Quantification of RNA damage by reverse transcription polymerase chain reactions

Analytical Biochemistry

Volumn 357, Issue 1, 2006, Pages 58-67

  Gong, Xin ^a   Tao, Rui ^a   Li, Zhongwei ^a  

^a FLORIDA ATLANTIC UNIVERSITY   (United States)

Author keywords

Oxidative stress; PCR; Reverse transcription; RNA damage

Indexed keywords

DAMAGE DETECTION; ESCHERICHIA COLI; OXIDATIVE STRESS; RNA;

CONTROL CULTURES; GEL-BASED; HIGH SENSITIVITY; MODIFYING AGENTS; REAL-TIME PCR; REVERSE TRANSCRIPTION; REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION; RNA FUNCTIONS;

POLYMERASE CHAIN REACTION;

COMPLEMENTARY DNA; RNA 16S;

ALZHEIMER DISEASE; ANALYTIC METHOD; ARTICLE; DEGENERATIVE DISEASE; DNA DAMAGE; DNA TEMPLATE; GEL ELECTROPHORESIS; OXIDATIVE STRESS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA DAMAGE; STEADY STATE;

ESCHERICHIA COLI;

EID: 33748312314     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.06.025     Document Type: Article

References (44)

1. Beckman K.B., and Ames B.N. The free radical theory of aging matures. Physiol. Rev. 78 (1998) 547-581
2. Bohr V.A. DNA damage and its processing: relation to human disease. J. Inherit. Metab. Dis. 25 (2002) 215-222
3. Moreira P.I., Smith M.A., Zhu X., Nunomura A., Castellani R.J., and Perry G. Oxidative stress and neurodegeneration. Ann. N.Y. Acad. Sci. 1043 (2005) 545-552
4. Ungvari Z., Gupte S.A., Recchia F.A., Batkai S., and Pacher P. Role of oxidative-nitrosative stress and downstream pathways in various forms of cardiomyopathy and heart failure. Curr. Vasc. Pharmacol. 3 (2005) 221-229
5. Kang D., and Hamasaki N. Alterations of mitochondrial DNA in common diseases and disease states: aging, neurodegeneration, heart failure, diabetes, and cancer. Curr. Med. Chem. 12 (2005) 429-441
6. Fiala E.S., Conaway C.C., and Mathis J.E. Oxidative DNA and RNA damage in the livers of Sprague-Dawley rats treated with the hepatocarcinogen 2-nitropropane. Cancer Res. 49 (1989) 5518-5522
7. Wamer W.G., Yin J.J., and Wei R.R. Oxidative damage to nucleic acids photosensitized by titanium dioxide. Free Radic. Biol. Med. 23 (1997) 851-858
8. Shen Z., Wu W., and Hazen S.L. Activated leukocytes oxidatively damage DNA, RNA, and the nucleotide pool through halide-dependent formation of hydroxyl radical. Biochemistry 39 (2000) 5474-5482
9. Hofer T., Badouard C., Bajak E., Ravanat J.L., Mattsson A., and Cotgreave I.A. Hydrogen peroxide causes greater oxidation in cellular RNA than in DNA. Biol. Chem. 386 (2005) 333-337
10. Shan X., and Lin C.L. Quantification of oxidized RNAs in Alzheimer's disease. Neurobiol. Aging 27 (2005) 657-662
11. Bellacosa A., and Moss E.G. RNA repair: damage control. Curr. Biol. 13 (2003) R482-R484
12. Nunomura A., Perry G., Pappolla M.A., Wade R., Hirai K., Chiba S., and Smith M.A. RNA oxidation is a prominent feature of vulnerable neurons in Alzheimer's disease. J. Neurosci. 19 (1999) 1959-1964
13. Nunomura A., Perry G., Hirai K., Aliev G., Takeda A., Chiba S., and Smith M.A. Neuronal RNA oxidation in Alzheimer's disease and Down's syndrome. Ann. N.Y. Acad. Sci. 893 (1999) 362-364
14. Abe T., Tohgi H., Isobe C., Murata T., and Sato C. Remarkable increase in the concentration of 8-hydroxyguanosine in cerebrospinal fluid from patients with Alzheimer's disease. J. Neurosci. Res. 70 (2002) 447-450
15. Zhang J., Perry G., Smith M.A., Robertson D., Olson S.J., Graham D.G., and Montine T.J. Parkinson's disease is associated with oxidative damage to cytoplasmic DNA and RNA in substantia nigra neurons. Am. J. Pathol. 154 (1999) 1423-1429
16. Nunomura A., Chiba S., Kosaka K., Takeda A., Castellani R.J., Smith M.A., and Perry G. Neuronal RNA oxidation is a prominent feature of dementia with Lewy bodies. Neuroreport 13 (2002) 2035-2039
17. Tateyama M., Takeda A., Onodera Y., Matsuzaki M., Hasegawa T., Nunomura A., Hirai K., Perry G., Smith M.A., and Itoyama Y. Oxidative stress and predominant Aβ42(43) deposition in myopathies with rimmed vacuoles. Acta Neuropathol. (Berl.) 105 (2003) 581-585
18. Martinet W., de Meyer G.R., Herman A.G., and Kockx M.M. Reactive oxygen species induce RNA damage in human atherosclerosis. Eur. J. Clin. Invest. 34 (2004) 323-327
19. Liu J., Head E., Gharib A.M., Yuan W., Ingersoll R.T., Hagen T.M., Cotman C.W., and Ames B.N. Memory loss in old rats is associated with brain mitochondrial decay and RNA/DNA oxidation: partial reversal by feeding acetyl-l-carnitine and/or R-α-lipoic acid. Proc. Natl. Acad. Sci. USA 99 (2002) 2356-2361
20. Ding Q., Markesbery W.R., Chen Q., Li F., and Keller J.N. Ribosome dysfunction is an early event in Alzheimer's disease. J. Neurosci. 25 (2005) 9171-9175
21. Shan X., Tashiro H., and Lin C.L. The identification and characterization of oxidized RNAs in Alzheimer's disease. J. Neurosci. 23 (2003) 4913-4921
22. Demple B., and Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu. Rev. Biochem. 63 (1994) 915-948
23. Poulsen H.E. Oxidative DNA modifications. Exp. Toxicol. Pathol. 57 Suppl. 1 (2005) 161-169
24. Kasai H., Crain P.F., Kuchino Y., Nishimura S., Ootsuyama A., and Tanooka H. Formation of 8-hydroxyguanine moiety in cellular DNA by agents producing oxygen radicals and evidence for its repair. Carcinogenesis 7 (1986) 1849-1851
25. Ames B.N., and Gold L.S. Endogenous mutagens and the causes of aging and cancer. Mutat. Res. 250 (1991) 3-16
26. Bessho T., Tano K., Kasai H., and Nishimura S. Deficiency of 8-hydroxyguanine DNA endonuclease activity and accumulation of the 8-hydroxyguanine in mutator mutant (mutM) of Escherichia coli. Biochem. Biophys. Res. Commun. 188 (1992) 372-378
27. Wood M.L., Dizdaroglu M., Gajewski E., and Essigmann J.M. Mechanistic studies of ionizing radiation and oxidative mutagenesis: genetic effects of a single 8-hydroxyguanine (7-hydro-8-oxoguanine) residue inserted at a unique site in a viral genome. Biochemistry 29 (1990) 7024-7032
28. Moriya M., Ou C., Bodepudi V., Johnson F., Takeshita M., and Grollman A.P. Site-specific mutagenesis using a gapped duplex vector: a study of translesion synthesis past 8-oxodeoxyguanosine in E. coli. Mutat. Res. 254 (1991) 281-288
29. Shibutani S., Takeshita M., and Grollman A.P. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxo-dG. Nature 349 (1991) 431-434
30. Cheng K.C., Cahill D.S., Kasai H., Nishimura S., and Loeb L.A. 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions. J. Biol. Chem. 267 (1992) 166-172
31. Furge L.L., and Guengerich F.P. Analysis of nucleotide insertion and extension at 8-oxo-7,8-dihydroguanine by replicative T7 polymerase exo- and human immunodeficiency virus-1 reverse transcriptase using steady-state and pre-steady-state kinetics. Biochemistry 36 (1997) 6475-6487
32. Taddei F., Hayakawa H., Bouton M., Cirinesi A., Matic I., Sekiguchi M., and Radman M. Counteraction by MutT protein of transcriptional errors caused by oxidative damage. Science 278 (1997) 128-130
33. Kim S.K., Lee S.H., Kwon O.S., and Moon B.J. DNA · RNA heteroduplex containing 8-oxo-7,8-dihydroguanosine: base pairing, structures, and thermodynamic stability. J. Biochem. Mol. Biol. 37 (2004) 657-662
34. Rhee Y., Valentine M.R., and Termini J. Oxidative base damage in RNA detected by reverse transcriptase. Nucleic Acids Res. 23 (1995) 3275-3282
35. de Souza-Pinto N.C., and Bohr V.A. The mitochondrial theory of aging: involvement of mitochondrial DNA damage and repair. Int. Rev. Neurobiol. 53 (2002) 519-534
36. Santos J.H., Mandavilli B.S., and Van Houten B. Measuring oxidative mtDNA damage and repair using quantitative PCR. Methods Mol. Biol. 197 (2002) 159-176
37. Zhang Z.W., and Heng Z.C. Randomized terminal linker-dependent PCR: a versatile and sensitive method for detection of DNA damage. Biomed. Environ. Sci. 15 (2002) 203-208
38. Cheng Z.F., Zuo Y., Li Z., Rudd K.E., and Deutscher M.P. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273 (1998) 14077-14080
39. Mo J., Maki H., and Sekiguchi M. Hydrolytic elimination of a mutagenic nucleotide, 8-oxo-dGTP, by human 18-kilodalton protein: sanitization of nucleotide pool. Proc. Natl. Acad. Sci. USA 89 (1992) 11021-11025
40. John G.St., Brot N., Ruan J., Erdjument-Bromage H., Tempst P., Weissbach H., and Nathan C. Peptide methionine sulfoxide reductase from Escherichia coli and Mycobacterium tuberculosis protects bacteria against oxidative damage from reactive nitrogen intermediates. Proc. Natl. Acad. Sci. USA 98 (2001) 9901-9906
41. Zheng M., Wang X., Templeton L.J., Smulski D.R., LaRossa R.A., and Storz G. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J. Bacteriol. 183 (2001) 4562-4570
42. Deutscher M.P. Degradation of stable RNA in bacteria. J. Biol. Chem. 278 (2003) 45041-45044
43. Bebenek K., Boyer J.C., and Kunkel T.A. The base substitution fidelity of HIV-1 reverse transcriptase on DNA and RNA templates probed with 8-oxo-deoxyguanosine triphosphate. Mutat. Res. 429 (1999) 149-158
44. Eberding A., Rehaume V., and Lee C.H. Detection of mRNA degradation intermediates in tissues using the 3′-end poly(A)-tailing polymerase chain reaction method. Anal. Biochem. 335 (2004) 58-65