One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes

Selective colorimetric polynucleotide detection based on Au nanoparticle probes which align in a 'tail-to-tail' fashion onto a target polynucleotide is described. In this new nanoparticle-based detection system, Au particles (~13 nm diameter), which are capped with 3'- and 5'- (alkanethiol)oligonucleotides, are used to complex a 24-base polynucleotide target. Hybridization of the target with the probes results in the formation of an extended polymeric Au nanoparticle/polynucleotide aggregate, which triggers a red to purple color change in solution. The color change is due to a red shift in the surface plasmon resonance of the Au nanoparticles. The aggregates exhibit characteristic, exceptionally sharp 'melting transitions' (monitored at 260 or 700 nm), which allows one to distinguish target sequences that contain one base end mismatches, deletions, or an insertion from the fully complementary target. When test solutions are spotted onto a C18 reverse-phase thin-layer chromatography plate, color differentiation is enhanced and a permanent record of the test is obtained, thereby providing a better method for distinguishing the aforementioned target sequences. Significantly, one-pot colorimetric detection of the target in the presence of four strands with single base imperfections can be accomplished with this new probe system.