Human APE1 and uracil-DNA glycosylase were purified to homogeneity as described previously (43 (link),44 (link)). E.coli endonuclease III and endonuclease IV were obtained from Trevigen. E.coli exonuclease III and BamHI restriction endonuclease were obtained from New England Biolabs. Topoisomerase I was obtained from Promega. Whole cell extracts were prepared by a method as described previously (45 (link)). Protein concentration was determined using the BioRad Coomassie blue assay with bovine serum albumin (BSA) as a standard.
MMS, 5-hydroxymethyl-2′-deoxyuridine (hmdUrd), camptothecin and mechlorethamine hydrochloride (nitrogen mustard) were all purchased from Sigma-Aldrich. Temozolomide was a gift from Prof. Malcolm Stevens, University of Nottingham, UK. Stock solutions of potential APE1 inhibitors and camptothecin were dissolved in DMSO. MMS, hmdUrd, temozolomide and mechlorethamine hydrochloride were dissolved in phosphate buffered saline (PBS).
The oligonucleotides; 5′-F-GCCCCCXGGGGACGTACGATATCCCGCTCC-3′ and 3′-Q-CGGGGGCCCCCTGCATGCTATAGGGCGAGG-5′ (where F is Fluorescein, Q is Dabcyl and X is Terahydrofuran, an abasic site analog) were custom-made by Eurogentec Ltd. A uracil-containing 18mer oligonucleotide 5′-CTCGCAAGUGGGTACCGA-3′ and its complementary oligonucleotide, 5′-TCGGTACCCGCTTGCGAG-3′ were synthesized by the Cancer Research UK central services laboratory (Clare Hall, UK). The 3′-phosphoglycolate (PG) substrate (5′-CAATAGAGTAACACGGpg-3′) was synthesized by Eurogentec using the method of Urata and Akagi (46 ), in which the 3′-phosphoglyceryl residue is oxidized sequentially by sodium periodate (NaIO4) and sodium chlorite (NaClO2). This oligonucleotide, which has been characterized previously (16 (link)), was purified by high-performance liquid chromatography (HPLC) and the presence of 3′-PG was confirmed by mass spectrometry.
MMS, 5-hydroxymethyl-2′-deoxyuridine (hmdUrd), camptothecin and mechlorethamine hydrochloride (nitrogen mustard) were all purchased from Sigma-Aldrich. Temozolomide was a gift from Prof. Malcolm Stevens, University of Nottingham, UK. Stock solutions of potential APE1 inhibitors and camptothecin were dissolved in DMSO. MMS, hmdUrd, temozolomide and mechlorethamine hydrochloride were dissolved in phosphate buffered saline (PBS).
The oligonucleotides; 5′-F-GCCCCCXGGGGACGTACGATATCCCGCTCC-3′ and 3′-Q-CGGGGGCCCCCTGCATGCTATAGGGCGAGG-5′ (where F is Fluorescein, Q is Dabcyl and X is Terahydrofuran, an abasic site analog) were custom-made by Eurogentec Ltd. A uracil-containing 18mer oligonucleotide 5′-CTCGCAAGUGGGTACCGA-3′ and its complementary oligonucleotide, 5′-TCGGTACCCGCTTGCGAG-3′ were synthesized by the Cancer Research UK central services laboratory (Clare Hall, UK). The 3′-phosphoglycolate (PG) substrate (5′-CAATAGAGTAACACGGpg-3′) was synthesized by Eurogentec using the method of Urata and Akagi (46 ), in which the 3′-phosphoglyceryl residue is oxidized sequentially by sodium periodate (NaIO4) and sodium chlorite (NaClO2). This oligonucleotide, which has been characterized previously (16 (link)), was purified by high-performance liquid chromatography (HPLC) and the presence of 3′-PG was confirmed by mass spectrometry.