Figure 2.

Chimeric substrates for detection of the polarity of strand exchange. The substrates used for fluorimetric assays of pairing and strand-displacement reactions. Thick and thin lines represent the GC-rich and AT-rich segments, respectively. Fluor location i and ii represent the placements of fluorescein (F) and rhodamine (R) on different strands for pairing and strand displacement, respectively. The dyes were placed at the right-hand ends of the symbolized strands: in the substrates shown in A, fluorescein was placed at the 3′ end of the single strand in the assay for pairing and at the 3′ end of the displaced strand in the assay for strand exchange; rhodamine was placed at the 5′ end of the plus strand in either assay. In B, the single-stranded oligonucleotides were the complements of those used in A, and fluorescein was located at the 5′ end of the single strand in the assay for pairing and at the 5′ end of the displaced strand in the assay for strand exchange, whereas rhodamine was at the 3′ end of the minus strand in either assay.