Genomes and Genes
Summary: A purine or pyrimidine base bonded to DEOXYRIBOSE.
- Evans M, Saparbaev M, Cooke M. DNA repair and the origins of urinary oxidized 2'-deoxyribonucleosides. Mutagenesis. 2010;25:433-42 pubmed publisher..The analysis of DNA oxidation, by measurement of oxidized 2'-deoxyribonucleosides in urine, particularly 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), has been reported extensively in the ..
- Kubelka T, Slavětínská L, Eigner V, Hocek M. Synthesis of 2,6-disubstituted pyridin-3-yl C-2'-deoxyribonucleosides through chemoselective transformations of bromo-chloropyridine C-nucleosides. Org Biomol Chem. 2013;11:4702-18 pubmed publisher2-Bromo-6-chloro- and 6-bromo-2-chloropyridin-3-yl deoxyribonucleosides were prepared by the Heck coupling of bromo-chloro-iodopyridines with TBS-protected deoxyribose glycal...
- Mannava S, Moparthy K, Wheeler L, Leonova K, Wawrzyniak J, Bianchi Smiraglia A, et al. Ribonucleotide reductase and thymidylate synthase or exogenous deoxyribonucleosides reduce DNA damage and senescence caused by C-MYC depletion. Aging (Albany NY). 2012;4:917-22 pubmed..Our data demonstrate the essential role of TS and RR in C-MYC-dependent suppression of senescence in melanoma cells. ..
- Horlacher J, Hottiger M, Podust V, Hubscher U, Benner S. Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns. Proc Natl Acad Sci U S A. 1995;92:6329-33 pubmed..These results are discussed in light of the crystal structure for pol beta and general considerations of how polymerases must interact with an incoming base pair to faithfully copy genetic information. ..
- Kodama E, Kohgo S, Kitano K, Machida H, Gatanaga H, Shigeta S, et al. 4'-Ethynyl nucleoside analogs: potent inhibitors of multidrug-resistant human immunodeficiency virus variants in vitro. Antimicrob Agents Chemother. 2001;45:1539-46 pubmed..Further development of 4'-E analogs as potential therapeutics for infection with multidrug-resistant HIV-1 is warranted. ..
- Hantke K. Phage T6--colicin K receptor and nucleoside transport in Escherichia coli. FEBS Lett. 1976;70:109-12 pubmed
- Gao J, Liu H, Kool E. Assembly of the complete eight-base artificial genetic helix, xDNA, and its interaction with the natural genetic system. Angew Chem Int Ed Engl. 2005;44:3118-22 pubmed
- Reddy M, Shibata N, Kondo Y, Nakamura S, Toru T. Design, synthesis, and spectroscopic investigation of zinc dodecakis(trifluoroethoxy)phthalocyanines conjugated with deoxyribonucleosides. Angew Chem Int Ed Engl. 2006;45:8163-6 pubmed
- Chen H, Hsieh C, Shen L, Chang C. Characterization of DNA--protein cross-links induced by oxanine: cellular damage derived from nitric oxide and nitrous acid. Biochemistry. 2007;46:3952-65 pubmed..Because the repair mechanism of DPCs is not extensively investigated, the characterization of oxanine-derived DPC structures should shed light on their detection in vivo and on their biological consequences...
- Danielsen M, Andersen H, Wind A. Use of folic acid casei medium reveals trimethoprim susceptibility of Lactobacillus species. Lett Appl Microbiol. 2004;38:206-10 pubmed..The results show that trimethoprim susceptibility testing of the tested Lactobacillus species is possible and indicate that transferable resistance genes are absent in all the tested strains. ..
- Choi Y, Moon H, Yoshimura Y, Marquez V. Recent advances in the synthesis of conformationally locked nucleosides and their success in probing the critical question of conformational preferences by their biological targets. Nucleosides Nucleotides Nucleic Acids. 2003;22:547-57 pubmed..The method developed for the latter class permitted access to a novel bicyclo[3.1.0]hexene-type nucleosides structurally similar to D4T and carbovir. A structural analysis and biological activities are discussed. ..
- Maga G, Amacker M, Hubscher U, Gosselin G, Imbach J, Mathe C, et al. Molecular basis for the enantioselectivity of HIV-1 reverse transcriptase: role of the 3'-hydroxyl group of the L-(beta)-ribose in chiral discrimination between D- and L-enantiomers of deoxy- and dideoxy-nucleoside triphosphate analogs. Nucleic Acids Res. 1999;27:972-8 pubmed
- Bae S, Lakshman M. Synthetic utility of an isolable nucleoside phosphonium salt. Org Lett. 2008;10:2203-6 pubmed publisher..Using this salt, a new synthesis of an acrolein-2'-deoxyguanosine adduct has also been accomplished. ..
- Liguori A, Napoli A, Sindona G. Survey of the proton affinities of adenine, cytosine, thymine and uracil dideoxyribonucleosides, deoxyribonucleosides and ribonucleosides. J Mass Spectrom. 2000;35:139-44 pubmed..The scale extends over a very narrow range of approximately 2 kcal mol(-1), thus demonstrating the sensitivity of the kinetic method in the evaluation of small differences in thermodynamic parameters. ..
- Embrechts J, Lemiere F, Van Dongen W, Esmans E. Equilenin-2'-deoxynucleoside adducts: analysis with nano-liquid chromatography coupled to nano-electrospray tandem mass spectrometry. J Mass Spectrom. 2001;36:317-28 pubmed
- Olsen R, Backman J, Molander P, Øvrebø S, Thorud S, Lundanes E, et al. Characterization of adducts formed in the reaction of glutaraldehyde with 2'-deoxyadenosine. Chem Res Toxicol. 2007;20:965-74 pubmed..Plausible mechanisms for the formation of the adducts are presented. In the reaction of glutaraldehyde with single and double stranded calf thymus DNA, the dA334 adduct was formed. ..
- Sandrini M, Söderbom F, Mikkelsen N, Piskur J. Dictyostelium discoideum salvages purine deoxyribonucleosides by highly specific bacterial-like deoxyribonucleoside kinases. J Mol Biol. 2007;369:653-64 pubmedThe salvage of deoxyribonucleosides in the social amoeba Dictyostelium discoideum, which has an extremely A+T-rich genome, was investigated. All native deoxyribonucleosides were phosphorylated by D...
- Ahluwalia D, Bienstock R, Schaaper R. Novel mutator mutants of E. coli nrdAB ribonucleotide reductase: insight into allosteric regulation and control of mutation rates. DNA Repair (Amst). 2012;11:480-7 pubmed publisher..These mutants provide new insight into the precise mechanisms by which RNR is regulated and how dNTP pool disturbances resulting from defects in RNR can lead to increased mutation. ..
- Wang M, Gupta R, Rastogi S, Kohli S, Zhang K, Lanfear D, et al. Acute intravenous infusion of an adenosine regulating agent improves left ventricular function in dogs with advanced heart failure. Cardiovasc Drugs Ther. 2013;27:489-98 pubmed publisher..These observations support the continued development of ARA's for the treatment of acute HF syndromes. ..
- Adema A, Bijnsdorp I, Sandvold M, Verheul H, Peters G. Innovations and opportunities to improve conventional (deoxy)nucleoside and fluoropyrimidine analogs in cancer. Curr Med Chem. 2009;16:4632-43 pubmed..We expect that combining different strategies could further increase the efficacy of these compounds. ..
- Reichardt C, Wen C, Vogt R, Crespo Hernandez C. Role of intersystem crossing in the fluorescence quenching of 2-aminopurine 2'-deoxyriboside in solution. Photochem Photobiol Sci. 2013;12:1341-50 pubmed publisher..Furthermore, the rate of formation and yield of the triplet state depend sensitively on the hydrogen-donor ability and polarity of the solvent. ..
- Shen R, Wheeler L, Mathews C. Molecular interactions involving Escherichia coli nucleoside diphosphate kinase. J Bioenerg Biomembr. 2006;38:255-9 pubmed..However, ndk disruption unbalances the dNTP pools and stimulates mutagenesis. We discuss our attempts to understand the basis for this enhanced mutagenesis. ..
- Wang Q, Li Y, Song C, Qian K, Chen C, Lee K, et al. Synthesis and anti-HIV activity of 2'-deoxy-2'-fluoro-4'-C-ethynyl nucleoside analogs. Bioorg Med Chem Lett. 2010;20:4053-6 pubmed publisher..Compound 2 was 35-fold more potent than AZT against wild-type virus, and also retained nanomolar antiviral activity against resistant strains, NL4-3 (K101E) and RTMDR. Thus, 2 merits further development as a novel NRTI drug. ..
- Munch Petersen B, Knecht W, Lenz C, Søndergaard L, Piskur J. Functional expression of a multisubstrate deoxyribonucleoside kinase from Drosophila melanogaster and its C-terminal deletion mutants. J Biol Chem. 2000;275:6673-9 pubmed..1998) J. Biol. Chem. 273, 3926-3931). To prove that the capacity to phosphorylate all four deoxyribonucleosides is in fact associated to one polypeptide chain, partially sequenced cDNA clones, originating from the ..
- Zhang Y, Craig J, Gallagher M. Location of the nupC gene on the physical map of Escherichia coli K-12. J Bacteriol. 1992;174:5758-9 pubmed
- Welin M, Kosinska U, Mikkelsen N, Carnrot C, Zhu C, Wang L, et al. Structures of thymidine kinase 1 of human and mycoplasmic origin. Proc Natl Acad Sci U S A. 2004;101:17970-5 pubmed..The TK1 structure differs fundamentally from the structures of the other deoxyribonucleoside kinases, indicating a different evolutionary origin. ..
- Rejman D, Masojidkova M, Rosenberg I. Nucleosidyl-O-Methylphosphonates: a pool of monomers for modified oligonucleotides. Nucleosides Nucleotides Nucleic Acids. 2004;23:1683-705 pubmedAn unique set of 5'-O- and 3'-O-phosphonomethyl derivatives of four natural 2'-deoxyribonucleosides, 1-(2-deoxy-beta-D-threo-pentofuranosyl)thymine, 5'-O- and 2'-O-phosphonomethyl derivatives of 1-(3-deoxy-beta-D-erythro-pentofuranosyl)..
- Kagawa K, Kagawa H. DNA modification in chick heart and cerebrum. Comp Biochem Physiol A Mol Integr Physiol. 2004;138:147-60 pubmed..We propose a model of the deoxynucleoside where a carbonyl residue exists between the base and the 2-deoxyribose moiety of the canonical deoxyribonucleoside. ..
- Rao P, Benner S. Fluorescent charge-neutral analogue of xanthosine: synthesis of a 2'-deoxyribonucleoside bearing a 5-aza-7-deazaxanthine base. J Org Chem. 2001;66:5012-5 pubmed..5.6. Furthermore, as part of the design, 4 is made capable of presenting an unshared pair of electrons to the DNA minor groove. ..
- Kaluzhny D, Mikhailov S, Efimtseva E, Borisova O, Florentiev V, Shchyolkina A, et al. Fluorescent 2-pyrimidinone nucleoside in parallel-stranded DNA. Nucleosides Nucleotides Nucleic Acids. 2003;22:1499-503 pubmed..Here we studied an effect of a pyrimidinone-G (PG) base pair on the stability and conformation of the ps DNA to explore whether P is useful as a structural probe. ..
- Vadhanam M, Horn J, Flesher J, Gupta R. Detection of benzylic adducts in DNA and nucleotides from 7-sulfooxymethyl-12-methylbenz[a]anthracene and related compounds by 32P-postlabeling using new TLC systems. Chem Biol Interact. 2003;146:81-7 pubmed..The methodology developed was also found applicable for highly lipophilic adducts resulting from sulfate esters of structurally-related metabolites of DMBA. ..
- Leroy F, Dukhan D, Durka M, Chaves D, Bragnier N, Storer R, et al. Synthesis of 2'-C-methyl-beta-D-ribofuranosylimidazo [4,5-d]-pyridazine derivatives (2-aza-3-deazapurine nucleoside analogues). Nucleosides Nucleotides Nucleic Acids. 2005;24:667-9 pubmed..In order to evaluate their antiviral properties, two imidazo[4,5-d]pyridazine 2'-C-methyl-beta-D-ribofuranonucleoside derivatives have been synthesized. ..
- Decosterd L, Cottin E, Chen X, Lejeune F, Mirimanoff R, Biollaz J, et al. Simultaneous determination of deoxyribonucleoside in the presence of ribonucleoside triphosphates in human carcinoma cells by high-performance liquid chromatography. Anal Biochem. 1999;270:59-68 pubmed
- Chabes A, Georgieva B, Domkin V, Zhao X, Rothstein R, Thelander L. Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase. Cell. 2003;112:391-401 pubmed..We propose that increased survival and mutation rates result from more efficient translesion DNA synthesis at elevated dNTP concentrations. ..
- Clausen A, Girandon L, Ali A, Knecht W, Rozpedowska E, Sandrini M, et al. Two thymidine kinases and one multisubstrate deoxyribonucleoside kinase salvage DNA precursors in Arabidopsis thaliana. FEBS J. 2012;279:3889-97 pubmed publisher..Deoxyribonucleoside kinases (EC 220.127.116.11) salvage deoxyribonucleosides by transfer of a phosphate group to the 5' of a deoxyribonucleoside...
- Poli J, Tsaponina O, Crabbe L, Keszthelyi A, Pantesco V, Chabes A, et al. dNTP pools determine fork progression and origin usage under replication stress. EMBO J. 2012;31:883-94 pubmed publisher..Since upregulation of RNR promotes fork progression in the presence of DNA lesions, we propose that CIN mutants adapt to chronic replication stress by upregulating dNTP pools. ..
- Amer A, Senior S, Fan X. 5-substituted pyrimidine L-2'-deoxyribonucleosides: synthetic, quantum chemical, and NMR studies. Nucleosides Nucleotides Nucleic Acids. 2012;31:42-54 pubmed publisher..The newly synthesized L-analogues show no significant activity against vaccinia and cowpox viruses. ..
- Garvey E, Lowen G, Almond M. Nucleotide and nucleoside analogues as inhibitors of cytosolic 5'-nucleotidase I from heart. Biochemistry. 1998;37:9043-51 pubmed..Because of the high selectivity for c-N-I versus both of the other 5'-nucleotidases, the nucleoside inhibitors of c-N-I may be useful biochemical tools in discerning the role that c-N-I plays in generating adenosine within myocardium. ..
- Kunz B, Kohalmi S, Kunkel T, Mathews C, McIntosh E, Reidy J. International Commission for Protection Against Environmental Mutagens and Carcinogens. Deoxyribonucleoside triphosphate levels: a critical factor in the maintenance of genetic stability. Mutat Res. 1994;318:1-64 pubmed
- McGhee J, von Hippel P. Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry. 1975;14:1281-96 pubmed
- Wilson T, Zhao Z, Maxwell K, Kontogiannis L, Lilley D. Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme. Biochemistry. 2001;40:2291-302 pubmed..This is consistent with a direct role for the nucleobase of G8 in the chemistry of cleavage. ..
- Katahira R, Ashihara H. Profiles of pyrimidine biosynthesis, salvage and degradation in disks of potato (Solanum tuberosum L.) tubers. Planta. 2002;215:821-8 pubmed..1.1.23), exhibited high activity. The rates of uptake of pyrimidine ribo- and deoxyribonucleosides by the disks were high, in the range 2.0-2.8 nmol (g FW)(-1) h(-1)...
- Stahlschmidt A, Machulla H, Reischl G, Knaus E, Wiebe L. Radioiodination of 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene (dRFIB), a putative thymidine mimic nucleoside for cell proliferation studies. Appl Radiat Isot. 2008;66:1221-8 pubmed publisher..The activation energy for dRFIB radioiodination was calculated from temperature-time RCY data to be approximately 100 kJ/mol using no-carrier-added [(124)I]iodide. ..
- Seela F, Peng X. Synthesis and properties of 7-substituted 7-deazapurine (pyrrolo[2,3-d]pyrimidine) 2'-deoxyribonucleosides. Curr Protoc Nucleic Acid Chem. 2005;Chapter 1:Unit 1.10 pubmed publisher7-Substituted 7-deazapurine (pyrrolo[2,3-d]pyrimidine) 2'-deoxyribonucleosides are synthesized by stereoselective nucleobase anion glycosylation...
- Shaikh K, Leonard P, Seela F. 7-deaza-2'-deoxyxanthosine: nucleobase protection and base pairing of oligonucleotides. Nucleosides Nucleotides Nucleic Acids. 2007;26:737-41 pubmed..The base pairing of nucleosides 1 and 2 with the four canonical DNA constituents as well as with 3 within the 12-mer duplexes is studied. ..
- Raunak -, Ravindra Babu B, Sørensen M, Parmar V, Harrit N, Wengel J. Oligodeoxynucleotides containing alpha-L-ribo configured LNA-type C-aryl nucleotides. Org Biomol Chem. 2004;2:80-9 pubmed..Thermal denaturation studies showed universal base pairing behavior for the pyrenyl monomer ([small alpha]L)Py(L) when incorporated into a DNA or an [small alpha]-L-LNA oligonucleotide. ..
- Qiu X, Qing F. Synthesis of 3'-deoxy-3'-difluoromethyl azanucleosides from trans-4-hydroxy-l-proline. J Org Chem. 2005;70:3826-37 pubmed
- Csapo Z, Keszler G, Safrany G, Spasokoukotskaja T, Talianidis I, Staub M, et al. Activation of deoxycytidine kinase by gamma-irradiation and inactivation by hyperosmotic shock in human lymphocytes. Biochem Pharmacol. 2003;65:2031-9 pubmed..These data provide evidence for the activation of dCK upon DNA damage and repair that seems to be mediated by phosphorylation of the enzyme, suggesting the role of dCK in DNA repair processes. ..
- Hartung R, Paquette L. Practical synthesis of enantiopure spiro[4.4]nonane C-(2'-deoxy)ribonucleosides. J Org Chem. 2005;70:1597-604 pubmed..Also reported is a highly practical and reliable means for the formation of novel 2'-deoxyribonucleosides of novel structural type from these spirocyclic cyclopentenones.
- Wang M, Chung F, Hecht S. Formation of 7-(4-oxobutyl)guanine in hepatic DNA of rats treated with N-nitrosopyrrolidine. Carcinogenesis. 1992;13:1909-11 pubmed..p. administration was 643 +/- 9 mumol/mol guanine, approximately one-third of the level of adduct 1. This study is the first to demonstrate the in vivo formation of a formylalkyl-substituted guanine adduct by a nitrosamine. ..