Fluorescent sequence-specific dsDNA binding oligomers

Sequence-specific detection methods for double-stranded DNA that obviate the need for denaturation would provide a powerful tool for bioorganic chemistry and genetics. As part of a sustained effort to develop sequence-specific fluorescent DNA detection methods, two programmable oligomers have been synthesized which target their respective sequences 5'-WTACGW-3' and 5'-WGGGGW-3' (W = A or T). The two oligomers were found to fluoresce weakly in the absence of DNA but showed significant fluorescence enhancement by the addition of match DNA. The fluorescence is shown to increase in a concentration-dependent manner, and the intensity varies depending on the number of mismatch sites incorporated into the DNA hairpins. This new class of oligomers provides a method to detect DNA sequences without denaturation and in the absence of conjugation to a dye molecule. This is a first step toward sequence-specific DNA-binding molecules containing a fluorescent switch integrated as part of the recognition modules.