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Medecine Sciences : M/S May 2009Nucleic acids offer an ample structural and functional plasticity enabling their industrial production and chemical diversification for therapeutic purposes as well as... (Review)
Review
Nucleic acids offer an ample structural and functional plasticity enabling their industrial production and chemical diversification for therapeutic purposes as well as the establishment in vivo and in vitro of informational processes that did not spontaneously occur during evolution.
Topics: Antiviral Agents; DNA; Deoxyribonucleotides; Deoxyribose; Industry; Phosphorylation; RNA; Science
PubMed: 19848190
DOI: 10.1051/medsci/2009252s27 -
Molekuliarnaia Biologiia 1994The data on the replacement of ribonucleotides within ribozymes with deoxyribonucleotides are reviewed. Resulting chimeric ribozymes ("nucleozymes") are many times more... (Review)
Review
The data on the replacement of ribonucleotides within ribozymes with deoxyribonucleotides are reviewed. Resulting chimeric ribozymes ("nucleozymes") are many times more stable than their precursors. Synthesis of minimized ribozymes or minimized nucleozymes ("minizymes") are discussed.
Topics: Base Sequence; Deoxyribonucleotides; Molecular Sequence Data; RNA, Catalytic; Ribonucleotides
PubMed: 8052243
DOI: No ID Found -
Nucleic Acids Research May 2020Cells maintain a fine-tuned, dynamic concentration balance in the pool of deoxyribonucleoside 5'-triphosphates (dNTPs). This balance is essential for physiological...
Cells maintain a fine-tuned, dynamic concentration balance in the pool of deoxyribonucleoside 5'-triphosphates (dNTPs). This balance is essential for physiological processes including cell cycle control or antiviral defense. Its perturbation results in increased mutation frequencies, replication arrest and may promote cancer development. An easily accessible and relatively high-throughput method would greatly accelerate the exploration of the diversified consequences of dNTP imbalances. The dNTP incorporation based, fluorescent TaqMan-like assay published by Wilson et al. has the aforementioned advantages over mass spectrometry, radioactive or chromatography based dNTP quantification methods. Nevertheless, the assay failed to produce reliable data in several biological samples. Therefore, we applied enzyme kinetics analysis on the fluorescent dNTP incorporation curves and found that the Taq polymerase exhibits a dNTP independent exonuclease activity that decouples signal generation from dNTP incorporation. Furthermore, we found that both polymerization and exonuclease activities are unpredictably inhibited by the sample matrix. To resolve these issues, we established a kinetics based data analysis method which identifies the signal generated by dNTP incorporation. We automated the analysis process in the nucleoTIDY software which enables even the inexperienced user to calculate the final and accurate dNTP amounts in a 96-well-plate setup within minutes.
Topics: Deoxyribonucleotides; Exodeoxyribonucleases; Fluorescence; Kinetics; Software; Taq Polymerase
PubMed: 32103262
DOI: 10.1093/nar/gkaa116 -
Nucleic Acids Research 2007DNA polymerases are identified that copy a non-standard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC...
DNA polymerases are identified that copy a non-standard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC pairs. 6-Amino-5-nitro-3-(1'-beta-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (dZ) implements the non-standard 'small' donor-donor-acceptor (pyDDA) hydrogen bonding pattern. 2-Amino-8-(1'-beta-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP) implements the 'large' acceptor-acceptor-donor (puAAD) pattern. These nucleobases were designed to present electron density to the minor groove, density hypothesized to help determine specificity for polymerases. Consistent with this hypothesis, both dZTP and dPTP are accepted by many polymerases from both Families A and B. Further, the dZ:dP pair participates in PCR reactions catalyzed by Taq, Vent (exo-) and Deep Vent (exo-) polymerases, with 94.4%, 97.5% and 97.5%, respectively, retention per round. The dZ:dP pair appears to be lost principally via transition to a dC:dG pair. This is consistent with a mechanistic hypothesis that deprotonated dZ (presenting a pyDAA pattern) complements dG (presenting a puADD pattern), while protonated dC (presenting a pyDDA pattern) complements dP (presenting a puAAD pattern). This hypothesis, grounded in the Watson-Crick model for nucleobase pairing, was confirmed by studies of the pH-dependence of mismatching. The dZ:dP pair and these polymerases, should be useful in dynamic architectures for sequencing, molecular-, systems- and synthetic-biology.
Topics: Base Pair Mismatch; DNA-Directed DNA Polymerase; Deoxyribonucleosides; Deoxyribonucleotides; Hydrogen Bonding; Hydrogen-Ion Concentration; Polymerase Chain Reaction; Pyridones; Triazines
PubMed: 17576683
DOI: 10.1093/nar/gkm395 -
The Journal of Chemical Physics Dec 2012Over 15 years ago, the ability to electrically detect and characterize individual polynucleotides as they are driven through a single protein ion channel was suggested...
Over 15 years ago, the ability to electrically detect and characterize individual polynucleotides as they are driven through a single protein ion channel was suggested as a potential method for rapidly sequencing DNA, base-by-base, in a ticker tape-like fashion. More recently, a variation of this method was proposed in which a nanopore would instead detect single nucleotides cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We analyze the exonuclease/nanopore-based DNA sequencing engine using analytical theory and computer simulations that describe nucleotide transport. The available data and analytical results suggest that the proposed method will be limited to reading <80 bases, imposed, in part, by the short lifetime each nucleotide spends in the vicinity of the detection element within the pore and the ability to accurately discriminate between the four mononucleotides.
Topics: DNA; Deoxyribonucleotides; Diffusion; Exodeoxyribonucleases; Models, Molecular; Nanopores; Nucleic Acid Conformation; Probability; Protein Conformation; Sequence Analysis, DNA
PubMed: 23231259
DOI: 10.1063/1.4766363 -
Nucleosides, Nucleotides & Nucleic Acids 2024This work catalogued oligonucleotide sequences and sequence compositions based on the overall yield of full-length product obtained by the phosphoramidite...
This work catalogued oligonucleotide sequences and sequence compositions based on the overall yield of full-length product obtained by the phosphoramidite chemistry-based solid phase synthesis. In total, 76 sequences with different dinucleotide and trinucleotide repeats were synthesized, and the fully-deprotected products were analyzed by denaturing anion exchange HPLC. Overall, sequences containing more 2'-deoxyadenosine residues were obtained in relatively lower yields, likely due to the relative ease of 2'-deoxyadenosine to undergo depurination during the detritylation reaction. Furthermore, dinucleotide steps, such as d(CG)/d(GC) and d(AG)/d(GA), likely contribute the overall lower yields of full-length products as well.
Topics: Solid-Phase Synthesis Techniques; Organophosphorus Compounds; Deoxyribonucleotides; Base Sequence; Oligonucleotides; Chromatography, High Pressure Liquid
PubMed: 38116988
DOI: 10.1080/15257770.2023.2295478 -
Seikagaku. the Journal of Japanese... 1972
Review
Topics: Chemical Phenomena; Chemistry; Deoxyribonucleotides; Nucleotides; Polynucleotides; Templates, Genetic
PubMed: 4554993
DOI: No ID Found -
ELife Jan 2016Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible...
Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR 'reads' the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.
Topics: Allosteric Regulation; Crystallography, X-Ray; Deoxyribonucleotides; Escherichia coli; Models, Molecular; Protein Conformation; Ribonucleotide Reductases; Substrate Specificity
PubMed: 26754917
DOI: 10.7554/eLife.07141 -
Basic Life Sciences 1985Excess dTMP is toxic and mutagenic with exponentially growing dTMP efficient uptaking yeast strains 831 rho+ and 833 rho. The respiratory deficient strain 833 exhibits a...
Excess dTMP is toxic and mutagenic with exponentially growing dTMP efficient uptaking yeast strains 831 rho+ and 833 rho. The respiratory deficient strain 833 exhibits a tenfold sensitivity to the genotoxicity of excess dTMP. Mutant yield in the forward mutation system CAN1----can1 after dTMP excess is comparable to that found after irradiation with UV254nm. Excess dTMP is a poor mutagen in stationary phase cells of both strains. Mutagenicity of excess dTMP is not found in an ochre mutant allele (ade2-1). Exposure of exponentially growing cells to other deoxyribonucleotides (dCMP, dAMP, and dGMP) reveal these nucleotides to have mutagenic potential as well.
Topics: Canavanine; Deoxyadenine Nucleotides; Deoxycytidine Monophosphate; Deoxyguanine Nucleotides; Deoxyribonucleotides; Dose-Response Relationship, Drug; Drug Resistance; Mutation; Saccharomyces cerevisiae; Thymidine Monophosphate
PubMed: 3888182
DOI: 10.1007/978-1-4613-2449-2_26 -
Ukrains'kyi Biokhimichnyi Zhurnal (1999... 2011Quantitative characteristics of structural flexibility of the DNA elementary monomer units -5'-deoxycytidylic, 5'-thymidylic, 5'-deoxyadenylic and 5'-deoxyguanylic acid...
Quantitative characteristics of structural flexibility of the DNA elementary monomer units -5'-deoxycytidylic, 5'-thymidylic, 5'-deoxyadenylic and 5'-deoxyguanylic acid molecules--have been calculated with original methods. Root-mean-square deviations from equilibrium for all conformational parameters, caused by nuclei thermal or quantum zero-point vibrations, have been found to lie within 4 degrees divided by 25 degrees at 0 K and 7 degrees divided by 50 degrees at 298 K and corresponding relaxed force constants--within 1 divided by 35 kcal/mol x rad(-2). Their values have been found to be sensitive to the molecule's conformation. It has been proven, that the torsion angle gamma is the most rigid one whereas relaxed force constants for all other conformational variables are lower and comparable to each other. The data obtained could serve for development of structural-dynamical models of the DNA.
Topics: Chemistry, Physical; DNA; Deoxyribonucleotides; Models, Molecular; Nucleic Acid Conformation; Pliability; Quantum Theory; Temperature; Thermodynamics
PubMed: 22276428
DOI: No ID Found