Single-molecular AFM probing of specific DNA sequencing using RecA-promoted homologous pairing and strand exchange

The specific sequence in a linearlized double-stranded DNA target has been identified at a single-molecular level by atomic force microscopy (AFM). Th is was accomplished using RecA-coated, single-stranded DNA probes which wer e paired with a specific complementary DNA sequence in a linear double-stra nded DNA target by strand-exchange reaction at a homologous sequence site w ith target DNA. The sites of interaction between the nucleoprotein filament s and the double-stranded DNA targets were directly visualized by AFM in so lution containing 4 mM magnesium acetate. Measurements of the position of R ecA-coated probes paired to individual target DNA showed that DNA probes sp ecifically paired at their corresponding homologous target sequences. Stran d exchange promoted by RecA and the visualization by AFM provided a rapid a nd efficient way to identify homologous sequence on a single-molecule targe t DNA.