Fig. 1.

Excision products and XR-seq libraries. (A) Detection of the excised oligonucleotides from kidney and liver of mice administered cisplatin at 10 mg/kg. Mice were killed 2 h after cisplatin injection at ZT02. Kidney and liver nuclei were isolated, lysed gently, and TFIIH was immunoprecipitated with anti-p89 and anti-p62 antibodies, which bring down the primary excision products tightly bound to TFIIH (11, 12). The excision products were further purified with anti–Pt-DNA (cisplatin) antibodies. A small fraction of the purified DNA was 3′ labeled with ³²P-cordycepin and analyzed on a sequencing gel, along with 17- and 24-nt-long size markers. The 50-mer was included in the labeling reactions as an internal control to measure labeling and recovery efficiency. (B) Analysis of dsDNA libraries generated from the excised oligomers at ZT04. The purified excised oligomers were treated with NaCN where indicated to reverse the Pt adduct and then subjected to the indicated PCR cycles and separated on a polyacrylamide gel (12).