-
Nucleic Acids Research Nov 2022The formation of triplex DNA is a site-specific recognition method that directly targets duplex DNA. However, triplex DNA formation is generally formed for the GC and AT...
Recognition of 5-methyl-CG and CG base pairs in duplex DNA with high stability using antiparallel-type triplex-forming oligonucleotides with 2-guanidinoethyl-2'-deoxynebularine.
The formation of triplex DNA is a site-specific recognition method that directly targets duplex DNA. However, triplex DNA formation is generally formed for the GC and AT base pairs of duplex DNA, and there are no natural nucleotides that recognize the CG and TA base pairs, or even the 5-methyl-CG (5mCG) base pair. Moreover, duplex DNA, including 5mCG base pairs, epigenetically regulates gene expression in vivo, and thus targeting strategies are of biological importance. Therefore, the development of triplex-forming oligonucleotides (TFOs) with artificial nucleosides that selectively recognize these base pairs with high affinity is needed. We recently reported that 2'-deoxy-2-aminonebularine derivatives exhibited the ability to recognize 5mCG and CG base pairs in triplex formation; however, this ability was dependent on sequences. Therefore, we designed and synthesized new nucleoside derivatives based on the 2'-deoxy-nebularine (dN) skeleton to shorten the linker length connecting to the hydrogen-bonding unit in formation of the antiparallel motif triplex. We successfully demonstrated that TFOs with 2-guanidinoethyl-2'-deoxynebularine (guanidino-dN) recognized 5mCG and CG base pairs with very high affinity in all four DNA sequences with different adjacent nucleobases of guanidino-dN as well as in the promoter sequences of human genes containing 5mCG base pairs with a high DNA methylation frequency.
Topics: Humans; Base Pairing; Oligonucleotides; DNA; Deoxyribonucleosides; Nucleosides; Nucleic Acid Conformation
PubMed: 36454012
DOI: 10.1093/nar/gkac1110 -
Journal of Bacteriology Aug 1968Inability to grow on deoxyribonucleosides as the sole carbon source is characteristic of deo mutants of Escherichia coli. Growth of deoC mutants, which lack deoxyribose...
Inability to grow on deoxyribonucleosides as the sole carbon source is characteristic of deo mutants of Escherichia coli. Growth of deoC mutants, which lack deoxyribose 5-phosphate aldolase, is reversibly inhibited by deoxyribonucleosides through inhibition of respiration. By contrast, deoB mutants are not sensitive to deoxyribonucleosides, and deoxyribose 5-phosphate aldolase and thymidine phosphorylase are present at normal levels but are not inducible by thymidine. Organisms with the genotype deoB(-)thy(-) or deoC(-)thy(-) are able to grow on low levels of thymine, whereas deoB(+)thy(-) or deoC(+)thy(-) strains require high levels of thymine for growth. The deoB and deoC mutations are transducible with and map on the counterclockwise side of the threonine marker. They are closely linked to deoA, a gene determining thymidine phosphorylase. Merodiploids heterozygous for either the deoB or deoC genes are resistant to deoxyribonucleosides and, in combination with the thy mutation, require high levels of thymine for growth. Cultures of thy(+)deoC(-) mutants are inhibited by thymidine until this compound has been completely degraded and excreted as deoxyribose and thymine, whereupon growth promptly resumes at a normal rate. The inhibition of respiration in deoC strains and the induction of thymidine phosphorylase and deoxyribose 5-phosphate aldolase in the wild-type organism are considered to result from the accumulation of deoxyribose 5-phosphate.
Topics: Bacterial Proteins; Chromosome Mapping; Conjugation, Genetic; DNA, Bacterial; Escherichia coli; Extrachromosomal Inheritance; Genes; Genetics, Microbial; Molecular Biology; Nucleosides; Oxygen Consumption; Pentoses; Phenotype; RNA, Bacterial; Thymidine; Thymine; Transduction, Genetic
PubMed: 4877128
DOI: 10.1128/jb.96.2.501-514.1968 -
PloS One 2016Telbivudine, a thymidine nucleoside analog, is a common therapeutic option for chronic hepatitis B infection. While raised serum creatine kinase is common, myopathy...
Telbivudine, a thymidine nucleoside analog, is a common therapeutic option for chronic hepatitis B infection. While raised serum creatine kinase is common, myopathy associated with telbivudine is rare. Reports on its myopathological features are few and immunohistochemical analyses of inflammatory cell infiltrates have not been previously described. We describe the clinical, myopathological and immunohistochemical features of four patients who developed myopathy after telbivudine therapy for chronic hepatitis B infection. All four patients presented with progressive proximal muscle weakness, elevation of serum creatine kinase and myopathic changes on electromyography. Muscle biopsies showed myofiber degeneration/necrosis, regeneration, and fibers with cytoplasmic bodies and cytochrome c oxidase deficiency. There was minimal inflammation associated with strong sarcolemmal overexpression of class I major histocompatibility complex (MHC class I). Upon withdrawal of telbivudine, muscle weakness improved in all patients and eventually completely resolved in three. In our series, telbivudine-associated myopathy is characterized by necrotizing myopathy which improved on drug withdrawal. Although the occasional loss of cytochrome c oxidase is consistent with mitochondrial toxicity, the overexpression of MHC class I in all patients could suggest an underlying immune-mediated mechanism which may warrant further investigation.
Topics: Aged; Female; Humans; Male; Middle Aged; Muscular Diseases; Telbivudine; Thymidine
PubMed: 27611456
DOI: 10.1371/journal.pone.0162760 -
Journal of the American Chemical Society Mar 2010Exposure to formaldehyde results in the formation of DNA-protein cross-links (DPCs) as a primary genotoxic effect. Although DPCs are biologically important and eight...
Exposure to formaldehyde results in the formation of DNA-protein cross-links (DPCs) as a primary genotoxic effect. Although DPCs are biologically important and eight amino acids have been reported to form stable adducts with formaldehyde, the structures of these cross-links have not yet been elucidated. We have characterized formaldehyde-induced cross-links of Lys, Cys, His, and Trp with dG, dA, and dC. dT formed no cross-links, nor did Arg, Gln, Tyr, or Asn. Reaction of formaldehyde with Lys and dG gave the highest yield of cross-linked products, followed by reaction with Cys and dG. Yields from the other coupling reactions were lower by a factor of 10 or more. Detailed structural examination by NMR and mass spectrometry established that the cross-links between amino acids and single nucleosides involve a formaldehyde-derived methylene bridge. Lys yielded two additional products with dG in which the linking structure is a 1,N(2)-fused triazino ring. The Lys cross-linked products were unstable at ambient temperature. Reactions between the reactive N(alpha)-Boc-protected amino acids and the trinucleotides d(T(1)B(2)T(3)) where B(2) is the target base G, A, or C and reactions between dG, dA and dC and 8-mer peptides containing a single reactive target residue at position 5 yielded cross-linked products with structures inferred from high resolution mass spectrometry and fragmentation patterns that are consistent with those between N(alpha)-Boc-protected amino acids and single nucleotides rigorously determined by NMR studies. These structures will provide a basis for investigation of the characteristics and properties of DPCs formed in vivo and will be helpful in identifying biomarkers for the evaluation of formaldehyde exposure both at the site of contact and at distant sites.
Topics: Amino Acids; Chromatography, High Pressure Liquid; Cross-Linking Reagents; Deoxyadenosines; Deoxycytidine; Deoxyguanosine; Formaldehyde; Formic Acid Esters; Nuclear Magnetic Resonance, Biomolecular; Nucleosides; Oligonucleotides; Oligopeptides; Spectroscopy, Fourier Transform Infrared; Tandem Mass Spectrometry; Thymidine
PubMed: 20178313
DOI: 10.1021/ja908282f -
PloS One 2014Thymidine analogues are powerful tools when studying DNA synthesis including DNA replication, repair and recombination. However, these analogues have been reported to...
Thymidine analogues are powerful tools when studying DNA synthesis including DNA replication, repair and recombination. However, these analogues have been reported to have severe effects on cell-cycle progression and growth, the very processes being investigated in most of these studies. Here, we have analyzed the effects of 5-ethynyl-2'-deoxyuridine (EdU) and 5-Chloro-2'-deoxyuridine (CldU) using fission yeast cells and optimized the labelling procedure. We find that both analogues affect the cell cycle, but that the effects can be mitigated by using the appropriate analogue, short pulses of labelling and low concentrations. In addition, we report sequential labelling of two consecutive S phases using EdU and 5-bromo-2'-deoxyuridine (BrdU). Furthermore, we show that detection of replicative DNA synthesis is much more sensitive than DNA-measurements by flow cytometry.
Topics: Bromodeoxyuridine; Cell Cycle; Cell Proliferation; DNA Replication; DNA, Fungal; Deoxyuridine; Schizosaccharomyces; Staining and Labeling; Thymidine
PubMed: 24551125
DOI: 10.1371/journal.pone.0088629 -
Chemical Research in Toxicology May 2017Genomic integrity is constantly challenged by a variety of endogenous and exogenous DNA damaging agents, which can lead to the formation of 10-10 DNA lesions per cell...
Genomic integrity is constantly challenged by a variety of endogenous and exogenous DNA damaging agents, which can lead to the formation of 10-10 DNA lesions per cell per day. Reactive oxygen species (ROS) represent a major type of DNA damaging agent. Specifically, a hydroxyl radical can attack the C1' position of 2-deoxyribose, and the ensuing carbon-centered radical, if improperly repaired, can cause the inversion of stereochemical configuration at the C1' to give α-anomeric lesions. In this study, we assessed the replicative bypass of α-dA, α-dT, α-dC, and α-dG in template DNA by conducting primer extension assays with the use of purified translesion synthesis DNA polymerases. Our results revealed that human polymerase (Pol) η, but not human Pol κ, Pol ι, or yeast Pol ζ, was capable of bypassing all of the α-dN lesions and extending the primer to generate full-length replication products. Data from steady-state kinetic measurements showed that Pol η was the most efficient in inserting the correct nucleotides opposite the modified nucleosides, with the relative efficiencies of nucleotide incorporation following the order of α-dA > α-dG > α-dT > α-dC. Additionally, human Pol η was found to misincorporate dTMP opposite α-dT and dCMP opposite α-dC at frequencies of 66% and 24%, respectively, whereas α-dA and α-dG were weakly miscoding. These findings provided important knowledge about the effects these α-dN lesions have on the fidelity and efficiency of DNA replication mediated by human Pol η.
Topics: DNA Damage; DNA Primers; DNA Replication; DNA-Directed DNA Polymerase; Deoxyribonucleosides; Humans; In Vitro Techniques; Kinetics; Reactive Oxygen Species
PubMed: 28388097
DOI: 10.1021/acs.chemrestox.6b00439 -
Biochemistry Jul 2017Reactive oxygen species (ROS), resulting from endogenous metabolism and/or environmental exposure, can induce damage to the 2-deoxyribose moiety in DNA. Specifically, a...
Reactive oxygen species (ROS), resulting from endogenous metabolism and/or environmental exposure, can induce damage to the 2-deoxyribose moiety in DNA. Specifically, a hydrogen atom from each of the five carbon atoms in 2-deoxyribose can be abstracted by hydroxyl radical, and improper chemical repair of the ensuing radicals formed at the C1', C3', and C4' positions can lead to the stereochemical inversion at these sites to yield epimeric 2-deoxyribose lesions. Although ROS-induced single-nucleobase lesions have been well studied, the biological consequences of the C3'-epimeric lesions of 2'-deoxynucleosides, i.e., 2'-deoxyxylonucleosides (dxN), have not been comprehensively investigated. Herein, we assessed the impact of dxN lesions on the efficiency and fidelity of DNA replication in Escherichia coli cells by conducting a competitive replication and adduct bypass assay with single-stranded M13 phage containing a site-specifically incorporated dxN. Our results revealed that, of the four dxN lesions, only dxG constituted a strong impediment to DNA replication, and intriguingly, dxT and dxC conferred replication bypass efficiencies higher than those of the unmodified counterparts. In addition, the three SOS-induced DNA polymerases (Pol II, Pol IV, and Pol V) did not play any appreciable role in bypassing these lesions. Among the four dxNs, only dxA directed a moderate frequency of dCMP misincorporation. These results provided important insights into the impact of the C3'-epimeric lesions on DNA replication in E. coli cells.
Topics: DNA Adducts; DNA Replication; DNA, Bacterial; DNA-Directed DNA Polymerase; Deoxyribonucleosides; Escherichia coli; Escherichia coli Proteins; Mutagenesis; SOS Response, Genetics
PubMed: 28650656
DOI: 10.1021/acs.biochem.7b00146 -
Nucleosides, Nucleotides & Nucleic Acids 2015The objective of this work was to design conjugates of anti-HIV nucleosides conjugated with fatty acids and cell-penetrating poly-L-arginine (polyArg) peptides. Three...
The objective of this work was to design conjugates of anti-HIV nucleosides conjugated with fatty acids and cell-penetrating poly-L-arginine (polyArg) peptides. Three conjugates of polyArg cell-penetrating peptides with fatty acyl derivatives of alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC) were synthesized. In general, the compounds exhibited anti-HIV activity against X4 and R5 cell-free virus with EC50 values of 1.5-16.6 μM. FLT-CO-(CH2)12-CO-(Arg)7 exhibited EC50 values of 2.9 μM and 3.1 μM against X4 and R5 cell-free virus, respectively. The FLT conjugate was selected for further preformulation studies by determination of solution state degradation and lipid solubility. The compound was found to be stable in neutral and oxidative conditions and moderately stable in heated conditions.
Topics: Anti-HIV Agents; Cell-Penetrating Peptides; Deoxycytidine; Deoxyribonucleosides; Dicarboxylic Acids; Dideoxynucleosides; Emtricitabine; Humans; Lamivudine; Peptides; Reverse Transcriptase Inhibitors
PubMed: 25513860
DOI: 10.1080/15257770.2014.945649 -
Antimicrobial Agents and Chemotherapy Apr 19923'-Fluoro-3'-deoxythymidine (FLT), a candidate anti-AIDS compound in clinical trials, showed anti-human immunodeficiency virus type 1 (HIV-1) potency (50% effective... (Comparative Study)
Comparative Study
Comparisons of anti-human immunodeficiency virus activities, cellular transport, and plasma and intracellular pharmacokinetics of 3'-fluoro-3'-deoxythymidine and 3'-azido-3'-deoxythymidine.
3'-Fluoro-3'-deoxythymidine (FLT), a candidate anti-AIDS compound in clinical trials, showed anti-human immunodeficiency virus type 1 (HIV-1) potency (50% effective concentration, 0.0052 microM) slightly better than or equal to that of 3'-azido-3'-deoxythymidine (AZT) in MT4 cells and was threefold more potent in H9 cells. There was no FLT resistance demonstrable in the AZT-resistant HIV-1 strains. Both FLT and AZT showed low cytotoxicity for MT4 cells, with selectivity indices (efficacy/toxicity ratio) of greater than 47,000 and greater than 33,000, respectively. Cellular permeation of FLT and thymidine (dThd) was greater than that of AZT, and FLT and dThd permeated the cell membranes by a carrier-mediated mechanism as well as by simple diffusion, as indicated by the existence of nitrobenzylthioinosine-5'-monophosphate-sensitive and -insensitive components. By contrast, transport of AZT into cells was by simple diffusion. The intracellular level of the triphosphate of FLT (FLTTP) in MT4 cells was two- to threefold higher than that of AZT (AZTTP) after exposure to 1.8 microM each compound for 12 h. The elimination kinetics of FLTTP and AZTTP in HIV-1-infected MT4 cells in fresh medium showed biphasic patterns, with initial half-lives of 1.03 and 1.09 h, respectively. In phytohemagglutinin-stimulated human peripheral blood lymphocytes, the FLTTP level was increased 59-fold compared with that in unstimulated cells at 12 h, was four- to sixfold higher than the level of AZTTP in stimulated cells at 12 h, and remained four- to fivefold higher during a 4-h elimination period in fresh medium and twofold higher at the end of a 12-h elimination period. Two- to eightfold more [3H]AZT than [3H]FLT was incorporated into the host cell DNA, and both [3H]AZT and [3H]FLT remained persistently incorporated for over 24 h. The incorporated [3H]AZT and [3H]FLT were alkali labile, whereas incorporated [3H]dThd was alkali stable. Pharmacokinetics of FLT in plasma of monkeys after intravenous (i.v.) administration showed that the FLT concentration in plasma declined, with a half-life of 1.19 +/- 0.1 h; the steady-state volume of distribution was 0.93 +/- 0.2 liter/kg of body weight, and total clearance was 0.56 +/- 0.15 liter/kg. Oral bioavailability of FLT was excellent and comparable to i.v. bioavailability in terms of areas under the concentration-time curves for three monkeys. Of the total dose, 41 to 61% was excreted in urine as unchanged FLT, and only 3.2 to 7.4% of the total dose was identified as glucuronide-conjugated FLT in urine 48 h after i.v. administration to monkeys. We conclude that FLT exhibits an anti-HIV-1 potency similar to that of AZT but with slightly better selectivity of effects and with higher intracellular active metabolite levels.
Topics: Animals; Antiviral Agents; Cell Membrane Permeability; Cells, Cultured; Chromatography, High Pressure Liquid; Dideoxynucleosides; Female; HIV; Humans; Macaca fascicularis; Male; Tritium; Zidovudine
PubMed: 1503443
DOI: 10.1128/AAC.36.4.808 -
PLoS Genetics Mar 2018Ribonucleotides (rNMPs) are frequently incorporated during replication or repair by DNA polymerases and failure to remove them leads to instability of nuclear DNA...
Ribonucleotides (rNMPs) are frequently incorporated during replication or repair by DNA polymerases and failure to remove them leads to instability of nuclear DNA (nDNA). Conversely, rNMPs appear to be relatively well-tolerated in mitochondrial DNA (mtDNA), although the mechanisms behind the tolerance remain unclear. We here show that the human mitochondrial DNA polymerase gamma (Pol γ) bypasses single rNMPs with an unprecedentedly high fidelity and efficiency. In addition, Pol γ exhibits a strikingly low frequency of rNMP incorporation, a property, which we find is independent of its exonuclease activity. However, the physiological levels of free rNTPs partially inhibit DNA synthesis by Pol γ and render the polymerase more sensitive to imbalanced dNTP pools. The characteristics of Pol γ reported here could have implications for forms of mtDNA depletion syndrome (MDS) that are associated with imbalanced cellular dNTP pools. Our results show that at the rNTP/dNTP ratios that are expected to prevail in such disease states, Pol γ enters a polymerase/exonuclease idling mode that leads to mtDNA replication stalling. This could ultimately lead to mtDNA depletion and, consequently, to mitochondrial disease phenotypes such as those observed in MDS.
Topics: Animals; DNA Polymerase gamma; DNA Replication; DNA, Mitochondrial; Deoxyribonucleosides; Mice; Mice, Inbred C57BL; Phosphates
PubMed: 29601571
DOI: 10.1371/journal.pgen.1007315