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 Fِrster 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 1 nM. 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.