Table 1. Sequences of oligonucleotides bearing a single base lesion used to identify the NIR activity and relative efficiency of the APE1-catalyzed cleavage of duplex DNA substrates.

Namea	Sequenceb	Lesion position	Sequence context	Cleavage efficiencyc
1. εA-DL10	d(AATTGCTATXTAGCTCCGCACGCTGGTACCCATCTCATGA)	10	TATXTAG	14.1%
2. εA-PP	d(CATCTCATGAAATTGCTATXTAGCTCCGCACGCTGGTACC)	20	TATXTAG	9.7%
3. εN22	d(CACTTCGGAXTGTGACTGATCC)	10	GGAXTGT	7%
4. εN-C21	d(GCTCTCGTCTGXACACCGAAG)	12	CTGXACA	4.2%
5. εN-RT	d(TGACTGCATAXGCATGTAGACGATGTGCAT)	11	ATAXGCA	11.7%
6. εN-DL	d(AATTGCTATCTAGCTCCGCXCGCTGGTACCCATCTCATGA)	20	CGCXCGC	Noned
7. εA28	d(CAGCTCTGTACXTGAGCGGTGGTGACAC)	12	TACXTGA	None
8. εN-MS	d(AAATACATCGTCACCTGGGXCATGTTGCAGATCC)	20	GGGXCAT	None
9. εN-PN	d(GGCTTCATCGTTATTXATGACCTGGTGGATACCG)	16	ATTXATG	None
10. Tg-RT	d(TGACTGCATAYGCATGTAGACGATGTGCAT)	11	ATAXGCA	2.3%
11. Tg-IW	d(ACAGACGCCAYCAACCAGG)	11	CCAXCAA	3.9%
12. 8oxoG-RT	d(TGACTGCATAZGCATGTAGACGATGTGCAT)	11	ATAXGCA	None
13. 8oxoG22	d(CACTTCGGAZTGTGACTGATCC)	10	GGAXTGT	None
14. THF-22e	d(CACTTCGGAPTGTGACTGATCC)	10	GGAXTGT	>90%

^aεN is either εA or εC.

^bX is the position of ε-base, Y is the position of thymine glycol, Z is the position of 8-oxoguanine, P is the position of a synthetic AP site.

^cCleavage efficiency was expressed as the percentage of incision product produced after 2 h incubation at 37°C in the presence of 10 nM DNA substrate and 10 nM of APE1 under NIR conditions.

^dNon-zero background levels of activity in non-treated oligonucleotides were subtracted when calculating APE1 activities. Background levels were varied from 0.3 to 2% and were due to non-specific spontaneous degradation and/or impurities of oligonucleotides.

^eTHF, 3-hydroxy-2-hydroxymethyltetrahydrofuran or tetrahydrofuran, is a synthetic analogue of an AP site. To measure cleavage efficiency a solution of 1 nM of 22 mer THF•T duplex oligonucleotide was incubated with 0.5 nM APE1 for 5 min at 37°C under NIR conditions.