Non-enzymatic depurination of nucleic acids: Factors and mechanisms

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  An, Ran ^a   Jia, Yu ^a   Wan, Baihui ^a   Zhang, Yanfang ^a   Dong, Ping ^a   Li, Jing ^a   Liang, Xingguo ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; OLIGODEOXYNUCLEOTIDE DERIVATIVE; SINGLE STRANDED DNA; SODIUM CHLORIDE; DNA; INORGANIC SALT; NUCLEIC ACID; OLIGODEOXYRIBONUCLEOTIDE; PROTON; PURINE DERIVATIVE;

ARTICLE; CHEMICAL PROCEDURES; DNA SEQUENCE; DNA STRUCTURE; IONIC STRENGTH; NON ENZYMATIC DEPURINATION; NUCLEIC ACID METABOLISM; PH; PROTON TRANSPORT; TEMPERATURE; CHEMISTRY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; KINETICS; METABOLISM; NUCLEOTIDE SEQUENCE; TIME;

BASE SEQUENCE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DNA; HYDROGEN-ION CONCENTRATION; KINETICS; NUCLEIC ACIDS; OLIGODEOXYRIBONUCLEOTIDES; PROTONS; PURINES; SALTS; TEMPERATURE; TIME FACTORS;

EID: 84920146914     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0115950     Document Type: Article

References (34)

1. Dekker CA (1960) Nucleic Acids Selected Topics Related to their Enzymology and Chemistry. Annu Rev Biochem 29: 453-474.
2. Loeb LA, Preston BD (1986) Mutagenesis by apurinic/apyrimidinic sites. Annu Rev Genet 20: 201-230.
3. Chakravarti D, Mailander PC, Li KM, Higginbotham S, Zhang HL, et al. (2001) Evidence that a burst of DNA depurination in SENCAR mouse skin induces error-prone repair and forms mutations in the H-ras gene. Oncogene 20: 7945-7953.
4. Sherchan J, Choi H, Lee ES (2009) Depurination of nucleosides and calf thymus DNA induced by 2-bromopropane at the physiological condition. Bull Korean Chem Soc 30: 2309-2317.
5. Schaaper RM, Loeb LA (1981) Depurination causes mutations in SOS-induced cells. Proc Natl Acad Sci U S A 78: 1773-1777.
6. Lindahl T, Andersson A (1972) Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 11: 3618-3623.
7. Schaaper RM, Glickman BW, Loeb LA (1982) Role of depurination in mutagenesis by chemical carcinogens. Cancer Res 42: 3480-3485.
8. Osborne M, Merrifield K (1985) Depurination of benzo [a] pyrene-diolepoxide treated DNA. Chem Biol Interact 53: 183-195.
9. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362: 709-715.
10. Lindahl T, Nyberg B (1972) Rate of depurination of native deoxyribonucleic acid. Biochemistry 11: 3610-3618.
11. Zhang L, Hou D, Chen X, Li D, Zhu L, et al. (2011) Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res 22: 107-126.
12. Luzio JP, Pryor PR, Bright NA (2007) Lysosomes: fusion and function. Nat Rev Mol Cell Bio 8: 622-632.
13. Garrett ER, Mehta P (1972) Solvolysis of adenine nucleosides. I. Effects of sugars and adenine substituents on acid solvolyses. J Am Chem Soc 94: 8532-8541.
14. Suzuki T, Ohsumi S, Makino K (1994) Mechanistic studies on depurination and apurinic site chain breakage in oligodeoxyribonucleotides. Nucleic Acids Res 22: 4997-5003.
15. Garrett ER (1960) Kinetics of the hydrolytic degradation of a nucleoside, the antibiotic psicofuranine. J Am Chem Soc 82: 827-832.
16. Tamm C, Hodes M, Chargaff E (1952) The formation of apurinic acid from the desoxyribonucleic acid of calf thymus. J Biol Chem 195: 49-63.
17. Lawley P, Brookes P (1963) Further studies on the alkylation of nucleic acids and their constituent nucleotides. Biochem J 89: 127.
18. Hevesi L, Wolfson-Davidson E, Nagy J, Nagy O, Bruylants A (1972) Contribution to the mechanism of the acid-catalyzed hydrolysis of purine nucleosides. J Am Chem Soc 94: 4715-4720.
19. Greer S, Zamenhof S (1962) Studies on depurination of DNA by heat. J Mol Biol 4: 123-141.
20. Zoltewicz JA, Clark DF, Sharpless TW, Grahe G (1970) Kinetics and mechanism of the acid-catalyzed hydrolysis of some purine nucleosides. J Am Chem Soc 92: 1741-1750.
21. Amosova O, Smith A, Fresco JR (2011) The consensus sequence for self-catalyzed site-specific G residue depurination in DNA. J Biol Chem 286: 36316-36321.
22. Amosova O, Coulter R, Fresco JR (2006) Self-catalyzed site-specific depurination of guanine residues within gene sequences. Proc Natl Acad Sci 103: 4392-4397.
23. Fresco JR, Amosova O, Wei P, Alvarez-Dominguez JR, Glumcher D, et al. (2011) Site-Specific Self-Catalyzed DNA Depurination, the Basis of a Spontaneous Mutagenic Mechanism of Wide Evolutionary Significance. Evolutionary Biology-Concepts, Biodiversity, Macroevolution and Genome Evolution: Springer. 3-19.
24. Frederico LA, Kunkel TA, Shaw BR (1990) A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry-us 29: 2532-2537.
25. Hotokka M, Lönnberg H (1996) Hydrolysis of adenosine. A semiempirical and ab initio study. J Mol Struct 363: 191-201.
26. Rios-Font R, Rodríguez-Santiago L, Bertran J, Sodupe M (2007) Influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2'-deoxyguanosine. A theoretical study. J Phys Chem B 111: 6071-6077.
27. Cavalieri E, Saeed M, Zahid M, Cassada D, Snow D, et al. (2012) Mechanism of DNA depurination by carcinogens in relation to cancer initiation. Iubmb Life 64: 169-179.
28. Tsuboi M, Kyogoku Y, Shimanouchi T (1962) Infrared absorption spectra of protonated and deprotonated nucleosides. Biochim Biophys Acta 55: 1-12.
29. Gut IG (1997) Depurination of DNA and matrix-assisted laser desorption/ionization mass spectrometry. Int J Mass Spectrom 169: 313-322.
30. Baik M-H, Friesner RA, Lippard SJ (2002) Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination? J Am Chem Soc 124: 4495-4503.
31. Cavalieri E, Vauthier E, Cossé-Barbi A, Fliszár S (2000) The glycosyl C1'-N9 bond of deoxyadenosine and deoxyguanosine: response to electrophilic attacks on the purinic nitrogen atoms. Theor Chem Acc 104: 235-239.
32. Nelson DL, Lehninger AL, Cox MM (2008) Lehninger principles of biochemistry: Macmillan.
33. Neidle S (2010) Principles of nucleic acid structure: Academic Press.
34. Lyons JW, Kotin L (1965) The effect of magnesium ion on the secondary structure of deoxyribonucleic acid. J Am Chem Soc 87: 1781-1785.