Figure 2
From: Development of a Cell-Based Assay for Measuring Base Excision Repair Responses
Hairpin DNA ORA Substrate and Blocking Potential of BER Damages. (A) The initial design of the hairpin was adapted from Shen et al.28, and contained three-components, here named Flag, Cassette, and Hairpin. The notable features of the three-component hairpin were biotinylation of the Flag oligo, a damage lesion (designated; but no 5′ phosphorylation in each of the eight different Cassette oligos), and a phosphorylation (P) and protective ddC group in the Hairpin oligo. Also shown is the positioning of the various damage sites in the three-component substrate, and the location of the qPCR primers. See Tables 1 and 2 for oligonucleotide information. (B) The blocking-potential of each lesion with a primer overlapping the lesion (BBRefTest). (C) The blocking-potential of each lesion with a primer that permits run-through (3C-Upstream-Test-Primer). Averages and standard deviations of at least three independent experimental replicates are shown in panels B and C.
