Nucleotides: Structure and Properties

Nucleotides consist of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Cells contain many types of nucleotides, which play a central role in a wide variety of cellular processes, including metabolic regulation and the storage and utilization of genetic information

Electronic signature of DNA nucleotides via transverse transport

We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries a unique signature due to the different electronic and chemical structure of the four bases. This signature is independent of the nearest-neighbor nucleotides. Furthermore, except for the nucleotides with Guanine and Cytosine bases, we find that the difference in conductance of the nucleotides is large for most orientations of the bases with respect to the electrodes. By exploiting these differences it may be possible to sequence single-stranded DNA by scanning its length with conducting probes.Comment: 4 pages, 5 figure

Gastroprotective effects of oral nucleotide administration

BACKGROUND AND AIMS: Nucleotides form the building blocks of DNA and are marketed as dietary supplements, alone or in combination with other ingredients, to promote general health. However, there has been only limited scientific study regarding the true biological activity of orally administered nucleotides. We therefore tested their efficacy in a variety of models of epithelial injury and repair. METHODS: Effects on proliferation ([(3)H] thymidine incorporation) and restitution (cell migration of wounded monolayers) were analysed using HT29 and IEC6 cells. The ability of a nucleotide mixture to influence gastric injury when administered orally and subcutaneously was analysed using a rat indomethacin (20 mg/kg) restraint model. RESULTS: In both cell lines, cell migration was increased by approximately twofold when added at 1 mg/ml (p<0.01); synergistic responses were seen when a mixture of nucleotides was used. Cell proliferation was stimulated by adenosine monophosphate (AMP) in HT29, but not in IEC6, cells. Gastric injury was reduced by approximately 60% when gavaged at 4–16 mg/ml (p<0.05), concentrations similar to those likely to be found in consumers taking nucleotide supplements. Systemic administration of nucleotides was unhelpful. CONCLUSIONS: Nucleotides possess biological activity when analysed in a variety of models of injury and repair and could provide a novel inexpensive approach for the prevention and treatment of the injurious effects of non steroidal anti‐inflammatory drugs and other ulcerative conditions of the bowel. Further studies on their potential benefits (and risks) appear justified

Relationship between promoter sequence and its strength in gene expression

In this study, through various tests one theoretical model is presented to describe the relationship between promoter strength and its nucleotide sequence. Our analysis shows that, promoter strength is greatly influenced by nucleotide groups with three adjacent nucleotides in its sequence. Meanwhile, nucleotides in different regions of promoter sequence have different effects on promoter strength. Based on experimental data for {\it E. coli} promoters, our calculations indicate, nucleotides in -10 region, -35 region, and the discriminator region of promoter sequence are more important than those in spacing region for determining promoter strength. With model parameter values obtained by fitting to experimental data, four promoter libraries are theoretically built for the corresponding experimental environments under which data for promoter strength in gene expression has been measured previously

Determination of total potentially available nucleosides in bovine milk

Bovine colostrum and milk samples were collected from two herds over the course of the first month post-partum, pooled for each herd by stage of lactation and total potentially available nucleosides were determined. Sample analysis consisted of parallel enzymatic treatments, phenylboronate clean-up, and liquid chromatography to quantify contributions of nucleosides, monomeric nucleotides, nucleotide adducts, and polymeric nucleotides to the available nucleosides pool. Bovine colostrum contained high levels of nucleosides and monomeric nucleotides, which rapidly decreased as lactation progressed into transitional milk. Mature milk was relatively consistent in nucleoside and monomeric nucleotide concentrations from approximately the tenth day post-partum. Differences in concentrations between summer-milk and winter-milk herds were largely attributable to variability in uridine and monomeric nucleotide concentrations

Transverse Electronic Transport through DNA Nucleotides with Functionalized Graphene Electrodes

Graphene nanogaps and nanopores show potential for the purpose of electrical DNA sequencing, in particular because single-base resolution appears to be readily achievable. Here, we evaluated from first principles the advantages of a nanogap setup with functionalized graphene edges. To this end, we employed density functional theory and the non-equilibrium Green's function method to investigate the transverse conductance properties of the four nucleotides occurring in DNA when located between the opposing functionalized graphene electrodes. In particular, we determined the electrical tunneling current variation as a function of the applied bias and the associated differential conductance at a voltage which appears suitable to distinguish between the four nucleotides. Intriguingly, we observe for one of the nucleotides a negative differential resistance effect.Comment: 19 pages, 7 figure

First-principles study of high conductance DNA sequencing with carbon nanotube electrodes

Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore both reduce conformational fluctuations and significantly improve the conductance. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several $\mu$A. Below 1 V the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second-largest, cytosine the third and finally thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations. Based on these results we propose a DNA sequencing protocol combining three possible data analysis strategies.Comment: 12 pages, 17 figures, 3 table

Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism

To be viable, organisms possess a number of (deoxy)nucleotide phosphohydrolases, which hydrolyze these nucleotides removing them from the active NTP and dNTP pools. Deamination of purine bases can result in accumulation of such nucleotides as ITP, dITP, XTP and dXTP. E. coli RdgB has been characterised as a deoxyribonucleoside triphosphate pyrophosphohydrolase that can act on these nucleotides. S. cerevisiae homologue encoded by YJR069C was purified and its (d)NTPase activity was assayed using fifteen nucleotide substrates. ITP, dITP, and XTP were identified as major substrates and kinetic parameters measured. Inhibition by ATP, dATP and GTP were established. On the basis of experimental and published data, modelling and simulation of ITP, dITP, XTP and dXTP metabolism was performed. (d)ITP/(d)XTPase is a new example of enzyme with multiple substrate-specificity demonstrating that multispecificity is not a rare phenomenon

Dependence of nucleotide physical properties on their placement in codons and determinative degree

Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (Austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependences of these variables from the place in the codon and the determinative degree were obtained. The difference of these variables for codons and anticodons is shown.Comment: 13 pages, 8 figures, PD