Interactions of human O⁶-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs

The O⁶-alkylguanine-DNA alkyltransferase (AGT) repairs O ⁶-alkylguanine and O⁴-alkylthymine adducts in single-stranded and duplex DNAs. Here we characterize the binding of AGT to single-stranded DNAs ranging in length from 5 to 78 nucleotides (nt). Binding is moderately cooperative (37.9 ± 3.0 ≤ ω ≤ 89.8 ± 8.9), resulting in an all-or-nothing association pattern on short templates. This cooperativity contrasts with the isolated binding seen in recent crystal structures of AGT-DNA complexes. The statistical binding site size S (mean = 5.2 ± 0.1) oscillates with increasing template length. The oscillation period (4.10 ± 0.02 nt/protein) is nearly identical to the binding site size obtained at the highest known binding density (S = 4 nt/protein) and is significantly smaller than the contour length (∼8 bp) occupied in crystalline complexes. A model in which AGT proteins overlap along the DNA contour is proposed to account for these features. Oscillations in intrinsic binding constant K_i and cooperativity factor ω have the same frequency but are of opposite phase to S with the result that the most stable protein-protein and protein-DNA interactions occur at the highest packing densities. We hypothesize that modest binding cooperativity and high binding densities are adaptations that allow AGT to efficiently search for lesions in the context of chromatin remodeling and DNA replication.