FRET detection of DNA sequence via electrostatic interaction of polycationic phenyleneethynylene dendrimer with DNA/PNA hybrid.

Interaction between a polycationic compound and DNA is a useful phenomenon for development of a new DNA sensing system. In this work, dendritic polycationic phenyleneethynylene fluorophores are investigated as a Förster resonance energy transfer (FRET) donor for the detection of DNA hybridization in conjunction with a fluorescein-labeled pyrrolidinyl peptide nucleic acid (Fl-acpcPNA) probe. The first generation dendrimer is an efficient energy donor for the fluorescein acceptor but also shows non-specific FRET signal with Fl-acpcPNA. The addition of N-methyl 2-pyrrolidone can virtually completely remove the non-specific interaction between Fl-acpcPNA and the dendrimer. Under the optimal condition, the complementary DNA gives a distinctively high FRET ratio (1.42) comparing with those of the non-complementary (0.26) and singly mismatched (0.51) DNAs. The FRET ratio responses linearly with the DNA concentration with the detection limit lower than 1nM. The FRET ratio is even higher for the complementary target DNAs with extra hanging nucleotide sequences, which is a more frequently encountered scenario in real applications.