Cationic fluorene-based conjugated polyelectrolytes induce compaction and bridging in DNA

The cationic conjugated polymer (CCP), poly{9,9-bis[N,N-(trimethylammonium)hexyl]fluorene-co-1,4-phenylene} iodide (PFP-NR3) induces compaction in DNA in an acetonitrile/water mixture, as seen by fluorescence microscopy. At high concentrations of PFP-NR3, some chain structures still appear to exist. However, these are larger than normal DNA coils and have "beads" of enhanced fluorescence along the chain. These structures have also been imaged on freshly cleaved mica surfaces using atomic force microscopy. Images obtained following deposition onto mica from mixtures of DNA and the polyelectrolyte PFP-NR3 in acetonitrile/water 25:75 show both the efficient compaction of DNA induced by the polymer and linking and bridging of DNA/PFP-NR3 aggregates. The strong interaction between DNA and PFP-NR3 results in the formation of DNA/PFP-NR3 networks across the mica surface in which several strands of DNA are linked with aggregated polymer/DNA structures at various points along these chains. The linking of DNA strands is confirmed by a large increase in the apparent length of the DNA, which increases from 775 (+/-82) nm (with no PFP-NR3 present) to 4050 (+/-800) nm in the presence of PFP-NR3. Larger aggregates, believed to be PFP-NR3/compacted DNA, which also link other DNA strands, can also be seen. The fluorescence of PFP-NR3 is quenched by DNA, and this is accompanied by a bathochromic wavelength shift of the CCP emission, indicating complexation. Although the quenching mechanism is not yet clear, it appears to be a consequence of DNA-CCP aggregate formation. These results have implications on the use of CCPs in DNA sensing and, because the particular polymer has a rigid backbone, on the effect of chain rigidity on compaction and on formation of extended and supramolecular structures, which may have implications in DNA nanotechnology.