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. 2013 Oct 24;42(2):1095–1110. doi: 10.1093/nar/gkt945

Figure 8.

Figure 8.

Deamination of dC in ss regions of a 40-bp DNA duplex and the effect of SSB proteins. (A) Schematic representation of a series of TBs in a ds nucleic acid. Unpaired bases are located in the center of a 40-bp DNA duplex that contains the TTCA sequence in the ss region of one strand. (B) Deaminase assay performed using duplexes (40 bp) containing TBs with different lengths of unpaired bases (1–9 nt). These duplexes were generated by heat annealing the ssDNA substrate (JL913) to oligonucleotides containing 1 nt (JL1088; TB-1), 3 (JL1089; TB-3), 5 (JL1090; TB-5) and 9 (JL1091; TB-9) that are not complementary to the corresponding residues in the other DNA strand. (C) Deaminase assay using the ssDNA substrate (JL913; 180 nM) after preincubation with SSB proteins (HIV-1 NC, T4 Gene 32 or E. coli SSB; each protein at 500 nM) for 15 min at 37°C before addition of A3A and incubation for 1 h. Bars: 1, 5 and 9, no proteins (negative control); 2, 6 and 10, A3A only (positive control); 3, 7, 11 and 4, 8, 12, A3A and ssDNA preincubated with 2.5 or 5 µM SSB protein, respectively.