the coordination of complex multistep chemistry. Structural biology of BER is, thus, an important prototype for understanding protein interactions controlling systems in the post-genomic area. Taken together, these papers provide a fundamental understanding of the DNA repair events, underlying the function of DNA, in the cell biology of life, especially, for the processes controlling genetic integrity.

Interaction of cyanine dyes with nucleic acids. XVII. Towards an aggregation of cyanine dyes in solutions as a factor facilitating nucleic acid detection

Spectral properties of newly synthesized cyanine dyes, namely 1-[6-(4-{6-[2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl)-1-pyridiniumyl]hexanoyl}piperazino)-6-oxohexyl]-2,6-dimethyl-4-(3-ethyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl)pyridinium (K-6) (bichromophoric dye) and 1-[5-di(3-{5-[2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl)-1-pyridiniumyl]pentylcarboxamido}propyl) carbamoylpentyl]-2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl) pyridinium (K-T) (trichromophoric dye) in solutions in the presence of and without deoxyribonucleic acid (DNA) were studied within a wide concentration range. It has been established that absorption, as well as fluorescence of investigated dye solutions, without DNA are mainly determined by H-aggregates of dye molecules. On the contrary, the fluorescence of dye solutions in the presence of DNA gives an intrinsic dye molecular fluorescence. H-aggregates are broken because of binding dye molecules with DNA. It has been suggested that both K-T and K-6 molecules bind mainly with DNA via the interaction of two chromophores. As the ratio of the number of dye molecules to that of DNA base pairs increases with an increase in dye concentration, a formation of dye molecule H-aggregates on DNA molecules are observed. Such aggregates have a different structure than those formed in the solutions without DNA. On the grounds of the data obtained, it is concluded that it is possible to use a dye aggregation capable of obtaining higher values for fluorescence enhancement of the DNA stains.

Application of chimeric RNA–DNA oligonucleotides to the detection of pathogenic microorganisms using surface plasmon resonance

Chimeric oligonucleotides consisting of 21 bases of ribonucleic acid (RNA) with six bases of deoxyribonucleic acid (DNA) at the 3′-hydroxyl terminus (chimeric RNA–DNA primer) and the recombinant thermostable DNA polymerase derived from Thermus thermophilus (r Tth DNA polymerase) were utilized to efficiently amplify DNA fragments using the conventional polymerase chain reaction (PCR). The reaction required the use of both DNA polymerase and reverse transcriptase during each thermal cycle to form a double-stranded DNA in which one terminus was an RNA : DNA hybrid. Due to the ability of r Tth DNA polymerase to function as both the DNA polymerase and reverse transcriptase, a chimeric RNA–DNA primer was shown to serve as a primer in the conventional PCR procedure. We further demonstrate the advantages of using these PCR products to identify microorganisms using surface plasmon resonance (SPR) technology. This detection system was able to distinguish Shiga toxin-producing Escherichia coli O157 : H7 strains from other bacteria such as Salmonella typhimurium and S. enteritidis.

The infrared frequencies of DNA bases: science and art.

If we could hear the body, delve into its rhythms and frequencies, what might it sound like? Would we recognize patterns pleasing to the ear, consider them beautiful, musical? Is our biology harmonically ordered in any way? And if so, so what? There are many ways to explore such questions, and one direct way is to access the frequencies of deoxyribonucleic acid (DNA), the primary carrier of genetic information for all living organisms. In 1988 the author, a composer, posed these questions to Dr. David Deamer, a cell biologist. One significant constraint with. this project required that, rather than mapping, or assigning arbitrary pitches to hear patterns, the actual vibrational frequencies were to be collected directly from the molecular realm. These frequencies would then be arranged as scales of tones and used as the basis for musical composition. In 1990 the cassette version of Sequencia was recorded, and in 1994 the CD with additional music was produced. Sequencia consists of three performances of original music-Eikos, Sequencia, and Pataphysical Thymine-performed on traditional instruments plus electronic keyboard, based entirely on a tuning system derived from certain frequencies that occur naturally in DNA.

The reactivity of chloramphenicol reduction products with DNA bases

Purpose : The interaction between the constituent bases of deoxyribonucleic acid and the reduction products of the nitro-aromatic compound chloramphenicol and its nitroso derivative have been studied using an electrochemical system. Methods and Materials : The changes to the voltammetry of chloramphenicol and nitrosochloramphenicol upon addition of adenine, cytosine, guanine, and thymine at various concentrations have been measured. The biological implications of reductive activation of both chloramphenicol and nitrosochloramphenicol were examined using a ΦX174 double transfection technique which measures biologically relevant deoxyribonucleic acid damage. Results : Measurement of the voltammetric response of chloramphenicol shows that the most noticeable change upon base addition is a decrease in the lifetime of the nitro radical anion in the following order of decreasing activity: adenine, thymine, and cytosine. No effect was observed with guanine. The reversible 2-electron nitrosochloramphenicol-hydroxychloramphenicol couple showed no interaction on the voltammetric timescale, although binding of the hydroxylamine to guanine was observed. Interaction of the azo derivative, formed as a consequence of further reduction plus chemical reaction of nitrosochloramphenicol was observed. Biological studies showed that no significant effect on deoxyribonucleic acid by chloramphenicol or nitrosochloramphenicol was observed under oxic conditions. Controlled reduction of nitrosochloramphenicol to the hydroxylamine gave considerably less damage than when nitrosochloramphenicol or chloramphenicol was completely reduced. Conclusion : The chloramphenicol nitro radical anion reacts selectively with the bases of deoxyribonucleic acid. Reduction products of nitrosochloramphenicol beyond the 2-electron hydroxylamine are highly reactive to deoxyribonucleic acid.

Estimation and Modelling Repeated Patterns in High Order Markov Chains with the Mixture Transition Distribution Model

The mixture transition distribution (MTD) model was introduced by Raftery as a parsimonious model for high order Markov chains. It is flexible, can represent a wide range of dependence patterns, can be physically motivated, fits data well and is in several ways a discrete-valued analogue for the class of autoregressive time series models. However, estimation has presented difficulties because the parameter space is highly non-convex, being defined by a large number of non-linear constraints. Here we propose a computational algorithm for maximum likelihood estimation which is based on a way of reducing the large number of constraints. This also allows more structured versions of the model, e.g. those involving structural zeros, to be fitted quite easily. A way of fitting the model by using GLIM is also discussed. The algorithm is applied to a sequence of wind directions, and also to two sequences of deoxyribonucleic acid bases from introns from mouse genes. In each case, the MTD model fits better than the conventional Markov chain model, and for the wind data it provides superior out-of-sample predictions. A modification of the model to represent repeated patterns is proposed and a very parsimonious version of this modified model is successfully applied to data representing bird songs.

Some Novel Aerobic Heparin-Degrading Bacterial Isolates

Sixteen heparinase producing strains were isolated from soil and activated sludge. Their taxonomic relationships were investigated by polyacrylamide gel electrophoresis of sodium dodecylsulphate denatured whole-cell proteins, by the determination of the guanine plus cytosine content of their genomic deoxyribonucleic acid (DNA) and by DNA : ribosomal ribonucleic acid (RNA) hybridizations with labelled rRNA of Cytophaga heparina LMG 10339 T . Three rRNA similarity groups were distinguished. Group I was found to be related to the type strain of Cytophaga heparina and was subdivided in two subgroups on the basis of protein electrophoretic profiling and differences in DNA base composition. Group II consisted of only one strain, which showed a lower T m(e) value with rRNA of C. heparina LMG 10339 T and revealed a different electrophoretic protein profile. Group III was found to be quite different from C. heparina . With a T m(e) difference of more than 7 °C and a separate position in a numerical analysis of the protein electrophoretic profiles, the latter strains probably constitute a separate genus.

Deoxyribonucleic acid relatedness among strains of the moderately halophilic speciesDeleya halophila

The genomic relatedness among 16 strains assigned to the moderately halophilic speciesDeleya halophila and other 20 representative strains of halophilic and nonhalophilic species was estimated by determination of deoxyribonucleic acid (DNA) base composition and by DNA-DNA hybridization studies. The guanine-plus-cytosine (G + C) base contents, determined from the melting temperature of DNAs ofD. halophila strains, were 66.0–68.8 mol %. DNA-DNA homology studies, determined by membrane filter technique, indicate that the 16 strains ofD. halophila comprise a genetically homogeneous group. High homology (≥70–100%) was obtained between the type strainD. halophila CCM 3662 and the otherD. halophila strains studied; however, very low DNA relatedness was found between the representative strains ofD. halophila and otherDeleya species (≤13-0%), as well as other moderately halophilic, marine, or nonhalophilic bacteria investigated.

核酸から蛋白質まで

Since elucidation of structure of deoxyribonucleic acid (DNA) as genetic material, it was established that DNA makes ribonucleic acid, which makes protein according to the original information given in DNA base as base sequences. From these basic idea of genetic flow system there was emerged the word "protein engineering". According to this principle, engineering of h-lysozyme, RNase H and their relevant proteins was described. A triosephosphate isomerase barrel type protein was designed and expressed.

Infrared spectroscopy and infrared linear dichroism of nucleic acids

The activities of this laboratory in the field of infrared spectroscopy of nucleic acids since 1964 are summarized. Vibrations of deoxyribonucleic acid (DNA) were assigned by inspection of spectra of DNA's differing in their base composition. The “melting” of DNA dissolved in D2O has been studied by infrared spectroscopy, and the base composition of DNA samples from different microorganisms has been determined both from absorbance differences of base vibrations and by measurrments of the “melting” temperature. Further studies have dealt with the structure of the copper(II) -DNA complex and the assignment of the out-of-plane NH vibration bands of the DNA bases. It was shown that the purine H-8 atoms undergo slow isotopic exchange at elevated temperature (55°C), allowing preparation of deuterium-labelled native DNA.The introduction of infrared linear dichroism enabled the B—A transition of oriented DNA films to be monitored as a function of the relative humidity. An infrared band at 1185 cm−1 was described as a new “marker” band for A-DNA. The infrared linear dichroism results were treated quantitatively to determine the phosphate group geometry of B-DNA and A-DNA, and to calculate the ligand-induced “freezing” of a fraction of the DNA in the B form. A new drug assay was presented based upon this “freezing” effect.

Hydrogen Peroxide-Induced Base Damage in Deoxyribonucleic Acid

Aqueous solutions of calf thymus deoxyribonucleic acid (DNA) were exposed to hydrogen peroxide in the presence of air. Base products formed in DNA were identified and quantitated following acid hydrolysis and trimethylsilylation using gas chromatography-mass spectrometry. The yields of these products were dependent upon the hydrogen peroxide concentration, and increased in the following order: 8-hydroxyadenine, cytosine glycol, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, 8-hydroxyguanine, thymine glycol, and 4,6-diamino-5-formamidopyrimidine. Previous studies have shown that these compounds are typically formed in DNA in aqueous solution by hydroxyl radicals generated by ionizing radiation. Hydrogen peroxide is thought to participate in a Fenton-like reaction with transition metals, which are readily bound to DNA in trace quantities, resulting in the production of hydroxyl radicals close to the DNA. This proposed mechanism was examined by exposing DNA to hydrogen peroxide either in the presence of a hydroxyl radical scavenger or following pretreatment of DNA with metal-ion chelators. The results indicate that trace quantities of transition metal ions can react readily with hydrogen peroxide to produce radical species. The production of radical species was monitored by determining the altered bases that resulted from the reaction between radicals and DNA. The yields of the base products were reduced by 40 to 60% with 10 mmol dm-3 of dimethyl sulfoxide. A 100-fold increase in the concentration of dimethyl sulfoxide did not result in a further reduction in hydrogen peroxide-induced base damage. DNA which was freed from bound metal ions by pretreatment with metal ion chelators followed by exhaustive dialysis was found to be an ineffective substrate for hydrogen peroxide. The yields of base products measured in this DNA were at background levels. These results support the role of metal ions bound to DNA in the site-specific formation of highly reactive radical species, most likely hydroxyl radicals, in hydrogen peroxide-induced damage to the bases in DNA.

Bacillus glucanolyticus, a New Species That Degrades a Variety of -Glucans

A new species, Bacillus glucanolyticus, is proposed for a group of facultatively anaerobic endospore-forming bacteria isolated from soil that hydrolyze various β-glucans, including carboxymethyl cellulose and pustulan. Of the 14 strains examined, 11 were phenotypically homogeneous, and five of these strains showed high levels of deoxyribonucleic acid (DNA) relatedness (>68%) to a reference strain. Two pustulan-hydrolyzing strains were atypical, with low levels of DNA relatedness (52 to 57%), and a third strain was not classified as B. glucanolyticus. B. glucanolyticus strains produce motile microcolonies similar to those of Bacillus alvei but can be distinguished from this taxon by several phenotypic characteristics and a higher DNA base composition (48 mol%). B. glucanolyticus is similar to Bacillus circulans and related species; indeed, four strains were received as B. circulans, but distinctive phenotypic characteristics and low levels of DNA homology with B. circulans, Bacillus amylolyticus, Bacillus lautus, Bacillus pabuli, and Bacillus validus strains support its introduction as a new species. The type strain of B. glucanolyticus is strain S93 (= DSM 5162T).

Streptococcus vestibularis sp. nov. from the Human Oral Cavity

Thirteen strains of gram-positive, catalase-negative, chain-forming cocci isolated from the vestibular mucosa of human oral cavities were compared with other oral streptococcal species. The new strains were unusual in that they formed acid from lactose, from salicin, and usually from cellobiose, but not from mannitol, sorbitol, inulin, or raffinose, and infrequently formed acid from trehalose. They hydrolyzed esculin, urea, and starch but not arginine, formed hydrogen peroxide, and were usually Voges-Proskauer positive. They did not produce extracellular glucan or fructan from sucrose. The strains were compared by analyzing long-chain fatty acids, by determining whole-cell polypeptide patterns by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and by performing deoxyribonucleic acid (DNA)-DNA hybridizations. They possessed fatty acid profiles with major amounts of hexadecanoic (C16:0) and octadecenoic (C18:1ω7; cw-vaccenic) acids together with tetradecanoic (C14:0; myristic), hexadecenoic (C16:1; palmitoleic), octadecanoic (C18:0; stearic), octadecenoic (C18:1ω9; oleic), and eicosenoic (C20:1) acids, as shown by capillary gas-liquid chromatography. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis polypeptide patterns of the isolates showed some similarity to the patterns obtained for strains of Streptococcus salivarius subsp. salivarius, although they were, nevertheless, clearly distinguishable from the latter. DNA-DNA hybridization studies demonstrated that the new strains are more closely related to S. salivarius than to the other species of oral streptococci, but are sufficiently dissimilar to warrant separate species status. The name Streptococcus vestibularis is proposed. The DNA base composition is 38 to 41 mol% guanine plus cytosine. The type strain is strain MM1 (= NCTC 12166).