for Methods strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays
Bin Liu and Guillermo C. Bazan
Departments of Chemistry and Biochemistry and Materials, Institute for Polymers and Organic Solids, University of California, Santa Barbara, CA 93106 Communicated by Alan J. Heeger, University of California, Santa Barbara, CA, November 17, 2004 (received for review October 11, 2004)
A strand-specic DNA sensory method is described based on surface-bound peptide nucleic acids and water-soluble cationic conjugated polymers. The main transduction mechanism operates by taking advantage of the net increase in negative charge at the peptide nucleic acid surface that occurs upon single-stranded DNA hybridization. Electrostatic forces cause the oppositely charged cationic conjugated polymer to bind selectively to the complementary surfaces. This approach circumvents the current need to label the probe or target strands. The polymer used in these assays is poly[9,9 -bis(6 -N,N,N-trimethylammonium)hexyl)uoreneco-alt-4,7-(2,1,3-benzothiadiazole) dibromide], which was specically designed and synthesized to be compatible with excitation sources used in commonly used DNA microarray readers. Furthermore, the utility of poly[9,9 -bis(6 -N,N,N-trimethylammonium)hexyl)uorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] has been demonstrated in homogenous and solid-state assays that involve uorescence resonance energy transfer to a reporter dye (Cy5) and that can benet from the light harvesting properties observed in water-soluble conjugated polymers.
peptide nucleic acid probe polyelectrolytes uorescence energy transfer
ethods for the detection of nucleic acids are highly significant in identifying specific target and in understanding their basic function. Hybridization probe technologies continue to be one of the most essential elements in the study of gene-related biomolecules (13). They are useful for a variety of commercial and scientific applications, including the identification of genetic mutations or single-nucleotide polymorphisms (SNPs), medical diagnostics, gene delivery, assessment of gene expression, and drug discovery (49). Heterogeneous formats for performing such hybridization probe assays have become increasingly common and powerful with the advancement of gene chip and DNA microarray technologies (1013). Such systems allow for high-throughput screening of hundreds to thousands of genes in a single experiment. Homogeneous DNA assays with increased sensitivity, relativ...
37 Proc Nat Acad Sci USA 102 589