Skip to main content
SpringerLink
Log in

Charged Conjugated Polymers

  • Chapter
  • First Online:
Detection of Non-Amplified Genomic DNA

Part of the book series: Soft and Biological Matter ((SOBIMA))

Abstract

Signal amplification property and versatility in molecular design of conjugated polymers make them attractive as signal transduction materials. Cationic conjugated polymers (CCP) have demonstrated great potential as DNA-sensing materials since electrostatic interactions between CCP and negatively charged DNA have been well developed to modify optical properties and thereby detect hybridization states. In this chapter, we focus on the state-of-art of CCP-based non-amplified genomic DNA detection in homogenous solution as well as on microarray format. Representative applications of poly(thiophene)-based DNA sensors which display colorimetric output due to conformational changes, and poly(fluorene)-based DNA sensors which utilize CCP as energy donors are highlighted. The developments of amplified single nucleotide polymorphisms and DNA methylation detection employing CCP as sensory signal are briefly discussed. Integrated signal amplification effect of CCP with high-throughput DNA microarray format will yield superior platform for genomic DNA detection.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Heeger, A.J.: Semiconducting and metallic polymers: the fourth generation of polymeric materials (nobel lecture). Angew. Chem. Int. Ed. 40, 2591–2611 (2001)

    Article  Google Scholar 

  2. Swager, T.M.: The molecular wire approach to sensory signal amplification. Acc. Chem. Res. 31, 201–207 (1998)

    Article  Google Scholar 

  3. McQuade, D.T., Pullen, A.E., Swager, T.M.: Conjugated polymer-based chemical sensors. Chem. Rev. 100, 2537–2574 (2000)

    Article  Google Scholar 

  4. Thomas, S.W., Joly, G.D., Swager, T.M.: Chemical sensors based on amplifying fluorescent conjugated polymers. Chem. Rev. 107, 1339–1386 (2007)

    Article  Google Scholar 

  5. Bernards, D.A., Malliaras, G.G.: Organic Semiconductors in Sensor Applications, vol. 107. Springer, Berlin (2008)

    Book  Google Scholar 

  6. Achyuthan, K.E., Bergstedt, T.S., Chen, L., Jones, R.M., Kumaraswamy, S., Kushon, S.A., Ley, K.D., Lu, L., McBranch, D., Mukundan, H., Rininsland, F., Shi, X., Xia, W., Whitten, D.G.: Fluorescence superquenching of conjugated polyelectrolytes: applications for biosensing and drug discovery. J. Mater. Chem. 15, 2648–2656 (2005)

    Article  Google Scholar 

  7. Liu, B., Bazan, G.C.: Homogeneous fluorescence-based DNA detection with water-soluble conjugated polymers. Chem. Mater. 16, 4467–4476 (2004)

    Article  Google Scholar 

  8. Ho, H.A., Najari, A., Leclerc, M.: Optical detection of DNA and proteins with cationic polythiophenes. Acc. Chem. Res. 41, 168–178 (2008)

    Article  Google Scholar 

  9. Zhou, Q., Swager, T.M.: Method for enhancing the sensitivity of fluorescent chemosensors: energy migration in conjugated polymers. J. Am. Chem. Soc. 117, 7017–7018 (1995)

    Article  Google Scholar 

  10. Leclerc, M.: Optical and electrochemical transducers based on functionalized conjugated polymers. Adv. Mater. 11, 1491–1498 (1999)

    Article  Google Scholar 

  11. Duarte, A., Pu, K.-Y., Liu, B., Bazan, G.C.: Recent advances in conjugated polyelectrolytes for emerging optoelectronic applications. Chem. Mater. 23, 501–515 (2010)

    Article  Google Scholar 

  12. Albert, K.J., Walt, D.R.: High-speed fluorescence detection of explosives-like vapors. Anal. Chem. 72, 1947–1955 (2000)

    Article  Google Scholar 

  13. He, F., Tang, Y., Wang, S., Li, Y., Zhu, D.: Fluorescent amplifying recognition for DNA G-quadruplex folding with a cationic conjugated polymer: a platform for homogeneous potassium detection. J. Am. Chem. Soc. 127, 12343–12346 (2005)

    Article  Google Scholar 

  14. Bunz, U.H.F.: Poly(aryleneethynylene)s: syntheses, properties, structures, and applications. Chem. Rev. 100, 1605–1644 (2000)

    Article  Google Scholar 

  15. Ho, H.-A., Béra-Abérem, M., Leclerc, M.: Optical sensors based on hybrid DNA/conjugated polymer complexes. Chem. Euro. J. 11, 1718–1724 (2005)

    Article  Google Scholar 

  16. Duan, X., Liu, L., Feng, F., Wang, S.: Cationic conjugated polymers for optical detection of DNA methylation, lesions, and single nucleotide polymorphisms. Acc. Chem. Res. 43, 260–270 (2010)

    Article  Google Scholar 

  17. Feng, X., Liu, L., Wang, S., Zhu, D.: Water-soluble fluorescent conjugated polymers and their interactions with biomacromolecules for sensitive biosensors. Chem. Soc. Rev. 39, 2411–2419 (2010)

    Article  Google Scholar 

  18. Feng, F., He, F., An, L., Wang, S., Li, Y., Zhu, D.: Fluorescent conjugated polyelectrolytes for biomacromolecule detection. Adv. Mater. 20, 2959–2964 (2008)

    Article  Google Scholar 

  19. Lee, J., Jun, H., Kim, J.: Polydiacetylene-liposome microarrays for selective and sensitive mercury(II) detection. Adv. Mater. 21, 3674–3677 (2009)

    Article  Google Scholar 

  20. Lee, J., Kim, H.J., Kim, J.: Polydiacetylene liposome arrays for selective potassium detection. J. Am. Chem. Soc. 130, 5010–5011 (2008)

    Article  Google Scholar 

  21. Lee, K., Rouillard, J.M., Pham, T., Gulari, E., Kim, J.: Signal-amplifying conjugated polymer-DNA hybrid chips. Angew. Chem. Int. Ed. 46, 4667–4670 (2007)

    Article  Google Scholar 

  22. Yang, J.-S., Swager, T.M.: Porous shape persistent fluorescent polymer films: an approach to TNT sensory materials. J. Am. Chem. Soc. 120, 5321–5322 (1998)

    Article  Google Scholar 

  23. Dubertret, B., Calame, M., Libchaber, A.J.: Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat. Biotech 19, 365–370 (2001)

    Article  Google Scholar 

  24. Wang, J.: Survey and summary. Nucleic Acids Res. 28, 3011–3016 (2000)

    Article  Google Scholar 

  25. Daar, A.S., Thorsteinsdottir, H., Martin, D.K., Smith, A.C., Nast, S., Singer, P.A.: Top ten biotechnologies for improving health in developing countries. Nat. Genet. 32, 229–232 (2002)

    Article  Google Scholar 

  26. Tumor Analysis Best Practices Working Group: Expression profiling—best practices for data generation and interpretation in clinical trials. Nat. Rev. Genet. 5, 229–237 (2004)

    Google Scholar 

  27. Gershon, D.: Microarray technology: an array of opportunities. Nature 416, 885–891 (2002)

    Article  ADS  Google Scholar 

  28. Heller, M.J.: DNA microarray technology: devices, systems, and applications. Annu. Rev. Biomed. Eng. 4, 129–153 (2002)

    Article  Google Scholar 

  29. Sassolas, A., Leca-Bouvier, B.D., Blum, L.J.: DNA biosensors and microarrays. Chem. Rev. 108, 109–139 (2008)

    Article  Google Scholar 

  30. Pinto, M.R., Schanze, K.S.: Conjugated polyelectrolytes: synthesis and applications. Synthesis 9, 1293–1309 (2002)

    Article  Google Scholar 

  31. Patil, A.O., Ikenoue, Y., Wudl, F., Heeger, A.J.: Water soluble conducting polymers. J. Am. Chem. Soc. 109, 1858–1859 (1987)

    Article  Google Scholar 

  32. Ho, H.-A., Boissinot, M., Bergeron, M.G., Corbeil, G., Doré, K., Boudreau, D., Leclerc, M.: Colorimetric and fluorometric detection of nucleic acids using cationic polythiophene derivatives. Angew. Chem. Int. Ed. 41, 1548–1551 (2002)

    Article  Google Scholar 

  33. Nilsson, K.P.R., Rydberg, J., Baltzer, L., Inganos, O.: Self-assembly of synthetic peptides control conformation and optical properties of a zwitterionic polythiophene derivative. Proc. Natl. Acad. Sci. U.S.A. 100, 10170–10174 (2003)

    Article  ADS  Google Scholar 

  34. McQuade, D.T., Hegedus, A.H., Swager, T.M.: Signal amplification of a turn-on sensor: harvesting the light captured by a conjugated polymer. J. Am. Chem. Soc. 122, 12389–12390 (2000)

    Article  Google Scholar 

  35. Bunz, U.H.F.: Poly(p-phenyleneethynylene)s by alkyne metathesis. Acc. Chem. Res. 34, 998–1010 (2001)

    Article  Google Scholar 

  36. Levitsky, I.A., Kim, J., Swager, T.M.: Energy migration in a poly(phenylene ethynylene): determination of interpolymer transport in anisotropic Langmuir Blodgett films. J. Am. Chem. Soc. 121, 1466–1472 (1999)

    Article  Google Scholar 

  37. Shi, S., Wudl, F.: Synthesis and characterization of a water-soluble poly(p-phenylenevinylene) derivative. Macromolecules 23, 2119–2124 (1990)

    Article  ADS  Google Scholar 

  38. Stork, M., Gaylord, B.S., Heeger, A.J., Bazan, G.C.: Energy transfer in mixtures of water- soluble oligomers: effect of charge, aggregation, and surfactant complexation. Adv. Mater. 14, 361–366 (2002)

    Article  Google Scholar 

  39. Kim, S., Jackiw, J., Robinson, E., Schanze, K.S., Reynolds, J.R., Baur, J., Rubner, M.F., Boils, D.: Water soluble photo- and electroluminescent alkoxy-sulfonated poly(p-phenylenes) synthesized via palladium catalysis. Macromolecules 31, 964–974 (1998)

    Article  ADS  Google Scholar 

  40. Gaylord, B.S., Wang, S., Heeger, A.J., Bazan, G.C.: Water-soluble conjugated oligomers: effect of chain length and aggregation on photoluminescence-quenching efficiencies. J. Am. Chem. Soc. 123, 6417–6418 (2001)

    Article  Google Scholar 

  41. Chen, L., McBranch, D.W., Wang, H.-L., Helgeson, R., Wudl, F., Whitten, D.G.: Highly sensitive biological and chemical sensors based on reversible fluorescence quenching in a conjugated polymer. Proc. Natl. Acad. Sci. U.S.A. 96, 12287–12292 (1999)

    Article  ADS  Google Scholar 

  42. Tan, C., Pinto, M.R., Schanze, K.S.: Photophysics, aggregation and amplified quenching of a water-soluble poly(phenylene ethynylene). Chem. Commun. 5, 446–447 (2002)

    Article  Google Scholar 

  43. Yang, R., Garcia, A., Korystov, D., Mikhailovsky, A., Bazan, G.C., Nguyen, T.-Q.: Control of interchain contacts, solid-state fluorescence quantum yield, and charge transport of cationic conjugated polyelectrolytes by choice of anion. J. Am. Chem. Soc. 128, 16532–16539 (2006)

    Article  Google Scholar 

  44. Yu, M., Tang, Y., He, F., Wang, S., Zheng, D., Li, Y., Zhu, D.: Synthesis of water-soluble dendritic conjugated polymers for fluorescent DNA assays. Macromol. Rapid Commun. 27, 1739–1745 (2006)

    Article  Google Scholar 

  45. Chen, L., Xu, S., McBranch, D., Whitten, D.: Tuning the properties of conjugated polyelectrolytes through surfactant complexation. J. Am. Chem. Soc. 122, 9302–9303 (2000)

    Article  Google Scholar 

  46. Kushon, S.A., Ley, K.D., Bradford, K., Jones, R.M., McBranch, D., Whitten, D.: Detection of DNA hybridization via fluorescent polymer superquenching. Langmuir 18, 7245–7249 (2002)

    Article  Google Scholar 

  47. Kushon, S.A., Bradford, K., Marin, V., Suhrada, C., Armitage, B.A., McBranch, D., Whitten, D.: Detection of single nucleotide mismatches via fluorescent polymer superquenching. Langmuir 19, 6456–6464 (2003)

    Article  Google Scholar 

  48. Yang, C.J., Pinto, M., Schanze, K., Tan, W.: Direct synthesis of an oligonucleotide-poly(phenylene ethynylene) conjugate with a precise one-to-one molecular ratio. Angew. Chem. Int. Ed. 44, 2572–2576 (2005)

    Article  Google Scholar 

  49. Lakowicz, J.R.: Principles of Fluorescence Spectroscopy, 2nd edn. Kluwer Academic/Plenum Publishers, New York (1999)

    Google Scholar 

  50. Nilsson, K.P.R., Inganas, O.: Chip and solution detection of DNA hybridization using a luminescent zwitterionic polythiophene derivative. Nat. Mater. 2, 419–424 (2003)

    Article  ADS  Google Scholar 

  51. Dore, K., Dubus, S., Ho, H.-A., Levesque, I., Brunette, M., Corbeil, G., Boissinot, M., Boivin, G., Bergeron, M.G., Boudreau, D., Leclerc, M.: Fluorescent polymeric transducer for the rapid, simple, and specific detection of nucleic acids at the zeptomole level. J. Am. Chem. Soc. 126, 4240–4244 (2004)

    Article  Google Scholar 

  52. Dubus, S., Gravel, J.-F., Le Drogoff, B., Nobert, P., Veres, T., Boudreau, D.: PCP-free DNA detection using a magnetic bead-supported polymeric transducer and microelectromagnetic traps. Anal. Chem. 78, 4457–4464 (2006)

    Article  Google Scholar 

  53. Ho, H.A., Dore, K., Boissinot, M., Bergeron, M.G., Tanguay, R.M., Boudreau, D., Leclerc, M.: Direct molecular detection of nucleic acids by fluorescence signal amplification. J. Am. Chem. Soc. 127, 12673–12676 (2005)

    Article  Google Scholar 

  54. Najari, A., Ho, H.A., Gravel, J.F., Nobert, P., Boudreau, D., Leclerc, M.: Reagentless ultrasensitive specific DNA array detection based on responsive polymeric biochips. Anal. Chem. 78, 7896–7899 (2006)

    Article  Google Scholar 

  55. Dueymes, C., Décout, J.L., Peltié, P., Fontecave, M.: Fluorescent deazaflavin–oligonucleotide probes for selective detection of DNA. Angew. Chem. Int. Ed. 41, 486–489 (2002)

    Article  Google Scholar 

  56. Dudley, A.M., Aach, J., Steffen, M.A., Church, G.M.: Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. U.S.A. 99, 7554–7559 (2002)

    Article  ADS  Google Scholar 

  57. Gaylord, B.S., Heeger, A.J., Bazan, G.C.: DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes. Proc. Natl. Acad. Sci. U.S.A. 99, 10954–10957 (2002)

    Article  ADS  Google Scholar 

  58. Gaylord, B.S., Massie, M.R., Feinstein, S.C., Bazan, G.C.: SNP detection using peptide nucleic acid probes and conjugated polymers: applications in neurodegenerative disease identification. Proc. Natl. Acad. Sci. U.S.A. 102, 34–39 (2005)

    Article  ADS  Google Scholar 

  59. Gaylord, B.S., Heeger, A.J., Bazan, G.C.: DNA hybridization detection with water-soluble conjugated polymers and chromophore-labeled single-stranded DNA. J. Am. Chem. Soc. 125, 896–900 (2003)

    Article  Google Scholar 

  60. Wang, Y., Liu, B.: Silica nanoparticle assisted DNA assays for optical signal amplification of conjugated polymer based fluorescent sensors. Chem. Commun. 34, 3553–3555 (2007)

    Article  Google Scholar 

  61. Wang, S., Gaylord, B.S., Bazan, G.C.: Fluorescein provides a resonance gate for fret from conjugated polymers to DNA intercalated dyes. J. Am. Chem. Soc. 126, 5446–5451 (2004)

    Article  Google Scholar 

  62. He, F., Tang, Y., Yu, M., Feng, F., An, L., Sun, H., Wang, S., Li, Y., Zhu, D., Bazan, G.C.: Quadruplex-to-duplex transition of g-rich oligonucleotides probed by cationic water-soluble conjugated polyelectrolytes. J. Am. Chem. Soc. 128, 6764–6765 (2006)

    Article  Google Scholar 

  63. He, F., Feng, F., Duan, X., Wang, S., Li, Y., Zhu, D.: Selective and homogeneous fluorescent DNA detection by target-induced strand displacement using cationic conjugated polyelectrolytes. Anal. Chem. 80, 2239–2243 (2008)

    Article  Google Scholar 

  64. Feng, X., Liu, L., Yang, Q., Wang, S.: Dual-amplified sensitive DNA detection based on conjugated polymers and recyclable autocatalytic hybridization of DNA. Chem. Commun. 47, 5783–5785 (2011)

    Article  Google Scholar 

  65. Liu, B., Bazan, G.C.: Interpolyelectrolyte complexes of conjugated copolymers and DNA platforms for multicolor biosensors. J. Am. Chem. Soc. 126, 1942–1943 (2004)

    Article  Google Scholar 

  66. Hong, J.W., Hemme, W.L., Keller, G.E., Rinke, M.T., Bazan, G.C.: Conjugated-polymer/DNA interpolyelectrolyte complexes for accurate DNA concentration determination. Adv. Mater. 18, 878–882 (2006)

    Article  Google Scholar 

  67. Liu, B., Bazan, G.C.: Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays. Proc. Natl. Acad. Sci. U.S.A. 102, 589–593 (2005)

    Article  ADS  Google Scholar 

  68. Sun, C., Gaylord, B.S., Hong, J.W., Liu, B., Bazan, G.C.: Application of cationic conjugated polymers in microarrays using label-free DNA targets. Nat. Protocols 2, 2148–2151 (2007)

    Article  Google Scholar 

  69. Raymond, F., Ho, H.-A., Peytavi, R., Bissonnette, L., Boissinot, M., Picard, F., Leclerc, M., Bergeron, M.: Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support. BMC Biotech. 5, 10 (2005)

    Article  Google Scholar 

  70. Kim, S., Misra, A.: SNP genotyping: technologies and biomedical applications. Annu. Rev. Biomed. Eng. 9, 289–320 (2007)

    Article  Google Scholar 

  71. Ding, C.: Other applications of single nucleotide polymorphisms. Trends Biotechnol. 25, 279–283 (2007)

    Article  Google Scholar 

  72. The International HapMap Consortium: A haplotype map of the human genome. Nature 437, 1299–1320 (2005)

    Article  ADS  Google Scholar 

  73. Duan, X., Li, Z., He, F., Wang, S.: A sensitive and homogeneous SNP detection using cationic conjugated polymers. J. Am. Chem. Soc. 129, 4154–4155 (2007)

    Article  Google Scholar 

  74. Duan, X., Yue, W., Liu, L., Li, Z., Li, Y., He, F., Zhu, D., Zhou, G., Wang, S.: Single-nucleotide polymorphism (SNP) genotyping using cationic conjugated polymers in homogeneous solution. Nat. Protocols 4, 984–991 (2009)

    Article  Google Scholar 

  75. Duan, X., Liu, L., Wang, S.: Homogeneous and one-step fluorescent allele-specific PCR for SNP genotyping assays using conjugated polyelectrolytes. Biosens. Bioelectron. 24, 2095–2099 (2009)

    Article  Google Scholar 

  76. Duan, X., Wang, S., Li, Z.: Conjugated polyelectrolyte-DNA complexes for multi-color and one-tube SNP genotyping assays. Chem. Commun. 21, 1302–1304 (2008)

    Article  Google Scholar 

  77. Li, Z.P., Tsunoda, H., Okano, K., Nagai, K., Kambara, H.: Microchip electrophoresis of tagged probes incorporated with one-colored ddNTP for analyzing single-nucleotide polymorphisms. Anal. Chem. 75, 3345–3351 (2003)

    Article  Google Scholar 

  78. Bird, A.: DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002)

    Article  Google Scholar 

  79. Reik, W., Walter, J.: Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2, 21–32 (2001)

    Article  Google Scholar 

  80. Robertson, K.D., Wolffe, A.P.: DNA methylation in health and disease. Nat. Rev. Genet. 1, 11–19 (2000)

    Article  Google Scholar 

  81. Feng, F., Wang, H., Han, L., Wang, S.: Fluorescent conjugated polyelectrolyte as an indicator for convenient detection of DNA methylation. J. Am. Chem. Soc. 130, 11338–11343 (2008)

    Article  Google Scholar 

  82. Sadri, R., Hornsby, P.J.: Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification. Nucleic Acids Res. 24, 5058–5059 (1996)

    Article  Google Scholar 

  83. Feng, F., Liu, L., Wang, S.: Fluorescent conjugated polymer-based FRET technique for detection of DNA methylation of cancer cells. Nat. Protocols 5, 1255–1264 (2010)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Beijing National Laboratory for Molecular Science, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China

    Fengting Lv & Shu Wang

Authors
  1. Fengting Lv
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shu Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shu Wang .

Editor information

Editors and Affiliations

  1. , Department of Chemical Science, University of Catania, Viale Andrea Doria 6, Catania, 95125, Italy

    Giuseppe Spoto

  2. , Faculty of Science, University of Parma, Parma, 43100, Italy

    Roberto Corradini

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Lv, F., Wang, S. (2012). Charged Conjugated Polymers. In: Spoto, G., Corradini, R. (eds) Detection of Non-Amplified Genomic DNA. Soft and Biological Matter. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1226-3_5

Download citation

Publish with us

Policies and ethics

Search

Navigation