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.

► A method to visualize a specific DNA sequence by using RecA was developed.
► The probe consisted of the ssDNA–RecA complex fluorescence-labeled with Qdots.
► A target strand of DNA was stretch-and-positioned using the electrostatic method.
► Clear fluorescent spots were observed on the stretched DNA molecules.
► The peak-binding frequency of the probe was at the site of sequence complementarity.