Polymer-DNA hybrids: Molecular recognition properties and applications in DNA detection

Ring-opening metathesis polymerization was used to make nearly monodisperse, comb, block copolymer-DNA hybrids with DNA strands and redox-active ferrocenyl groups as the side-chains. By varying the ratio of two ferrocenyl blocks in the polymer, triblock copolymer DNA hybrids were formed that had distinctive, electrochemical signals, allowing them to be used as highly selective probes in DNA detection assays. The selectivity stemmed from the very sharp dissociation, or melting, transitions observed for aggregates formed from complementary polymer-DNA hybrids. Structure-variation studies of the homopolymer-DNA hybrids revealed that neither changing the polymer length, nor increasing the spacer sequence connecting the polymer backbone to the hybridizing sequence, had any affect on the melting behavior. A comparison of the hybridization behavior of our polymer-DNA system with that of organic, small molecule-DNA hybrids (containing 1--4 DNA strands depending on the structure) suggested that both the presence of multiple DNA strands on the polymer-DNA hybrids as well as their geometrical arrangement were important parameters that strongly influence melting behavior.; When polymer-DNA hybrids were hybridized with complementary DNA-modified gold nanoparticles in a three-strand experiment, the melting behavior of the mixed hybrid system was similar to the behavior of the polymer-DNA and DNA-modified gold nanoparticle homoaggregates, with an intermediate melting temperature and sharpness. When a peptide nucleic acid (PNA) strand was substituted for the linker strand, both the PNA-linked polymer-DNA and GNP-DNA homoaggregates displayed sharp melting transitions and unusual salt dependence.; These results support a contribution from neighbor-neighbor cooperative effects based on overlapping ion clouds of neighboring duplexes as described by the Schatz and Mirkin groups. To evaluate the extent of this contribution, a dual-duplex polymer-DNA system was developed where the melting of one type of duplex within a pre-formed aggregate did not lead to aggregate dissolution. Excitingly, the resulting sharp melting transitions for both duplexes supported a predominant contribution of neighbor-neighbor cooperativity to the sharpness of the melting transitions instead of a phase transition mechanism requiring aggregate dissolution.