|
1
|
Cadet J and Wagner JR: DNA base damage by
reactive oxygen species, oxidizing agents, and UV radiation. Cold
Spring Harb Perspect Biol. 5:a0125592013. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Li Z, Pearlman AH and Hsieh P: DNA
mismatch repair and the DNA damage response. DNA Repair (Amst).
38:94–101. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Altaf M, Saksouk N and Côté J: Histone
modifications in response to DNA damage. Mutat Res. 618:81–90.
2007. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Lord CJ and Ashworth A: The DNA damage
response and cancer therapy. Nature. 481:287–294. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Cao LL, Shen C and Zhu WG: Histone
modifications in DNA damage response. Sci China Life Sci.
59:257–270. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Schipler A and Iliakis G: DNA
double-strand-break complexity levels and their possible
contributions to the probability for error-prone processing and
repair pathway choice. Nucleic Acids Res. 41:7589–7605. 2013.
View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Grimaldi KA, McGurk CJ, McHugh PJ and
Hartley JA: PCR-based methods for detecting DNA damage and its
repair at the sub-gene and single nucleotide levels in cells. Mol
Biotechnol. 20:181–196. 2002. View Article : Google Scholar : PubMed/NCBI
|
|
8
|
Osborne DJ: Technologies for detection of
DNA damage and mutations. Endeavour. 21:178–179. 1997. View Article : Google Scholar
|
|
9
|
Furda A, Santos JH, Meyer JN and van
Houten B: Quantitative PCR-based measurement of nuclear and
mitochondrial DNA damage and repair in mammalian cellsMolecular
Toxicology Protocols. Keohavong P and Grant GS: Humana Press;
Totowa, NJ: pp. 419–437. 2014, View Article : Google Scholar
|
|
10
|
Senoo T, Yamanaka M, Nakamura A, Terashita
T, Kawano S and Ikeda S: Quantitative PCR for detection of DNA
damage in mitochondrial DNA of the fission yeast
Schizosaccharomyces pombe. J Microbiol Methods. 127:77–81. 2016.
View Article : Google Scholar : PubMed/NCBI
|
|
11
|
De Boer JG and Glickman BW: Mutations
recovered in the Chinese hamster aprt gene after exposure to
carboplatin: A comparison with cisplatin. Carcinogenesis. 13:15–17.
1992. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Van Houten B, Cheng S and Chen Y:
Measuring gene-specific nucleotide excision repair in human cells
using quantitative amplification of long targets from nanogram
quantities of DNA. Mutat Res. 460:81–94. 2000. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Strauss EC and Orkin SH: Guanine-adenine
ligation-mediated PCR in vivo footprinting. Methods. 11:164–170.
1997. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Pfeifer GP and Tornaletti S: Footprinting
with UV irradiation and LMPCR. Methods. 11:189–196. 1997.
View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Pfeifer GP, Chen HH, Komura J and Riggs
AD: Chromatin structure analysis by ligation-mediated and terminal
transferase-mediated polymerase chain reaction. Methods Enzymol.
304:548–571. 1999. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Chang L, Li J and Wang L: Immuno-PCR: An
ultrasensitive immunoassay for biomolecular detection. Anal Chim
Acta. 910:12–24. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Karakoula A, Evans MD, Podmore ID,
Hutchinson PE, Lunec J and Cooke MS: Quantification of UVR-induced
DNA damage: Global-versus gene-specific levels of thymine dimers. J
Immunol Methods. 277:27–37. 2003. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Wang G, Hallberg LM and Englander EW:
Rapid SINE-mediated detection of cisplatin: DNA adduct formation in
vitro and in vivo in blood. Mutat Res. 434:67–74. 1999. View Article : Google Scholar : PubMed/NCBI
|
|
19
|
Wang G, Hallberg LM, Saphier E and
Englander EW: Short interspersed DNA element-mediated detection of
UVB-induced DNA damage and repair in the mouse genome, in vitro,
and in vivo in skin. Mutat Res. 433:147–157. 1999. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Featherstone C and Jackson SP: Ku, a DNA
repair protein with multiple cellular functions? Mutat Res.
434:3–15. 1999. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Jones JM, Gellert M and Yang W: A Ku
bridge over broken DNA. Structure. 9:881–884. 2001. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Gullo C, Au M, Feng G and Teoh G: The
biology of Ku and its potential oncogenic role in cancer. Biochim
Biophys Acta. 1765:223–234. 2006.PubMed/NCBI
|
|
23
|
Doherty AJ and Jackson SP: DNA repair: How
Ku makes ends meet. Curr Biol. 11:R920–R924. 2001. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
Walker JR, Corpina RA and Goldberg J:
Structure of the Ku heterodimer bound to DNA and its implications
for double-strand break repair. Nature. 412:607–614. 2001.
View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Paull TT, Rogakou EP, Yamazaki V,
Kirchgessner CU, Gellert M and Bonner WM: A critical role for
histone H2AX in recruitment of repair factors to nuclear foci after
DNA damage. Curr Biol. 10:886–895. 2000. View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Rogakou EP, Boon C, Redon C and Bonner WM:
Megabase chromatin domains involved in DNA double-strand breaks in
vivo. J Cell Biol. 146:905–916. 1999. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Henderson DS: DNA repair protocolsMethods
in Molecular Biology. 2nd. Humana Press; New Jersey, NJ: pp.
4982006
|
|
28
|
Levy N, Martz A, Bresson A, Spenlehauer C,
De Murcia G and Ménissier-De Murcia J: Xrcc1 is phosphorylated by
DNA-dependent protein kinase in response to DNA damage. Nucleic
Acids Res. 34:32–41. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Caldecott KW: Protein-protein interactions
during mammalian DNA single-strand break repair. Biochem Soc Trans.
31:247–251. 2003. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Brem R and Hall J: XRCC1 is required for
DNA single-strand break repair in human cells. Nucleic Acids Res.
33:2512–2520. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Goode EL, Ulrich CM and Potter JD:
Polymorphisms in DNA repair genes and associations with cancer
risk. Cancer Epidemiol Biomarkers Prev. 11:1513–1530.
2002.PubMed/NCBI
|
|
32
|
Strom CE, Mortusewicz O, Finch D, Parsons
JL, Lagerqvist A, Johansson F, Schultz N, Erixon K, Dianov GL and
Helleday T: CK2 phosphorylation of XRCC1 facilitates dissociation
from DNA and single-strand break formation during base excision
repair. DNA Repair (Amst). 10:961–969. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Caldecott KW: XRCC1 and DNA strand break
repair. DNA Repair (Amst). 2:955–969. 2003. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Collins AR: The comet assay for DNA damage
and repair: Principles, applications, and limitations. Mol
Biotechnol. 26:249–261. 2004. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Collins AR: Measuring oxidative damage to
DNA and its repair with the comet assay. Biochim Biophys Acta.
1840:794–800. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Collins AR and Azqueta A: DNA repair as a
biomarker in human biomonitoring studies; further applications of
the comet assay. Mutat Res. 736:122–129. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Kent CR, Eady JJ, Ross GM and Steel GG:
The comet moment as a measure of DNA damage in the comet assay. Int
J Radiat Biol. 67:655–660. 1995. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Jyoti S, Khan S, Naz F, Ali Rahul F and
Siddique YH: Assessment of DNA damage by panmasala, gutkha chewing
and smoking in buccal epithelial cells using alkaline single cell
gel electrophoresis (SCGE). Egyptian J Med Human Gen. 14:391–394.
2013. View Article : Google Scholar
|
|
39
|
Ostling O and Johanson KJ:
Microelectrophoretic study of radiation-induced DNA damages in
individual mammalian cells. Biochem Biophys Res Commun.
123:291–298. 1984. View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Glei M, Hovhannisyan G and Pool-Zobel BL:
Use of comet-FISH in the study of DNA damage and repair: Review.
Mutat Res. 681:33–43. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Collins AR, Dobson VL, Dušinská M, Kennedy
G and Štětina R: The comet assay: What can it really tell us? Mutat
Res. 375:183–193. 1997. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Rojas E, Lopez MC and Valverde M: Single
cell gel electrophoresis assay: Methodology and applications. J
Chromatogr B Biomed Sci Appl. 722:225–254. 1999. View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Angelis KJ, Dusinská M and Collins AR:
Single cell gel electrophoresis: Detection of DNA damage at
different levels of sensitivity. Electrophoresis. 20:2133–2138.
1999. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Collins AR and Azqueta A: Chapter
4-single-cell gel electrophoresis combined with lesion-specific
enzymes to measure oxidative damage to DNAMethods in Cell Biology.
Conn PM: Academic Press; Burlington, MA: pp. 69–92. 2012,
View Article : Google Scholar
|
|
45
|
Kumari S, Rastogi R, Singh K, Singh S and
Sinha R: DNA damage: Detection strategies. EXCLI J. 7:44–62.
2008.
|
|
46
|
Roti Roti JL and Wright WD: Visualization
of DNA loops in nucleoids from HeLa cells: Assays for DNA damage
and repair. Cytometry. 8:461–467. 1987. View Article : Google Scholar : PubMed/NCBI
|
|
47
|
Gavrieli Y, Sherman Y and Ben-Sasson SA:
Identification of programmed cell death in situ via specific
labeling of nuclear DNA fragmentation. J Cell Biol. 119:493–501.
1992. View Article : Google Scholar : PubMed/NCBI
|
|
48
|
Walker PR, Carson C, Leblanc J and
Sikorska M: Labeling DNA damage with terminal transferase, in in
situ detection of DNA damageMethods and Protocols. Didenko VV:
Humana Press; Totowa, NJ: pp. 3–19. 2002
|
|
49
|
Loo DT: TUNEL assay. An overview of
techniques. Methods Mol Biol. 203:21–30. 2002.PubMed/NCBI
|
|
50
|
Kanoh M, Takemura G, Misao J, Hayakawa Y,
Aoyama T, Nishigaki K, Noda T, Fujiwara T, Fukuda K, Minatoguchi S
and Fujiwara H: Significance of myocytes with positive DNA in situ
nick end-labeling (TUNEL) in hearts with dilated cardiomyopathy:
Not apoptosis but DNA repair. Circulation. 99:2757–2764. 1999.
View Article : Google Scholar : PubMed/NCBI
|
|
51
|
Otsuki Y and Ito Y: Quantitative
differentiation of both free 3′ oh and 5′ oh DNA ends using
terminal transferase-based labeling combined with transmission
electron microscopy, in in situ detection of DNA damageMethods and
Protocols. Didenko VV: Humana Press; Totowa, NJ: pp. 41–54.
2002
|
|
52
|
Didenko VV and Hornsby PJ: Presence of
double-strand breaks with single-base 3′ overhangs in cells
undergoing apoptosis but not necrosis. J Cell Biol. 135:1369–1376.
1996. View Article : Google Scholar : PubMed/NCBI
|
|
53
|
Didenko VV: Detection of specific
double-strand DNA breaks and apoptosis in situ using T4 DNA ligase.
Methods Mol Biol. 203:143–151. 2002.PubMed/NCBI
|
|
54
|
Levsky JM and Singer RH: Fluorescence in
situ hybridization: Past, present and future. J Cell Sci.
116:2833–2838. 2003. View Article : Google Scholar : PubMed/NCBI
|
|
55
|
Gall JG and Pardue ML: Formation and
detection of RNA-DNA hybrid molecules in cytological preparations.
Proc Natl Acad Sci USA. 63:378–383. 1969. View Article : Google Scholar : PubMed/NCBI
|
|
56
|
Halling KC and Kipp BR: Fluorescence in
situ hybridization in diagnostic cytology. Hum Pathol.
38:1137–1144. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
57
|
Cortés-Gutiérrez EI, Fernández JL,
Dávila-Rodríguez MI, López-Fernández C and Gosálvez J: Use of
DBD-FISH for the study of cervical cancer progression, in cervical
cancerMethods and Protocols. Keppler D and Lin WA: Springer; New
York, NY: pp. 291–301. 2015
|
|
58
|
Fernández JL, Vázquez-Gundín F, Rivero MT,
Genescá A, Gosálvez J and Goyanes V: DBD-fish on neutral comets:
Simultaneous analysis of DNA single- and double-strand breaks in
individual cells. Exp Cell Res. 270:102–109. 2001. View Article : Google Scholar : PubMed/NCBI
|
|
59
|
Fink SL and Cookson BT: Apoptosis,
pyroptosis, and necrosis: Mechanistic description of dead and dying
eukaryotic cells. Infect Immun. 73:1907–1916. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
60
|
Basiji D and O'Gorman MR: Imaging flow
cytometry. J Immunol Methods. 423:1–2. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
61
|
Muehlbauer PA and Schuler MJ: Detection of
numerical chromosomal aberrations by flow cytometry: A novel
process for identifying aneugenic agents. Mutat Res. 585:156–169.
2005. View Article : Google Scholar : PubMed/NCBI
|
|
62
|
Henry CM, Hollville E and Martin SJ:
Measuring apoptosis by microscopy and flow cytometry. Methods.
61:90–97. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
63
|
Huerta S, Goulet EJ, Huerta-Yepez S and
Livingston EH: Screening and detection of apoptosis. J Surg Res.
139:143–156. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
64
|
Vermes I, Haanen C, Steffens-Nakken H and
Reutelingsperger C: A novel assay for apoptosis. Flow cytometric
detection of phosphatidylserine expression on early apoptotic cells
using fluorescein labelled Annexin V. J Immunol Methods. 184:39–51.
1995. View Article : Google Scholar : PubMed/NCBI
|
|
65
|
Pietkiewicz S, Schmidt JH and Lavrik IN:
Quantification of apoptosis and necroptosis at the single cell
level by a combination of imaging flow cytometry with classical
Annexin V/propidium iodide staining. J Immunol Methods. 423:99–103.
2015. View Article : Google Scholar : PubMed/NCBI
|
|
66
|
Berton TR and Mitchell DL: Quantification
of DNA photoproducts in mammalian cell DNA using radioimmunoassay.
Methods Mol Biol. 920:177–187. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
67
|
Santella RM: Immunological methods for
detection of carcinogen-DNA damage in humans. Cancer Epidemiol
Biomarkers Prev. 8:733–739. 1999.PubMed/NCBI
|
|
68
|
Yatabe Y: ALK FISH and IHC: You cannot
have one without the other. J Thorac Oncol. 10:548–550. 2015.
View Article : Google Scholar : PubMed/NCBI
|
|
69
|
Kriste AG, Martincigh BS and Salter LF: A
sensitive immunoassay technique for thymine dimer quantitation in
UV-irradiated DNA. J Photochem Photobiol A: Chemistry. 93:185–192.
1996. View Article : Google Scholar
|
|
70
|
El-Yazbi AF and Loppnow GR: Detecting
UV-induced nucleic-acid damage. TrAC Trends Analytical Chemistry.
61:83–91. 2014. View Article : Google Scholar
|
|
71
|
Toyokuni S: Oxidative stress as an iceberg
in carcinogenesis and cancer biology. Arch Biochem Biophys.
595:46–49. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
72
|
Rindgen D, Turesky RJ and Vouros P:
Determination of in vitro formed DNA adducts of
2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine using capillary
liquid chromatography/electrospray ionization/tandem mass
spectrometry. Chem Res Toxicol. 8:1005–1013. 1995. View Article : Google Scholar : PubMed/NCBI
|
|
73
|
Mullins EA, Rubinson EH, Pereira KN,
Calcutt MW, Christov PP and Eichman BF: An HPLC-tandem mass
spectrometry method for simultaneous detection of alkylated base
excision repair products. Methods. 64:59–66. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
74
|
Caldecott KW: DNA single-strand break
repair. Exp Cell Res. 329:2–8. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
75
|
Cadet J, Douki T, Frelon S, Sauvaigo S,
Pouget JP and Ravanat JL: Assessment of oxidative base damage to
isolated and cellular DNA by HPLC-MS/MS measurement. Free Radic
Biol Med. 33:441–449. 2002. View Article : Google Scholar : PubMed/NCBI
|
|
76
|
Pouget JP, Douki T, Richard MJ and Cadet
J: DNA damage induced in cells by gamma and UVA radiation as
measured by HPLC/GC-MS and HPLC-EC and comet assay. Chem Res
Toxicol. 13:541–549. 2000. View Article : Google Scholar : PubMed/NCBI
|
|
77
|
Gowda GA and Djukovic D: Overview of mass
spectrometry-based metabolomics: Opportunities and challenges.
Methods Mol Biol. 1198:3–12. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
78
|
Dizdaroglu M, Coskun E and Jaruga P:
Measurement of oxidatively induced DNA damage and its repair, by
mass spectrometric techniques. Free Radic Res. 49:525–548. 2015.
View Article : Google Scholar : PubMed/NCBI
|
|
79
|
Sato K and Greenberg MM: Selective
detection of 2-deoxyribonolactone in DNA. J Am Chem Soc.
127:2806–2807. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
80
|
Dizdaroglu M: Substrate specificities and
excision kinetics of DNA glycosylases involved in base-excision
repair of oxidative DNA damage. Mutat Res. 531:109–126. 2003.
View Article : Google Scholar : PubMed/NCBI
|
|
81
|
Reddy PT, Jaruga P, Nelson BC, Lowenthal M
and Dizdaroglu M: Stable isotope-labeling of DNA repair proteins
and their purification, and characterization. Protein Expr Purif.
78:94–101. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
82
|
Gajewski E and Dizdaroglu M: Hydroxyl
radical induced cross-linking of cytosine and tyrosine in
nucleohistone. Biochemistry. 29:977–980. 1990. View Article : Google Scholar : PubMed/NCBI
|
|
83
|
Koivisto P and Peltonen K: Analytical
methods in DNA and protein adduct analysis. Anal Bioanal Chem.
398:2563–2572. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
84
|
Dizdaroglu M and Gajewski E: Structure and
mechanism of hydroxyl radical-induced formation of a DNA-protein
cross-link involving thymine and lysine in nucleohistone. Cancer
Res. 49:3463–3467. 1989.PubMed/NCBI
|
|
85
|
Fojta M, Daňhel A, Havran L and Vyskočil
V: Recent progress in electrochemical sensors and assays for DNA
damage and repair. TrAC Trends Analytical Chemistry. 79:160–167.
2016. View Article : Google Scholar
|
|
86
|
Boal AK and Barton JK: Electrochemical
detection of lesions in DNA. Bioconjug Chem. 16:312–321. 2005.
View Article : Google Scholar : PubMed/NCBI
|
|
87
|
Boon EM, Ceres DM, Drummond TG, Hill MG
and Barton JK: Mutation detection by electrocatalysis at
DNA-modified electrodes. Nat Biotechnol. 18:1096–1100. 2000.
View Article : Google Scholar : PubMed/NCBI
|