Fluorescent probes for the analysis of DNA strand scission in base excision repair.
We have developed fluorescent probes for the detection of strand scission in the excision repair of oxidatively damaged bases. They were hairpin-shaped oligonucleotides, each containing an isomer of thymine glycol or 5,6-dihydrothymine as a damaged base in the center, with a fluorophore and a quencher at the 5'- and 3'-ends, respectively. Fluorescence was detected when the phosphodiester linkage at the damage site was cleaved by the enzyme, because the short fragment bearing the fluorophore could not remain in a duplex form hybridized to the rest of the molecule at the incubation temperature. The substrate specificities of Escherichia coli endonuclease III and its human homolog, NTH1, determined by using these probes agreed with those determined previously by gel electrophoresis using (32)P-labeled substrates. Kinetic parameters have also been determined by this method. Since different fluorophores were attached to the oligonucleotides containing each lesion, reactions with two types of substrates were analyzed separately in a single tube, by changing the excitation and detection wavelengths. These probes were degraded during an incubation with a cell extract. Therefore, phosphorothioate linkages were incorporated to protect the probes from nonspecific nucleases, and the base excision repair activity was successfully detected in HeLa cells.
Matsumoto
Naoyuki
N
Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
Toga
Tatsuya
T
Hayashi
Ryosuke
R
Sugasawa
Kaoru
K
Katayanagi
Katsuo
K
Ide
Hiroshi
H
Kuraoka
Isao
I
Iwai
Shigenori
S
D053837:DNA Cleavage; D004249:DNA Damage; D004260:DNA Repair; D043224:Deoxyribonuclease (Pyrimidine Dimer) / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000737:chemistry*; D006367:HeLa Cells; D006801:Humans; D015345:Oligonucleotide Probes / Q000737:chemistry*; D054735:Phosphorothioate Oligonucleotides / Q000737:chemistry; D013379:Substrate Specificity
D029968:Escherichia coli Proteins; D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D054735:Phosphorothioate Oligonucleotides; D043224:Deoxyribonuclease (Pyrimidine Dimer); C106403:NTH protein, E coli; C468347:NTHL1 protein, human