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Ratiometric molecular beacons based on the perylene bisimide as a dimeric internal DNA base substitution

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Abstract

Molecular beacons with an excitonically interacting perylene bisimide base pair show the presence of the complementary olignucleotide sequence by both absorption and fluorescence changes.

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Notes and references

  1. S. Tyagi and F. R. Kramer, Molecular Beacons: Probes that Fluoresce upon Hybridization, Nat. Biotechnol., 1996, 14, 303–308

    Article  CAS  Google Scholar 

  2. X. H. Fang, J. J. Li and W. H. Tan, Using Molecular Beacons To Probe Molecular Interactions between Lactate Dehydrogenase and Single-Stranded DNA, Anal. Chem., 2000, 72, 3280–3285

    Article  CAS  Google Scholar 

  3. J. J. Li, X. Fang, S. M. Schuster and W. Tan, Molecular Beacons: A Novel Approach to Detect Protein - DNA Interactions, Angew. Chem., Int. Ed., 2000, 39, 1049–1052

    Article  CAS  Google Scholar 

  4. D. P. Bratu, B.-J. Cha, M. M. Mhlanga, F. R. Kramer and S. Tyagi, Visualizing the distribution and transport of mRNAs in living cells, Proc. Natl. Acad. Sci. U. S. A., 2003, 100, 13308–13313

    Article  CAS  Google Scholar 

  5. C. D. Medley, T. J. Drake, J. M. Tomasini, R. J. Rogers and W. H. Tan, Simultaneous Monitoring of the Expression of Multiple Genes Inside of Single Breast Carcinoma Cells, Anal. Chem., 2005, 77, 4713–4718.

    Article  CAS  Google Scholar 

  6. G. T. Hwang, Y. J. Seo and B. H. Kim, A Highly Discriminating Quencher-Free Molecular Beacon for Probing DNA, J. Am. Chem. Soc., 2004, 126, 6528–6529

    Article  CAS  Google Scholar 

  7. N. Venkatesan, Y. J. Seo and B. H. Kim, Quencher-free molecular beacons: a new strategy in fluorescence based nucleic acid analysis, Chem. Soc. Rev., 2008, 37, 648–663.

    Article  CAS  Google Scholar 

  8. E. Socher, L. Bethge, A. Knoll, N. Jungnick, A. Herrmann and O. Seitz, Low-Noise Stemless PNA Beacons for Sensitive DNA and RNA Detection, Angew. Chem., Int. Ed., 2008, 47, 9555–9559.

    Article  CAS  Google Scholar 

  9. P. Zhang, T. Beck and W. Tan, Design of a Molecular Beacon DNA Probe with Two Fluorophores, Angew. Chem., Int. Ed., 2001, 40, 402–405

    Article  CAS  Google Scholar 

  10. S. Tyagi, S. A. E. Marras and F. R. Kramer, Wavelength-shifting molecular beacons, Nat. Biotechnol., 2000, 18, 1191–1196

    Article  CAS  Google Scholar 

  11. P. J. Santangelo, B. Nix, A. Tsourkas and G. Bao, Dual FRET molecular beacons for mRNA detection in living cells, Nucleic Acids Res., 2004, 32, e57.

    Article  Google Scholar 

  12. Y. Chen, C. J. Yang, Y. Wu, P. Conlon, Y. Kim, H. Lin and W. Tan, Light-Switching Excimer Beacon Assays For Ribonuclease H Kinetic Study, ChemBioChem, 2008, 9, 355–359

    Article  CAS  Google Scholar 

  13. P. Conlon, C. J. Yang, Y. Wu, Y. Chen, K. Martinez, Y. Kim, N. Stevens, A. A. Marti, S. Jockusch, N. J. Turro and W. Tan, Pyrene Excimer Signaling Molecular Beacons for Probing Nucleic Acids, J. Am. Chem. Soc., 2008, 130, 336–342.

    Article  CAS  Google Scholar 

  14. H. Kashida, H. Asanuma and M. Komiyama, Insertion of two pyrene moieties into oligodeoxyribonucleotides for the efficient detection of deletion polymorphisms, Chem. Commun., 2006, 2768–2770

    Google Scholar 

  15. I. Trkulja and R. Häner, Monomeric and Heterodimeric Triple Helical DNA Mimics, J. Am. Chem. Soc., 2007, 129, 7982–7989

    Article  CAS  Google Scholar 

  16. V. L. Malinovskii, F. Samain and R. Häner, Monomeric and Heterodimeric Triple Helical DNA Mimics, Angew. Chem., Int. Ed., 2007, 46, 4464–4467

    Article  CAS  Google Scholar 

  17. K. Seio, M. Mizuta, K. Tasaki, K. Tamaki, A. Ohkubo and M. Sekine, Hybridization-dependent fluorescence of oligodeoxynucleotides incorporating new pyrene-modified adenosine residues, Bioorg. Med. Chem., 2008, 16, 8287–8293.

    Article  CAS  Google Scholar 

  18. C. Wagner and H.-A. Wagenknecht, Perylene-3,4:9,10-tetracarboxylic Acid Bisimide Dye as an Artificial DNA Base Surrogate, Org. Lett., 2006, 8, 4191–4194.

    Article  CAS  Google Scholar 

  19. D. Baumstark and H.-A. Wagenknecht, Perylene Bisimide Dimers as Fluorescent “Glue” for DNA and for Base-Mismatch Detection, Angew. Chem., Int. Ed., 2008, 47, 2652–2654

    Article  Google Scholar 

  20. D. Baumstark and H.-A. Wagenknecht, Fluorescent Hydrophobic Zippers inside Duplex DNA: Interstrand Stacking of Perylene-3,4:9,10-tetracarboxylic Acid Bisimides as Artificial DNA Base Dyes, Chem.-Eur. J., 2008, 14, 6640–6645.

    Article  CAS  Google Scholar 

  21. Y. Zheng, H. Long, G. C. Schatz and F. D. Lewis, Duplex and hairpin dimer structures for perylene diimide-oligonucleotide conjugates, Chem. Commun., 2005, 4795–4797

    Google Scholar 

  22. M. Hariharan, Y. Zheng, H. Long, T. A. Zeidan, G. C. Schatz, J. Vura-Weis, M. R. Wasielewski, X. Zuo, D. M. Tiede and F. D. Lewis, Hydrophobic Dimerization and Thermal Dissociation of Perylenediimide-Linked DNA Hairpins, J. Am. Chem. Soc., 2009, 131, 5920–5929

    Article  CAS  Google Scholar 

  23. P. P. Neelakandan, Z. Pan, M. Hariharan, Y. Zheng, H. Weissman, B. Rybtchinski and F. D. Lewis, Hydrophobic Self-Assembly of a Perylenediimide-Linked DNA Dumbbell into Supramolecular Polymers, J. Am. Chem. Soc., 2010, 132, 15808–15813

    Article  CAS  Google Scholar 

  24. T. A. Zeidan, M. Hariharan, K. Siegmund and F. D. Lewis, DNA base-pair flipping with fluorescent perylenediimide pincers, Photochem. Photobiol. Sci., 2010, 9, 916–922.

    Article  CAS  Google Scholar 

  25. S. Bevers, S. Schutte and L. W. McLaughlin, Naphthalene- and Perylene-Based Linkers for the Stabilization of Hairpin Triplexes, J. Am. Chem. Soc., 2000, 122, 5905–5915.

    Article  CAS  Google Scholar 

  26. N. Rahe, C. Rinn and T. Carell, Development of donor-acceptor modified DNA hairpins for the investigation of charge hopping kinetics in DNA, Chem. Commun., 2003, 2120–2121.

    Google Scholar 

  27. W. Wang, L.-S. Li, G. Helms, H.-H. Zhou and A. D. Q. Li, To Fold or to Assemble?, J. Am. Chem. Soc., 2003, 125, 1120–1121.

    Article  CAS  Google Scholar 

  28. R. Häner, S. M. Biner, S. M. Langenegger, T. Meng and V. L. Malinovskii, A Highly Sensitive, Excimer-Controlled Molecular Beacon, Angew. Chem., Int. Ed., 2010, 49, 1227–1230.

    Article  Google Scholar 

  29. H. Kashida, K. Sekiguchi and H. Asanuma, Insulator Base Pairs for Lighting-up Perylenediimide in a DNA Duplex, Chem.-Eur. J., 2010, 16, 11554–11557.

    Article  CAS  Google Scholar 

  30. T. A. Zeidan, R. Carmieli, R. F. Kelley, T. M. Wilson, F. D. Lewis and M. R. Wasielewski, Charge-Transfer and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide as a Base-Pair Surrogate, J. Am. Chem. Soc., 2008, 130, 13945–13955.

    Article  CAS  Google Scholar 

  31. S. Berndl and H.-A. Wagenknecht, Fluorescent Color Readout of DNA Hybridization with Thiazole Orange as an Artificial DNA Base, Angew. Chem., Int. Ed., 2009, 48, 2418–2421.

    Article  CAS  Google Scholar 

  32. K. Fujimoto, H. Shimizu and M. Inouye, Unambiguous Detection of Target DNAs by Excimer-Monomer Switching Molecular Beacons, J. Org. Chem., 2004, 69, 3271–3275

    Article  CAS  Google Scholar 

  33. K. Fujimoto, Y. Muto and M. Inouye, A general and versatile molecular design for host molecules working in water: a duplex-based potassium sensor consisting of three functional regions, Chem. Commun., 2005, 4780–4782.

    Google Scholar 

  34. N. Dave and J. Liu, Fast Molecular Beacon Hybridization in Organic Solvents with Improved Target Specificity, J. Phys. Chem. B, 2010, 114, 15694–15699.

    Article  CAS  Google Scholar 

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Author notes

  1. Hans-Achim Wagenknecht

    Present address: Institute for Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany

Authors and Affiliations

  1. Institute for Organic Chemistry, University of Regensburg, D-93040, Regensburg, Germany

    Florian Menacher & Hans-Achim Wagenknecht

Authors
  1. Florian Menacher
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  2. Hans-Achim Wagenknecht
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Correspondence to Hans-Achim Wagenknecht.

Additional information

Electronic supplementary information (ESI) available. See DOI: 10.1039/c1pp05091e

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Menacher, F., Wagenknecht, HA. Ratiometric molecular beacons based on the perylene bisimide as a dimeric internal DNA base substitution. Photochem Photobiol Sci 10, 1275–1278 (2011). https://doi.org/10.1039/c1pp05091e

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