Genomes and Genes
Summary: Adenine nucleotides which contain deoxyribose as the sugar moiety.
- Brieba L, Eichman B, Kokoska R, DOUBLIE S, Kunkel T, Ellenberger T. Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. EMBO J. 2004;23:3452-61 pubmed..This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG...
- Fairman J, Wijerathna S, Ahmad M, Xu H, Nakano R, Jha S, et al. Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization. Nat Struct Mol Biol. 2011;18:316-22 pubmed publisher..Site-directed mutagenesis and functional assays confirm that hexamerization is a prerequisite for inhibition by dATP. Our data indicate a mechanism for regulating RR activity by dATP-induced oligomerization. ..
- Reineks E, Berdis A. Evaluating the contribution of base stacking during translesion DNA replication. Biochemistry. 2004;43:393-404 pubmed..These kinetic differences are interpreted with regard to the differences in various structural components between the two enzymes and are consistent with the proposed model for DNA polymerization. ..
- Hendrickson C, Devine K, Benner S. Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine. Nucleic Acids Res. 2004;32:2241-50 pubmed..Each interpretation is significant for understanding the planetary biology of polymerases. ..
- Ghadessy F, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, et al. Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol. 2004;22:755-9 pubmed..Such 'unfussy' polymerases have immediate utility, as we demonstrate by the generation of microarray probes with up to 20-fold brighter fluorescence. ..
- Berdis A. Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase. Biochemistry. 2001;40:7180-91 pubmed..Extension from the G:abasic or A:abasic site mispair generates significant elemental effects (between 5 and 20) and suggests that chemistry is at least partially rate-limiting for extension beyond either mispair. ..
- Carrasco B, Ayora S, Lurz R, Alonso J. Bacillus subtilis RecU Holliday-junction resolvase modulates RecA activities. Nucleic Acids Res. 2005;33:3942-52 pubmed
- Li P, Nijhawan D, Budihardjo I, Srinivasula S, Ahmad M, Alnemri E, et al. Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade. Cell. 1997;91:479-89 pubmed
- Ingemarson R, Thelander L. A kinetic study on the influence of nucleoside triphosphate effectors on subunit interaction in mouse ribonucleotide reductase. Biochemistry. 1996;35:8603-9 pubmed
- Wang L, Broyde S. A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Nucleic Acids Res. 2006;34:785-95 pubmed..Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed. ..
- Fiala K, Brown J, Ling H, Kshetry A, Zhang J, Taylor J, et al. Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase. J Mol Biol. 2007;365:590-602 pubmed publisher..This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation...
- Nair D, Johnson R, Prakash L, Prakash S, Aggarwal A. DNA synthesis across an abasic lesion by human DNA polymerase iota. Structure. 2009;17:530-7 pubmed publisher..These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Poliota's small preference for insertion of dGTP over other nucleotides opposite this common lesion. ..
- Roettger M, Fiala K, Sompalli S, Dong Y, Suo Z. Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu. Biochemistry. 2004;43:13827-38 pubmed..In addition to a slow and distributive DNA polymerase activity, Polmu was identified to possess a weak strand-displacement activity. The potential biological roles of Polmu are discussed. ..
- Cramer J, Restle T. Pre-steady-state kinetic characterization of the DinB homologue DNA polymerase of Sulfolobus solfataricus. J Biol Chem. 2005;280:40552-8 pubmed..Thus, unlike replicative polymerases, an "induced fit" mechanism to select and incorporate nucleotides during DNA polymerization could not be detected for Dbh. ..
- Wu W, Stupi B, LITOSH V, Mansouri D, Farley D, Morris S, et al. Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates. Nucleic Acids Res. 2007;35:6339-49 pubmed..A five-base experiment, illustrating the exquisite, stepwise addition through a homopolymer repeat, demonstrates the applicability of the N(6)-(2-nitrobenzyl)-dATP as an ideal RT for CRT sequencing. ..
- Uppsten M, F rneg rdh M, Jordan A, Eliasson R, Eklund H, Uhlin U. Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors. J Mol Biol. 2003;330:87-97 pubmed..The low affinity for ATP at the specificity site is explained by a tyrosine, which hinders nucleotides containing a 2'-OH group to bind...
- Perlow R, Broyde S. Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen. J Mol Biol. 2001;309:519-36 pubmed
- Krahn J, Beard W, Miller H, Grollman A, Wilson S. Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure. 2003;11:121-7 pubmed..Our results provide insights into the mechanisms employed by polymerases to select the complementary dNTP. ..
- Kashlan O, Cooperman B. Comprehensive model for allosteric regulation of mammalian ribonucleotide reductase: refinements and consequences. Biochemistry. 2003;42:1696-706 pubmed
- Kamiya H, Murata Kamiya N, Iida E, Harashima H. Hydrolysis of oxidized nucleotides by the Escherichia coli Orf135 protein. Biochem Biophys Res Commun. 2001;288:499-502 pubmed..Murata-Kamiya, N., Osaki, T., Yasumoto, K., Kasai, H. (1998) J. Biol. Chem. 273, 11069-11074). These results suggest that this protein may be involved in the prevention of mutations induced by these oxidized deoxynucleotides. ..
- Shahgholi M, Garcia B, Chiu N, Heaney P, Tang K. Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved. Nucleic Acids Res. 2001;29:E91 pubmed..During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization. ..
- Nunoshiba T, Watanabe T, Nakabeppu Y, Yamamoto K. Mutagenic target for hydroxyl radicals generated in Escherichia coli mutant deficient in Mn- and Fe- superoxide dismutases and Fur, a repressor for iron-uptake systems. DNA Repair (Amst). 2002;1:411-418 pubmed..coli was similar to that in sodAB fur strain. These results suggested that the targets contributing to oxidative mutagenesis in sodAB fur strain are nucleotides such as dGTP and dATP, rather than DNA. ..
- Kurahashi M, Zheng H, Dwyer L, Ward S, Koh S, Sanders K. A functional role for the 'fibroblast-like cells' in gastrointestinal smooth muscles. J Physiol. 2011;589:697-710 pubmed publisher..We characterized these responses, and our results provide a new hypothesis about the role of fibroblast-like cells in smooth muscle tissues. ..
- Brut M, Esteve A, Landa G, Renvez G, Djafari Rouhani M. The Static Modes: an alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility. Eur Phys J E Soft Matter. 2009;28:17-25 pubmed publisher..We also discuss how this procedure allows "induced-fit" flexible molecular docking, beyond state-of-the-art semi-rigid methods. ..
- Taanman J, Muddle J, Muntau A. Mitochondrial DNA depletion can be prevented by dGMP and dAMP supplementation in a resting culture of deoxyguanosine kinase-deficient fibroblasts. Hum Mol Genet. 2003;12:1839-45 pubmed
- Koedrith P, Seo Y. Development of quantitative DNA cleavage assay for XPG endonuclease activity using endogenous nuclear proteins in human cell lines. Oncol Rep. 2011;26:1235-41 pubmed publisher..8 resulted in optimal endonucleolytic activity. Based on these results, our modified methodology has potential for quantitative monitoring of XPG cleavage activity in any cell type or tissue of interest. ..
- Truett G, Heeger P, Mynatt R, Truett A, Walker J, Warman M. Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). Biotechniques. 2000;29:52, 54 pubmed
- Balu N, Padgett W, Nelson G, Lambert G, Ross J, Nesnow S. Benzo[a]pyrene-7,8-quinone-3'-mononucleotide adduct standards for 32P postlabeling analyses: detection of benzo[a]pyrene-7,8-quinone-calf thymus DNA adducts. Anal Biochem. 2006;355:213-23 pubmed
- O Donnell M, Kornberg A. Dynamics of DNA polymerase III holoenzyme of Escherichia coli in replication of a multiprimed template. J Biol Chem. 1985;260:12875-83 pubmed..Based on these findings, schemes can be considered for holoenzyme action at the replication fork of a duplex chromosome. ..
- Chen L, Plunkett W, Gandhi V. Polyadenylation inhibition by the triphosphates of deoxyadenosine analogues. Leuk Res. 2008;32:1573-81 pubmed publisher..Taken together, our results suggest that polyadenylation inhibition may be a component in the mechanism of action of adenosine analogues. ..
- Cafarelli T, Rands T, Godoy V. The DinB•RecA complex of Escherichia coli mediates an efficient and high-fidelity response to ubiquitous alkylation lesions. Environ Mol Mutagen. 2014;55:92-102 pubmed publisher..Kinetic analyses are important to gain insights into the mechanism(s) regulating TLS DNA polymerases. ..
- Bao J, Ryu D. Biosynthesis reaction mechanism and kinetics of deoxynucleoside triphosphates, dATP and dGTP. Biotechnol Bioeng. 2005;89:485-91 pubmed..There is a significant advantage of using enzymatic biosyntheses of dATP and dGTP as compared to the chemical method that has been in commercial use. ..
- Begleiter A, Pugh L, Israels L, Johnston J. Enhanced cytotoxicity and inhibition of DNA damage repair in irradiated murine L5178Y lymphoblasts and human chronic lymphocytic leukemia cells treated with 2'-deoxycoformycin and deoxyadenosine in vitro. Cancer Res. 1988;48:3981-6 pubmed..These results suggest that 2'-deoxycoformycin/deoxyadenosine can function as a radiosensitizer, and this effect is associated with the cellular accumulation of dATP and inhibition of repair of DNA single strand breaks...
- Cattaneo M, Lecchi A, Ohno M, Joshi B, Besada P, Tchilibon S, et al. Antiaggregatory activity in human platelets of potent antagonists of the P2Y 1 receptor. Biochem Pharmacol. 2004;68:1995-2002 pubmed..Thus, all three of the bisphosphate derivatives are highly selective antagonists of the platelet P2Y(1) receptor, and MRS2500 is the most potent such antagonist yet reported. ..
- Garrido C, Bruey J, Fromentin A, Hammann A, Arrigo A, Solary E. HSP27 inhibits cytochrome c-dependent activation of procaspase-9. FASEB J. 1999;13:2061-70 pubmed..We conclude that HSP27 inhibits etoposide-induced apoptosis by preventing cytochrome c and dATP-triggered activity of caspase-9, downstream of cytochrome c release. ..
- Xu S, He M, Yu H, Cai X, Tan X, Lu B, et al. A quantitative method to measure telomerase activity by bioluminescence connected with telomeric repeat amplification protocol. Anal Biochem. 2001;299:188-93 pubmed..Because TRAP-ELIDA measures telomerase activity with a luminometer, it could be applied to a large number of clinical samples at the same time. ..
- Li Y, Waksman G. Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: insights into nucleotide incorporation and selectivity. Protein Sci. 2001;10:1225-33 pubmed..These hydrogen-bonding interactions may provide a means of detecting misincorporation at this position. ..
- Hou R, Gu J, Xie Y, Yi X, Schaefer III H. The 2'-deoxyadenosine-5'-phosphate anion, the analogous radical, and the different hydrogen-abstracted radical anions: molecular structures and effects on DNA damage. J Phys Chem B. 2005;109:22053-60 pubmed..This result should be important in understanding the reactive properties of these H-abstraction-produced anion radicals. ..
- Gallego D, Gil V, Aleu J, Martinez Cutillas M, Clave P, Jimenez M. Pharmacological characterization of purinergic inhibitory neuromuscular transmission in the human colon. Neurogastroenterol Motil. 2011;23:792-e338 pubmed publisher..We found that ?-NAD partially fulfills the criteria to be considered an inhibitory neurotransmitter in the human colon, but the relative contribution of each purine (ATP/ADP vs?-NAD) requires further studies. ..
- Svendsen K, Overgaard Hansen K, Frederiksen S. Synergistic effect of 3'-deoxyadenosine N1-oxide and adenosine deaminase inhibitors on growth of Ehrlich ascites tumor cells in vivo. Cancer Chemother Pharmacol. 1988;21:35-9 pubmed..The development of resistance to 3'-dANO was studied in cell cultures and found to be accompanied by changes in the enzyme activities of the reductase, the adenosine kinase, and the adenosine deaminase. ..
- Chae J, Kim Y, Cho Y. Crystal structure of the NurA-dAMP-Mn2+ complex. Nucleic Acids Res. 2012;40:2258-70 pubmed publisher..The 3' OH group of the ribose ring is directed toward the channel entrance, explaining the 5'-3' nuclease activity of Pf?NurA. We provide a DNA binding and cleavage model for Pf?NurA...
- Lang X, Yin P, You T, Jiang L, Guo L. A DFT investigation of surface-enhanced Raman scattering of adenine and 2'-deoxyadenosine 5'-monophosphate on Ag20 nanoclusters. Chemphyschem. 2011;12:2468-75 pubmed publisher..Furthermore, the spectrum of dAMP bound to the Ag(20) cluster via N7 approaches the experimental SERS spectra on silver colloids. ..
- Hooker L, Strong R, Adams R, Handa B, Merrett J, Martin J, et al. A sensitive, single-tube assay to measure the enzymatic activities of influenza RNA polymerase and other poly(A) polymerases: application to kinetic and inhibitor analysis. Nucleic Acids Res. 2001;29:2691-8 pubmed..4-0.6 microM) is approximately 100-fold lower than the K(m) value for ATP (50 microM) in the case of yeast PAP. ..
- Song S, Wheeler L, Mathews C. Deoxyribonucleotide pool imbalance stimulates deletions in HeLa cell mitochondrial DNA. J Biol Chem. 2003;278:43893-6 pubmed..Our finding of dTTP and dGTP elevations and dATP depletion in mitochondrial dNTP pools are consistent with a mutagenic mechanism involving T-G mispairing followed by a next-nucleotide effect involving T insertion opposite A...
- de Castro S, Maruoka H, Hong K, Kilbey S, Costanzi S, Hechler B, et al. Functionalized congeners of P2Y1 receptor antagonists: 2-alkynyl (N)-methanocarba 2'-deoxyadenosine 3',5'-bisphosphate analogues and conjugation to a polyamidoamine (PAMAM) dendrimer carrier. Bioconjug Chem. 2010;21:1190-205 pubmed publisher..This is the first example of attaching a strategically functionalized P2Y receptor antagonist to a PAMAM dendrimer to produce a multivalent conjugate exhibiting a desired biological effect, i.e., antithrombotic action. ..
- Pelletier M, Oliver L, Meflah K, Vallette F. Caspase-3 can be pseudo-activated by a Ca2+-dependent proteolysis at a non-canonical site. FEBS Lett. 2005;579:2364-8 pubmed..Altogether, our data suggest that calcium could favour a necrotic mechanism by inducing the generation of a form of C3 insensitive to mitochondrial activation. ..
- Kirouac K, Basu A, Ling H. Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase. Nucleic Acids Res. 2013;41:2060-71 pubmed publisher..This work provides one of the molecular mechanisms for G to T transversions, a signature mutation in human lung cancer. ..
- Rothwell P, Allen W, Sisamakis E, Kalinin S, Felekyan S, Widengren J, et al. dNTP-dependent conformational transitions in the fingers subdomain of Klentaq1 DNA polymerase: insights into the role of the "nucleotide-binding" state. J Biol Chem. 2013;288:13575-91 pubmed publisher..After nucleotide binding, correct dNTPs are transported to the closed state, whereas incorrect dNTPs are delivered to the open state. ..