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Published online on January 10, 2005, 10.1073/pnas.0408561102
PNAS | January 18, 2005 | vol. 102 | no. 3 | 589-593


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BIOCHEMISTRY
Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays

Bin Liu {dagger}, and Guillermo C. Bazan {dagger}

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-specific 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)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide], which was specifically 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)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] has been demonstrated in homogenous and solid-state assays that involve fluorescence resonance energy transfer to a reporter dye (Cy5) and that can benefit from the light harvesting properties observed in water-soluble conjugated polymers.

peptide nucleic acid probe | polyelectrolytes | fluorescence energy transfer

Author contributions: B.L. and G.C.B. designed research; B.L. performed research; B.L. contributed new reagents/analytic tools; B.L. analyzed data; and B.L. and G.C.B. wrote the paper.

Abbreviations: PNA, peptide nucleic acid; CCP, cationic conjugated polymers; PFBT, poly[9,9'-bis(6''-N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide]; DI, diionized.

{dagger} To whom correspondence may be addressed. E-mail: bliu{at}chem.ucsb.edu or bazan{at}chem.ucsb.edu.

© 2005 by The National Academy of Sciences of the USA


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