Figure 2.

Assays of homologous pairing and strand displacement on the basis of FRET. The fluorescein and rhodamine fluorophores were present on the 3′ and 5′ ends of the complementary strands, respectively. The assays are based on the nonradiative transfer of energy from fluorescein to rhodamine when the fluorescein is excited at its absorption maximum and the two dyes are in close proximity. (A) The quenching in fluorescein intensity or the subsequent increase in rhodamine emission, the so-called sensitized emission, is measured to detect homologous pairing. (B) The increase in fluorescein intensity or the decrease in the sensitized emission from rhodamine is measured to detect strand exchange.