Atomic Scissors: A New Method of Tracking the 5-Bromo-2′-Deoxyuridine-Labeled DNA In Situ

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Ligasová, Anna ^a,b   Strunin, Dmytro ^a,b   Liboska, Radek ^c   Rosenberg, Ivan ^c   Koberna, Karel ^a,b  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

^b INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

^c INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; BROXURIDINE; COPPER; DEOXYRIBOSE; DNA; HYDROGEN; MITOCHONDRIAL DNA; NUCLEIC ACID BASE; OXYGEN; RNA;

ARTICLE; ATOMIC SCISSORS; CELL NUCLEUS; CONTROLLED STUDY; DNA CLEAVAGE; DNA DETERMINATION; DNA REPLICATION; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; METHODOLOGY; MICROSCOPY; PROTEIN ANALYSIS; PROTEIN DENATURATION; PROTEIN DNA BINDING; RNA SYNTHESIS;

ANIMALS; ASCORBIC ACID; BROMODEOXYURIDINE; CELL NUCLEUS; COPPER SULFATE; DEOXYRIBONUCLEASE I; DNA CLEAVAGE; DNA REPLICATION; DNA, MITOCHONDRIAL; FLUORESCENT ANTIBODY TECHNIQUE, INDIRECT; HELA CELLS; HUMANS; OXIDATION-REDUCTION; OXYGEN; STAINING AND LABELING; SUPEROXIDE DISMUTASE; SUPEROXIDES;

EID: 84871565984     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052584     Document Type: Article

References (31)

1. Ageno M, Dore E, Frontali C, (1969) The alkaline denaturation of DNA. Biophys J 9: 1281-1311.
2. Dimitrova DS, Berezney R, (2002) The spatio-temporal organization of DNA replication sites is identical in primary, immortalized and transformed mammalian cells. J Cell Sci 115: 4037-4051.
3. Jackson DA, Pombo A, (1998) Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J Cell Biol 140: 1285-1295.
4. Kennedy BK, Barbie DA, Classon M, Dyson N, Harlow E, (2000) Nuclear organization of DNA replication in primary mammalian cells. Genes Dev 14: 2855-2868.
5. Stanojcic S, Lemaitre JM, Brodolin K, Danis E, Mechali M, (2008) In Xenopus egg extracts, DNA replication initiates preferentially at or near asymmetric AT sequences. Mol Cell Biol 28: 5265-5274.
6. Tkatchenko AV, (2006) Whole-mount BrdU staining of proliferating cells by DNase treatment: application to postnatal mammalian retina. Biotechniques 40: 29-30, 32.
7. Salic A, Mitchison TJ, (2008) A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc Natl Acad Sci U S A 105: 2415-2420.
8. Diermeier-Daucher S, Clarke ST, Hill D, Vollmann-Zwerenz A, Bradford JA, et al. (2009) Cell type specific applicability of 5-ethynyl-2′-deoxyuridine (EdU) for dynamic proliferation assessment in flow cytometry. Cytometry A 75: 535-546.
9. Meneni S, Ott I, Sergeant CD, Sniady A, Gust R, et al. (2007) 5-Alkynyl-2′-deoxyuridines: chromatography-free synthesis and cytotoxicity evaluation against human breast cancer cells. Bioorg Med Chem 15: 3082-3088.
10. Davis AF, Clayton DA, (1996) In situ localization of mitochondrial DNA replication in intact mammalian cells. J Cell Biol 135: 883-893.
11. Haines KM, Feldman EL, Lentz SI, Visualization of mitochondrial DNA replication in individual cells by EdU signal amplification. J Vis Exp.
12. Iborra FJ, Kimura H, Cook PR, (2004) The functional organization of mitochondrial genomes in human cells. BMC Biol 2: 9.
13. Koberna K, Stanek D, Malinsky J, Eltsov M, Pliss A, et al. (1999) Nuclear organization studied with the help of a hypotonic shift: its use permits hydrophilic molecules to enter into living cells. Chromosoma 108: 325-335.
14. Ligasova A, Raska I, Koberna K, (2009) Organization of human replicon: singles or zipping couples? J Struct Biol 165: 204-213.
15. Pogozelski WK, Tullius TD, (1998) Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety. Chem Rev 98: 1089-1108.
16. Drouin R, Rodriguez H, Gao SW, Gebreyes Z, O'Connor TR, et al. (1996) Cupric ion/ascorbate/hydrogen peroxide-induced DNA damage: DNA-bound copper ion primarily induces base modifications. Free Radic Biol Med 21: 261-273.
17. Lloyd DR, Phillips DH, (1999) Oxidative DNA damage mediated by copper(II), iron(II) and nickel(II) fenton reactions: evidence for site-specific mechanisms in the formation of double-strand breaks, 8-hydroxydeoxyguanosine and putative intrastrand cross-links. Mutat Res 424: 23-36.
18. Reed CJ, Douglas KT, (1989) Single-strand cleavage of DNA by Cu(II) and thiols: a powerful chemical DNA-cleaving system. Biochem Biophys Res Commun 162: 1111-1117.
19. Stoewe R, Prutz WA, (1987) Copper-catalyzed DNA damage by ascorbate and hydrogen peroxide: kinetics and yield. Free Radic Biol Med 3: 97-105.
20. Johnson GRA, Nazhat NB, Saadallanazhat RA, (1988) Reaction of the Aquacopper(I) Ion with Hydrogen-Peroxide- Evidence for a Cuiii (Cupryl) Intermediate. J Chem Soc, Faraday Trans 1 84: 501-510.
21. Masarwa M, Cohen H, Meyerstein D, Hickman DL, Bakac A, et al. (1988) Reactions of Low-Valent Transition-Metal Complexes with Hydrogen-Peroxide- Are They Fenton-Like or Not. 1. The Case of Cu+Aq and Cr-2+Aq. J Am Chem Soc 110: 4293-4297.
22. Sagripanti JL, Kraemer KH, (1989) Site-specific oxidative DNA damage at polyguanosines produced by copper plus hydrogen peroxide. J Biol Chem 264: 1729-1734.
23. Yamamoto K, Kawanishi S, (1989) Hydroxyl free radical is not the main active species in site-specific DNA damage induced by copper (II) ion and hydrogen peroxide. J Biol Chem 264: 15435-15440.
24. Aruoma OI, Halliwell B, Gajewski E, Dizdaroglu M, (1991) Copper-ion-dependent damage to the bases in DNA in the presence of hydrogen peroxide. Biochem J 273 (Pt 3) (): 601-604.
25. Burrows CJ, Muller JG, (1998) Oxidative Nucleobase Modifications Leading to Strand Scission. Chem Rev 98: 1109-1152.
26. Sporbert A, Gahl A, Ankerhold R, Leonhardt H, Cardoso MC, (2002) DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters. Mol Cell 10: 1355-1365.
27. Ligasová A, Koberna K, (2010) In situ reverse transcription: the magic of strength and anonymity. Nucleic Acids Res 38: e167.
28. Sirbu BM, Couch FB, Feigerle JT, Bhaskara S, Hiebert SW, et al. (2011) Analysis of protein dynamics at active, stalled, and collapsed replication forks. Genes Dev 25: 1320-1327.
29. Rush JD, Koppenol WH, (1988) Reactions of FeIInta and FeIIedda with hydrogen peroxide. J Am Chem Soc 110: 4957-4963.
30. Sawyer DT, Kang C, Llobet A, Redman C, (1993) Fenton Reagents (1:1 FeIILx/HOOH) React via [LxFeIIOOH(BH+)] (1) as Hydroxylases (Rh→ROH), not as Generators of Free Hydroxyl Radicals (HO). J Am Chem Soc 115: 5817-5818.
31. Yamazaki I, Piette LH, (1991) EPR spin-trapping study on the oxidizing species fomed in reaction of the ferrous ion with hydrogen peroxide. J Am Chem Soc 113: 7588-7593.