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.

a<p>εN is either εA or εC.</p>b<p>X 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.</p>c<p>Cleavage 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.</p>d<p>Non-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.</p>e<p>THF, 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.