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International Journal of Molecular... May 2023Genetic information stored in a DNA base sequence is continuously exposed to harmful factors. It has been determined that 9 × 10 different DNA damage events occur in a...
Genetic information stored in a DNA base sequence is continuously exposed to harmful factors. It has been determined that 9 × 10 different DNA damage events occur in a single human cell every 24 h. Of these, 7,8-dihydro-8-oxo-guanosine (G) is one of the most abundant and can undergo further transformations towards spirodi(iminohydantoin) (Sp). Sp is highly mutagenic in comparison to its precursor if not repaired. In this paper, the influence of both Sp diastereomers 4 and 4 as well as their and conformers on charge transfer through the double helix was taken into theoretical consideration. In addition, the electronic properties of four modelled double-stranded oligonucleotides (ds-oligos) were also discussed, i.e., d[ASpAGA] * [TCTCT]. Throughout the study, the M06-2X/6-31++G** level theory was used. Solvent-solute non-equilibrated and equilibrated interactions were also considered. The subsequent results elucidated that the 7,8-dihydro-8-oxo-guanosine:cytidine (GC) base pair is the settled point of a migrated radical cation in each of the discussed cases, due to its low adiabatic ionization potential, i.e., 5.55 [eV]. The opposite was noted for excess electron transfer through ds-oligos containing ()-Sp or ()-Sp. The radical anion was found on the GC moiety, whereas in the presence of ()-Sp or ()-Sp, an excess electron was found on the distal AT or AT base pair, respectively. Furthermore, a spatial geometry analysis of the discussed ds-oligos revealed that the presence of ()-Sp in the ds-oligo caused only a slight deformation to the double helix, while ()-Sp formed an almost ideal base pair with a complementary dC. The above results are in strong agreement with the final charge transfer rate constant, as calculated according to Marcus' theory. In conclusion, DNA damage such as spirodi(iminohydantoin), especially when becoming part of clustered DNA damage, can affect the effectiveness of other lesion recognition and repair processes. This can lead to the acceleration of undesired and deleterious processes such as carcinogenesis or aging. However, in terms of anticancer radio-/chemo- or combined therapy, the slowing down of the repair machinery can result in increased effectiveness. With this in mind, the influence of clustered damage on charge transfer and its subsequent effect on single-damage recognition by glycosylases justifies future investigation.
Topics: Humans; 8-Hydroxy-2'-Deoxyguanosine; DNA; Guanosine; DNA Damage; Mutagenesis; Deoxyguanosine
PubMed: 37239917
DOI: 10.3390/ijms24108570 -
PloS One 2014Efficient and adequate generation of deoxyribonucleotides is critical to successful DNA repair. We show that ataxia telangiectasia mutated (ATM) integrates the DNA...
Efficient and adequate generation of deoxyribonucleotides is critical to successful DNA repair. We show that ataxia telangiectasia mutated (ATM) integrates the DNA damage response with DNA metabolism by regulating the salvage of deoxyribonucleosides. Specifically, ATM phosphorylates and activates deoxycytidine kinase (dCK) at serine 74 in response to ionizing radiation (IR). Activation of dCK shifts its substrate specificity toward deoxycytidine, increases intracellular dCTP pools post IR, and enhances the rate of DNA repair. Mutation of a single serine 74 residue has profound effects on murine T and B lymphocyte development, suggesting that post-translational regulation of dCK may be important in maintaining genomic stability during hematopoiesis. Using [(18)F]-FAC, a dCK-specific positron emission tomography (PET) probe, we visualized and quantified dCK activation in tumor xenografts after IR, indicating that dCK activation could serve as a biomarker for ATM function and DNA damage response in vivo. In addition, dCK-deficient leukemia cell lines and murine embryonic fibroblasts exhibited increased sensitivity to IR, indicating that pharmacologic inhibition of dCK may be an effective radiosensitization strategy.
Topics: Animals; Ataxia Telangiectasia Mutated Proteins; B-Lymphocytes; Cell Line, Tumor; DNA Damage; DNA Repair; Deoxycytidine; Deoxycytidine Kinase; Deoxyribonucleosides; Genomic Instability; Hematopoiesis; Humans; Mice; Mice, Inbred BALB C; Mice, Knockout; Mutagenesis, Site-Directed; Phosphorylation; Protein Processing, Post-Translational; Substrate Specificity; T-Lymphocytes
PubMed: 25101980
DOI: 10.1371/journal.pone.0104125 -
European Journal of Nuclear Medicine... Apr 2011Deoxycytidine kinase (dCK) is a rate-limiting enzyme in deoxyribonucleoside salvage, a metabolic pathway involved in the production and maintenance of a balanced pool of... (Clinical Trial)
Clinical Trial
PURPOSE
Deoxycytidine kinase (dCK) is a rate-limiting enzyme in deoxyribonucleoside salvage, a metabolic pathway involved in the production and maintenance of a balanced pool of deoxyribonucleoside triphosphates (dNTPs) for DNA synthesis. dCK phosphorylates and therefore activates nucleoside analogs such as cytarabine, gemcitabine, decitabine, cladribine, and clofarabine that are used routinely in cancer therapy. Imaging probes that target dCK might allow stratifying patients into likely responders and nonresponders with dCK-dependent prodrugs. Here we present the biodistribution and radiation dosimetry of three fluorinated dCK substrates, (18)F-FAC, L: -(18)F-FAC, and L: -(18)F-FMAC, developed for positron emission tomography (PET) imaging of dCK activity in vivo.
METHODS
PET studies were performed in nine healthy human volunteers, three for each probe. After a transmission scan, the radiopharmaceutical was injected intravenously and three sequential emission scans acquired from the base of the skull to mid-thigh. Regions of interest encompassing visible organs were drawn on the first PET scan and copied to the subsequent scans. Activity in target organs was determined and absorbed dose estimated with OLINDA/EXM. The standardized uptake value was calculated for various organs at different times.
RESULTS
Renal excretion was common to all three probes. Bone marrow had higher uptake for L: -(18)F-FAC and L: -(18)F-FMAC than (18)F-FAC. Prominent liver uptake was seen in L: -(18)F-FMAC and L: -(18)F-FAC, whereas splenic activity was highest for (18)F-FAC. Muscle uptake was also highest for (18)F-FAC. The critical organ was the bladder wall for all three probes. The effective dose was 0.00524, 0.00755, and 0.00910 mSv/MBq for (18)F-FAC, L: -(18)F-FAC, and L: -(18)F-FMAC, respectively.
CONCLUSION
The biodistribution of (18)F-FAC, L: -(18)F-FAC, and L: -(18)F-FMAC in humans reveals similarities and differences. Differences may be explained by different probe affinities for nucleoside transporters, dCK, and catabolic enzymes such as cytidine deaminase (CDA). Dosimetry demonstrates that all three probes can be used safely to image the deoxyribonucleoside salvage pathway in humans.
Topics: Adult; Deoxycytidine; Deoxyribonucleosides; Female; Humans; Lymphoma; Male; Metabolic Networks and Pathways; Ovarian Neoplasms; Positron-Emission Tomography; Radiometry; Young Adult
PubMed: 21127859
DOI: 10.1007/s00259-010-1666-z -
Molecules (Basel, Switzerland) Mar 2020Nucleoside analogs are widely used for the treatment of viral diseases (Hepatitis B/C, herpes and human immunodeficiency virus, HIV) and various malignancies. ALS-8176,...
Nucleoside analogs are widely used for the treatment of viral diseases (Hepatitis B/C, herpes and human immunodeficiency virus, HIV) and various malignancies. ALS-8176, a prodrug of the 4'-chloromethyl-2'-deoxy-2'-fluoro nucleoside ALS-8112, was evaluated in hospitalized infants for the treatment of respiratory syncytial virus (RSV), but was abandoned for unclear reasons. Based on the structure of ALS-8112, a series of novel 4'-modified-2'-deoxy-2'-fluoro nucleosides were synthesized. Newly prepared compounds were evaluated against RSV, but also against a panel of RNA viruses, including Dengue, West Nile, Chikungunya, and Zika viruses. Unfortunately, none of the compounds showed marked antiviral activity against these viruses.
Topics: Animals; Antiviral Agents; Cell Line, Tumor; Chikungunya virus; Cricetulus; Dengue Virus; Deoxycytidine; Deoxyribonucleosides; Epithelial Cells; Hepatocytes; Humans; Leukocytes, Mononuclear; Microbial Sensitivity Tests; Primary Cell Culture; Prodrugs; Respiratory Syncytial Virus, Human; T-Lymphocytes; Treatment Failure; Virus Replication; West Nile virus; Zika Virus
PubMed: 32168734
DOI: 10.3390/molecules25061258 -
Proceedings of the National Academy of... Aug 2007
Topics: 8-Hydroxy-2'-Deoxyguanosine; DNA; Deoxyguanosine; Substrate Specificity
PubMed: 17699620
DOI: 10.1073/pnas.0706878104 -
Molecules (Basel, Switzerland) Feb 2014Synthetic routes to 5'-azidoribonucleosides are reported for adenosine, cytidine, guanosine, and uridine, resulting in a widely applicable one-pot methodology for the...
Synthetic routes to 5'-azidoribonucleosides are reported for adenosine, cytidine, guanosine, and uridine, resulting in a widely applicable one-pot methodology for the synthesis of these and related compounds. The target compounds are appropriate as precursors in a variety of purposive syntheses, as the synthetic and therapeutic relevance of azido- and amino-modified nucleosides is expansive. Furthermore, in the conversion of alcohols to azides, these methods offer a tractable alternative to the Mitsunobu and other more difficult reactions.
Topics: Adenosine; Alcohols; Azides; Cytidine; Deoxyribonucleosides; Uridine
PubMed: 24566312
DOI: 10.3390/molecules19022434 -
The Journal of Biological Chemistry Sep 1978Cell-free preparations from Rhodotorula glutinis catalyzed the conversion of deoxyribonucleosides to ribonucleosides in a pyrimidine deoxyribonucleoside 2' -hydroxylase...
Cell-free preparations from Rhodotorula glutinis catalyzed the conversion of deoxyribonucleosides to ribonucleosides in a pyrimidine deoxyribonucleoside 2' -hydroxylase reaction. The reaction occurred with only thymidine or deoxyuridine, of the common deoxyribonucleosides, without detachment of the deoxyribose moiety, at the nucleoside level. The same enzyme preparations catalyzed the conversion of thymine to 5-hydroxymethyluracil in a thymine 7-hydroxylase reaction. Requirements for molecular oxygen, alpha-ketoglutarate, Fe2+, and ascorbate indicated that the 2' -hydroxylase and 7-hydroxylase reactions are of the alpha-keto-acid dioxygenases class. The requirements for alpha-ketoglutarate and Fe2+ were very stringent. During the course of the 2' -hydroxylase and 7-hydroxylase reactions, alpha-ketoglutarate was decarboxylated to form succinate and CO2 so that the ratio of hydroxylated nucleoside or pyrimidine to CO2 was 1:1.5-Hydroxymethyluracil and 5-formyluracil also stimulated the decarboxylation of alpha-ketoglutarate and thus appeared to undergo 7-hydroxylase reactions.
Topics: Deoxyribonucleosides; Iron; Ketoglutaric Acids; Mitosporic Fungi; Mixed Function Oxygenases; Rhodotorula; Ribonucleosides; Substrate Specificity; Thymidine; Thymine
PubMed: 567220
DOI: No ID Found -
Methods in Molecular Biology (Clifton,... 2019Formation of adducts to DNA is of great benefit to DNA sequencing and damage detection technology and to enzymology. Here we describe the synthesis and characterization...
Formation of adducts to DNA is of great benefit to DNA sequencing and damage detection technology and to enzymology. Here we describe the synthesis and characterization procedures of 18-crown-6 adducts formed to abasic (AP) sites, 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG), and 2'-deoxycytidine (C) residues in DNA oligodeoxynucleotides. These crown ether adducts were used as site-specific modifications to facilitate nanopore technology. The methods described can be readily expanded to attach other suitable primary amines of interest.
Topics: 8-Hydroxy-2'-Deoxyguanosine; Crown Ethers; DNA; DNA Adducts; Deoxycytidine; Deoxyguanosine; Nanopores; Oligodeoxyribonucleotides
PubMed: 31016693
DOI: 10.1007/978-1-4939-9216-4_2 -
The EMBO Journal Nov 2001Here we report the first characterization of replication timing and its regulation in the fission yeast Schizosaccharomyces pombe. We used three different...
Here we report the first characterization of replication timing and its regulation in the fission yeast Schizosaccharomyces pombe. We used three different synchronization methods: centrifugal elutriation, cdc10 temperature-shift and release, and starvation for deoxyribonucleoside triphosphates (dNTPs) by treatment with hydroxyurea (HU) followed by removal of HU, to study the times when specific autonomously replicating sequence elements (ARS elements; potential replication origins) replicate during S phase. We found that individual ARS elements replicate at characteristic times, some early and some late, independently of synchronization method. In wild-type cells treated with HU, early ARS elements replicated but late ones did not. However, in HU-treated mutant cells lacking the Rad3 (similar to human ATR and ATM) or Cds1 (similar to human CHK2) checkpoint kinase, both early and late ARS elements were able to replicate. Thus under conditions of dNTP starvation the Rad3 and Cds1 kinases are needed to suppress the replication of normally late-replicating regions.
Topics: Adenosine Triphosphatases; Cell Cycle Proteins; Cell Division; Centrifugation; Checkpoint Kinase 2; DNA Helicases; DNA Replication; Deoxyribonucleosides; Electrophoresis, Gel, Two-Dimensional; Flow Cytometry; Genes, cdc; Hydroxyurea; Mutation; Protein Kinases; Protein Serine-Threonine Kinases; S Phase; Saccharomyces cerevisiae Proteins; Schizosaccharomyces; Schizosaccharomyces pombe Proteins; Sequence Deletion; Temperature; Time Factors; Transcription Factors
PubMed: 11689451
DOI: 10.1093/emboj/20.21.6115 -
Current Protocols in Nucleic Acid... Mar 20204-Cyanoindole-2'-deoxyribonucleoside (4CIN) is a fluorescent isomorphic nucleoside analogue with superior spectroscopic properties in terms of Stokes shift and quantum...
4-Cyanoindole-2'-deoxyribonucleoside (4CIN) is a fluorescent isomorphic nucleoside analogue with superior spectroscopic properties in terms of Stokes shift and quantum yield in comparison to the widely utilized isomorphic nucleoside analogue, 2-aminopurine-2'-deoxyribonucleoside (2APN). Notably, when inserted into single- or double-stranded DNA, 4CIN experiences substantially less in-strand fluorescence quenching compared to 2APN. Given the utility of these properties for a spectrum of research applications involving oligonucleotides and oligonucleotide-protein interactions (e.g., enzymatic processes, DNA hybridization, DNA damage), we envision that additional reagents based on 4-cyanoindole nucleosides may be widely utilized. This protocol expands on the previously published synthesis of 4CIN to include synthetic routes to both 4-cyanoindole-ribonucleoside (4CINr) and 4-cyanoindole-2'-deoxyribonucleoside-5'-triphosphate (4CIN-TP), as well as a method for the enzymatic incorporation of 4CIN-TP into DNA by a polymerase. These methods are anticipated to further enable the utilization of 4CIN in diverse applications involving DNA and RNA oligonucleotides. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of 4-cyanoindole-2'-deoxyribonucleoside (4CIN) and 4CIN phosphoramidite 4 Basic Protocol 2: Synthesis of 4-cyanoindole-ribonucleoside (4CINr) Basic Protocol 3: Synthesis of 4-cyanoindole-2'-deoxyribonucleoside-5'-triphosphate (4CIN-TP) Basic Protocol 4: Steady state incorporation kinetics of 2AP-TP and 4CIN-TP by a DNA polymerase.
Topics: Carbon-13 Magnetic Resonance Spectroscopy; Cyanides; DNA; Deoxyribonucleosides; Indoles; Mass Spectrometry; Nucleosides; Proton Magnetic Resonance Spectroscopy
PubMed: 31909864
DOI: 10.1002/cpnc.101