(a) Close up view of one of the flipped target adenines in the Mos1 STC crystal structure showing the hydrogen bond interactions (dotted cyan lines, distance in Å) with the V214 backbone atoms and the 2 and 6 positions of the adenine ring. The simulated annealing composite omit 2Fo-Fc electron density map (grey mesh) is contoured at 1.2σ. (b) Chemical structures and base-pairing of adenine, A, and its analogues 2-aminopurine, P, and 2,6-diaminopurine, D, with thymine, T or 2-thio-thymine, S. A steric clash between the 2-thio group of S and the 2-amino group of D tilts the bases relative to each other, and thus only one H-bond forms. (c) Denaturing PAGE of the products of strand transfer reactions with target DNA containing adenine and/or thymine analogues, as indicated above lanes 4 to 11. (d) Quantification of the 40 nt and 68 nt strand transfer products for each target DNA duplex, as a percentage of total DNA. Error bars represent the standard deviation, calculated from 2 experiments.