Sequence-Specific Fluorescence Detection of DNA by Polyamide−Thiazole Orange Conjugates

Publisher Website
Google Scholar
Abstract
Fluorescent methods to detect specific double-stranded DNA sequences without the need for denaturation may be useful in the field of genetics. Three hairpin pyrrole-imidazole polyamides 2 − 4 that target their respective sequences 5‘-WGGGWW-3‘, 5‘-WGGCCW-3‘, and 5‘-WGWWCW-3‘ (W = A or T) were conjugated to thiazole orange dye at the C-termini to examine their fluorescence properties in the presence and absence of match duplex DNA. The conjugates fluoresce weakly in the absence of DNA but showed significant enhancement (>1000-fold) upon the addition of 1 equiv of match DNA and only slight enhancement with the addition of mismatch DNA. The polyamide−dye conjugates bound specific DNA sequences with high affinity (Ka > 108 M-1) and unwound the DNA duplex through intercalation (unwinding angle, φ, ∼8°). This new class of polyamides provides a method to specifically detect DNA sequences without denaturation.