FIGURE 1.

Effect of mismatches on Dmc1-promoted strand exchange. A, experimental scheme to study Dmc1-catalyzed recombination in vitro. T, TAMRA (λ excitation: 556 nm; λ emission: 580 nm). C, Cy5 (λ excitation: 649 nm; λ emission: 665 nm). B, labeled duplex and the corresponding invading unlabeled ssDNA sequences used in the experiment. Variable nucleotides are highlighted in red. Hom, 100% homologous oligonucleotide; Het, heterologous; 60% of divergence; 5′TG, midTG, and 3′TG refers to a single TG mismatch at 5′ end, middle, or 3′ end, respectively, of the incoming strand; 3MMunif, three mismatches uniformly distributed; 3MM3′ and 3MMmid, three mismatches clustered on the 3′ end or near the central region of the incoming strand. C and D, fraction of exchange as a function of Dmc1 concentration for one TG mismatch in different positions or three TG mismatches with different distributions. Reactions shown in panels C and D were carried out for 40 min. Each data point represents an average of three independent determinations. Error bars are the S.D. E and F, effect of reporter dye placement on Dmc1 strand exchange between homologous DNA substrates or containing one mismatch at the 5′ or 3′ end.