Genomes and Genes
Summary: Guanine nucleotides which contain deoxyribose as the sugar moiety.
- Powell R, Holland P, Hollis T, Perrino F. Aicardi-Goutieres syndrome gene and HIV-1 restriction factor SAMHD1 is a dGTP-regulated deoxynucleotide triphosphohydrolase. J Biol Chem. 2011;286:43596-600 pubmed publisher..We show that SAMHD1 contains a dGTP-regulated deoxynucleotide triphosphohydrolase. We propose that Vpx targets SAMHD1 for degradation in a viral strategy to control cellular deoxynucleotide levels for efficient replication...
- Suzuki T, Yamamoto K, Harashima H, Kamiya H. Base excision repair enzyme endonuclease III suppresses mutagenesis caused by 8-hydroxy-dGTP. DNA Repair (Amst). 2008;7:88-94 pubmed..These results suggest that E. coli endonuclease III also acts as a defense against the mutations caused by 8-OH-dGTP in the nucleotide pool. ..
- Kakuma T, Nishida J, Tsuzuki T, Sekiguchi M. Mouse MTH1 protein with 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphatase activity that prevents transversion mutation. cDNA cloning and tissue distribution. J Biol Chem. 1995;270:25942-8 pubmed..In embryonic stem cells, an exceedingly high level of the enzyme was present. ..
- Satou K, Kawai K, Kasai H, Harashima H, Kamiya H. Mutagenic effects of 8-hydroxy-dGTP in live mammalian cells. Free Radic Biol Med. 2007;42:1552-60 pubmed..coli. These results constitute the first direct evidence to show that 8-OH-dGTP actually induces mutations in living mammalian cells. ..
- Ferraro P, Nicolosi L, Bernardi P, Reichard P, Bianchi V. Mitochondrial deoxynucleotide pool sizes in mouse liver and evidence for a transport mechanism for thymidine monophosphate. Proc Natl Acad Sci U S A. 2006;103:18586-91 pubmed..At nM external dTMP the nucleotide is concentrated 100-fold inside the mt matrix. Export of thymidine phosphates was much slower and possibly occurred at the level of dTDP. ..
- MacPherson P, Barone F, Maga G, Mazzei F, Karran P, Bignami M. 8-oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSalpha. Nucleic Acids Res. 2005;33:5094-105 pubmed..These findings are consistent with a contribution of oxidative DNA damage to frameshifts. They also suggest how mismatch repair might reduce the burden of DNA 8-oxoG and prevent frameshift formation. ..
- Vaisman A, Ling H, Woodgate R, Yang W. Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. EMBO J. 2005;24:2957-67 pubmed..The correct incoming nucleotide allows DNA synthesis to overcome pyrophosphorolysis, but an incorrect incoming nucleotide does not. ..
- Mishima M, Sakai Y, Itoh N, Kamiya H, Furuichi M, Takahashi M, et al. Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates. J Biol Chem. 2004;279:33806-15 pubmed..We also show that MTH1 catalyzes hydrolysis of 8-oxo-dGTP through nucleophilic substitution of water at the beta-phosphate. ..
- Jenuth J, Dilay J, Fung E, Mably E, Snyder F. Absence of dGTP accumulation and compensatory loss of deoxyguanosine kinase in purine nucleoside phosphorylase deficient mice. Adv Exp Med Biol. 1991;309B:273-6 pubmed
- Yang G, Wang J, Konigsberg W. Base selectivity is impaired by mutants that perturb hydrogen bonding networks in the RB69 DNA polymerase active site. Biochemistry. 2005;44:3338-46 pubmed..We have interpreted our results within the context of the crystal structure of the RB69 pol ternary complex [Franklin, M. C., et al. (2001) Cell 105, 657-667]. ..
- Nakamura T, Doi T, Sekiguchi M, Yamagata Y. Crystallization and preliminary X-ray analysis of Escherichia coli MutT in binary and ternary complex forms. Acta Crystallogr D Biol Crystallogr. 2004;60:1641-3 pubmed..1 A(3) Da(-1). Crystals of the ternary complex were prepared by soaking crystals of the binary complex in 1 mM MnCl(2) solution. They diffracted to 1.96 and 2.56 A resolution, respectively. ..
- Miller H, Prasad R, Wilson S, Johnson F, Grollman A. 8-oxodGTP incorporation by DNA polymerase beta is modified by active-site residue Asn279. Biochemistry. 2000;39:1029-33 pubmed..This suggests that interactions of 8-oxodGTP with Asn279 in the polymerase active site may alter the conformation of 8-oxodGTP and therefore alter its misincorporation. ..
- Ishibashi T, Hayakawa H, Sekiguchi M. A novel mechanism for preventing mutations caused by oxidation of guanine nucleotides. EMBO Rep. 2003;4:479-83 pubmed
- Snyder F, Jenuth J, Mably E, Mangat R. Point mutations at the purine nucleoside phosphorylase locus impair thymocyte differentiation in the mouse. Proc Natl Acad Sci U S A. 1997;94:2522-7 pubmed..The progressive T cell deficit is similar to the human disorder. ..
- Bialkowski K, Kasprzak K. A novel assay of 8-oxo-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase (8-oxo-dGTPase) activity in cultured cells and its use for evaluation of cadmium(II) inhibition of this activity. Nucleic Acids Res. 1998;26:3194-201 pubmed..The cells cultured with 0.3-3 microM cadmium(II) acetate for up to 24 h had their 8-oxo-dGTPase activity suppressed in a Cd(II) concentration-dependent manner, down to 70% of the control value. ..
- Colussi C, Parlanti E, Degan P, Aquilina G, Barnes D, MacPherson P, et al. The mammalian mismatch repair pathway removes DNA 8-oxodGMP incorporated from the oxidized dNTP pool. Curr Biol. 2002;12:912-8 pubmed..Increased expression of MTH1 in MMR-defective cells significantly reduces steady-state and H(2)O(2)-induced DNA 8-oxoG levels. This reduction dramatically diminishes the spontaneous mutation rate of Msh2(-/-) MEFs. ..
- Cai J, Ishibashi T, Takagi Y, Hayakawa H, Sekiguchi M. Mouse MTH2 protein which prevents mutations caused by 8-oxoguanine nucleotides. Biochem Biophys Res Commun. 2003;305:1073-7 pubmed..coli mutT(-) cells. Thus, MTH2 has a potential to protect the genetic material from the untoward effects of endogenous oxygen radicals. MTH2 could act as an MTH1 redundancy factor. ..
- Hori M, Satou K, Harashima H, Kamiya H. Suppression of mutagenesis by 8-hydroxy-2'-deoxyguanosine 5'-triphosphate (7,8-dihydro-8-oxo-2'-deoxyguanosine 5'-triphosphate) by human MTH1, MTH2, and NUDT5. Free Radic Biol Med. 2010;48:1197-201 pubmed publisher..These results indicate that all three of the human MTH1, MTH2, and NUDT5 proteins act as a defense against the mutagenesis induced by oxidized dGTP. ..
- Nakamura T, Meshitsuka S, Kitagawa S, Abe N, Yamada J, Ishino T, et al. Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. J Biol Chem. 2010;285:444-52 pubmed publisher..These results indicate that MutT specifically recognizes 8-oxoguanine nucleotides by the ligand-induced conformational change. ..
- Goldstone D, Ennis Adeniran V, Hedden J, Groom H, Rice G, Christodoulou E, et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature. 2011;480:379-82 pubmed publisher..We propose that SAMHD1, which is highly expressed in dendritic cells, restricts HIV-1 replication by hydrolysing the majority of cellular dNTPs, thus inhibiting reverse transcription and viral complementary DNA (cDNA) synthesis. ..
- Tassotto M, Mathews C. Assessing the metabolic function of the MutT 8-oxodeoxyguanosine triphosphatase in Escherichia coli by nucleotide pool analysis. J Biol Chem. 2002;277:15807-12 pubmed..These findings lead us to question the conclusion that 8-oxo-dGTP is the most significant physiological substrate for the MutT protein. ..
- Shimizu M, Gruz P, Kamiya H, Masutani C, Xu Y, Usui Y, et al. Efficient and erroneous incorporation of oxidized DNA precursors by human DNA polymerase eta. Biochemistry. 2007;46:5515-22 pubmed..We propose that human DNA polymerase eta may participate in oxidative mutagenesis through the efficient and erroneous incorporation of oxidized dNTPs during DNA synthesis. ..
- Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R. The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J Mol Biol. 2012;417:179-96 pubmed publisher..The ability to bind to either syn-dNTP or anti-dNTP and the involvement of a Theorell-Chance mechanism are key aspects of the strong nucleotide-binding and efficient gap-filling activities of ttPolX...
- Satou K, Hori M, Kawai K, Kasai H, Harashima H, Kamiya H. Involvement of specialized DNA polymerases in mutagenesis by 8-hydroxy-dGTP in human cells. DNA Repair (Amst). 2009;8:637-42 pubmed publisher..These results indicate that specialized DNA polymerases are involved in the mutagenesis induced by the oxidized dGTP. ..
- Sakumi K, Furuichi M, Tsuzuki T, Kakuma T, Kawabata S, Maki H, et al. Cloning and expression of cDNA for a human enzyme that hydrolyzes 8-oxo-dGTP, a mutagenic substrate for DNA synthesis. J Biol Chem. 1993;268:23524-30 pubmed..In such cells, the frequency of spontaneous mutation was greatly reduced. We propose that the human 8-oxo-dGTPase protects genetic information from the untoward effects of endogenous oxygen radicals. ..
- Taddei F, Hayakawa H, Bouton M, Cirinesi A, Matic I, Sekiguchi M, et al. Counteraction by MutT protein of transcriptional errors caused by oxidative damage. Science. 1997;278:128-30 pubmed..Such control of transcriptional fidelity by the ubiquitous MutT function has implications for evolution of RNA-based life, phenotypic expression, adaptive mutagenesis, and functional maintenance of nondividing cells. ..
- Huang X, Kolbanovskiy A, Wu X, Zhang Y, Wang Z, Zhuang P, et al. Effects of base sequence context on translesion synthesis past a bulky (+)-trans-anti-B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol kappa. Biochemistry. 2003;42:2456-66 pubmed..The base sequence-dependent features of translesion bypass are discussed in terms of the possible conformations of the adducts and the known structural features of bypass polymerases. ..
- Denofrio M, Hatz S, Lorente C, Cabrerizo F, Ogilby P, Thomas A. The photosensitizing activity of lumazine using 2'-deoxyguanosine 5'-monophosphate and HeLa cells as targets. Photochem Photobiol Sci. 2009;8:1539-49 pubmed publisher..The data reported herein illustrate how the irradiation of an endogenous biological compound can have various effects which, depending on the system, can be manifested in different ways. ..
- Ji X, Wu Y, Yan J, Mehrens J, Yang H, Delucia M, et al. Mechanism of allosteric activation of SAMHD1 by dGTP. Nat Struct Mol Biol. 2013;20:1304-9 pubmed publisher..The SAMHD1 tetramer structure provides the basis for a mechanistic understanding of its function in HIV restriction and the pathogenesis of AGS. ..
- Feng F, Wang H, Han L, Wang S. Fluorescent conjugated polyelectrolyte as an indicator for convenient detection of DNA methylation. J Am Chem Soc. 2008;130:11338-43 pubmed publisher..The isolation steps employed in other typical assays were avoided to simplify operations and increase repeatability. These features make the system promising for future use for early cancer diagnosis. ..
- Feng J, Anderson K. Mechanistic studies examining the efficiency and fidelity of DNA synthesis by the 3TC-resistant mutant (184V) of HIV-1 reverse transcriptase. Biochemistry. 1999;38:9440-8 pubmed
- Pelemans H, Esnouf R, Min K, Parniak M, De Clercq E, Balzarini J. Mutations at amino acid positions 63, 189, and 396 of human immunodeficiency virus type 1 reverse transcriptase (RT) partially restore the DNA polymerase activity of a Trp229Tyr mutant RT. Virology. 2001;287:143-50 pubmed..Therefore, amino acid position 229 may be regarded as an excellent amino acid target within the NNRTI pocket for rational drug design. ..
- Zhang X, Liu S, Jiao K, Gao H, Shi Y. Rapid and cost-effective detection of sequence-specific DNA by monitoring the electrochemical response of 2'-deoxyguanosine 5'-triphosphate in a PCR sample. Analyst. 2008;133:1729-35 pubmed publisher..The result was in good accordance with that obtained with gel electrophoresis. ..
- Wamer W, Yin J, Wei R. Oxidative damage to nucleic acids photosensitized by titanium dioxide. Free Radic Biol Med. 1997;23:851-8 pubmed..These results suggest that nucleic acids are a potential target for photooxidative damage sensitized by TiO2, and support the view that TiO2 photocatalyzes free radical formation. ..
- Serrano M, Lorente C, Vieyra F, Borsarelli C, Thomas A. Photosensitizing properties of biopterin and its photoproducts using 2'-deoxyguanosine 5'-monophosphate as an oxidizable target. Phys Chem Chem Phys. 2012;14:11657-65 pubmed publisher..The biological implications of the results obtained are also discussed. ..
- Fotouhi A, Skiöld S, Shakeri Manesh S, Osterman Golkar S, Wojcik A, Jenssen D, et al. Reduction of 8-oxodGTP in the nucleotide pool by hMTH1 leads to reduction in mutations in the human lymphoblastoid cell line TK6 exposed to UVA. Mutat Res. 2011;715:13-8 pubmed publisher..The results indicate that the nucleotide pool is a significant target for UVA-induced mutations and implicates that hMTH1 plays an important role in protecting cells from UVA-induced oxidative stress. ..
- Sankatsing S, Hoggard P, Huitema A, Sparidans R, Kewn S, Crommentuyn K, et al. Effect of mycophenolate mofetil on the pharmacokinetics of antiretroviral drugs and on intracellular nucleoside triphosphate pools. Clin Pharmacokinet. 2004;43:823-32 pubmed..There were no consistent effects of mycophenolic acid on the intracellular concentrations of dCTP, dGTP or 3TCTP. ..
- Choi S, Cooley R, Voutchkova A, Leung C, Vastag L, Knowles D. Oxidation of guanosine derivatives by a platinum(IV) complex: internal electron transfer through cyclization. J Am Chem Soc. 2005;127:1773-81 pubmed..The results indicate that a good nucleophilic group at the 5' position is required for the redox reaction between guanosine and the Pt(IV) complex. ..
- Kawate T, Allerson C, Wolfe J. Regioselective syntheses of 7-nitro-7-deazapurine nucleosides and nucleotides for efficient PCR incorporation. Org Lett. 2005;7:3865-8 pubmed..These modified nucleosides were converted to nucleotide triphosphates, each of which can replace the corresponding, naturally occurring triphosphate to support PCR amplification. [structure: see text] ..
- Wang S, Chang Y. Combinatorial synthesis of benzimidazolium dyes and its diversity directed application toward GTP-selective fluorescent chemosensors. J Am Chem Soc. 2006;128:10380-1 pubmed..Highly selective fluorescence turn-on GTP sensor, GTP Green, was discovered by a diversity directed sensor approach, combined by solid-phase combinatorial synthesis of a benzimidazolium library and high-throughput screening. ..
- Suzuki T, Harashima H, Kamiya H. Effects of base excision repair proteins on mutagenesis by 8-oxo-7,8-dihydroguanine (8-hydroxyguanine) paired with cytosine and adenine. DNA Repair (Amst). 2010;9:542-50 pubmed publisher..These results indicate that all of the above DNA glycosylases suppress mutations caused by 8-oxo-Gua:C in DNA. In contrast, it appears that MUTYH enhances A:T-->C:G mutations caused by 8-oxo-dGTP. ..
- Olejnik K, Kraszewska E. Cloning and characterization of an Arabidopsis thaliana Nudix hydrolase homologous to the mammalian GFG protein. Biochim Biophys Acta. 2005;1752:133-41 pubmed..2 mM and 2.7 s(-1) respectively. The products of ADP-ribose hydrolysis were AMP and ribose-5-phosphate. The optimal activity was at alkaline pH (8.5) with Mg2+ (5 mM) ions as the cofactor. The protein exists as a dimmer in solution. ..
- Vrana O, Brabec V. L-methionine inhibits reaction of DNA with anticancer cis-diamminedichloroplatinum(II). Biochemistry. 2002;41:10994-9 pubmed..Thus, the possibility that cisplatin bound to methionine residues serves as a drug reservoir available for platination of DNA in the nucleus of tumor cells appears unlikely. ..
- Bi L, Kim D, Ju J. Design and synthesis of a chemically cleavable fluorescent nucleotide, 3'-O-allyl-dGTP-allyl-bodipy-FL-510, as a reversible terminator for DNA sequencing by synthesis. J Am Chem Soc. 2006;128:2542-3 pubmed..The resulting DNA product is successfully used as a primer for further extension in polymerase reaction. This one-pot dual-deallylation reaction thus allows the reinitiation of the polymerase reaction and increases the SBS efficiency. ..
- Kamerlin S, McKenna C, Goodman M, Goondman M, Warshel A. A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases. Biochemistry. 2009;48:5963-71 pubmed publisher..An understanding of the mechanism of this reaction in solution could thereby provide a steppingstone for understanding the factors governing the fidelity of DNA polymerases. ..
- Sucato C, Upton T, Kashemirov B, Osuna J, Oertell K, Beard W, et al. DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Biochemistry. 2008;47:870-9 pubmed..Solvent pH and deuterium isotope-effect data are also used to evaluate mechanistic differences between correct and mispaired incorporation. ..
- Abeygunawardana C, Weber D, Gittis A, Frick D, Lin J, Miller A, et al. Solution structure of the MutT enzyme, a nucleoside triphosphate pyrophosphohydrolase. Biochemistry. 1995;34:14997-5005 pubmed..1995) Biochemistry 34, 5577-5586].(ABSTRACT TRUNCATED AT 250 WORDS) ..