Optical sequence probing with the homologous recombination protein RecA.

In this study, we used the homologous recombination protein RecA to locate a specific sequence on DNA. Single-stranded (ss) DNA (80-mer, 5'-biotinylated), complementary to the sequence of interest, was labeled with quantum dots (Qdots(®)) via biotin-avidin binding. The DNA was then mixed with RecA to form a fluorescent-labeled ssDNA-RecA complex. λ DNA, which was used as the target DNA, was stretch-and-positioned onto microelectrodes by using the electrostatic method. When the ssDNA-RecA complex was fed to the suspended target DNA, clear fluorescence spots were observed on individual target DNA molecules. The histogram of the probe-binding position along the target DNA was measured, and the peak was found to correspond to the location complementary to the probe ssDNA. This result shows a potential use for recombination proteins in facilitating the optical detection of DNA sequences.