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.
Similar content being viewed by others
Notes and references
S. Tyagi and F. R. Kramer, Molecular Beacons: Probes that Fluoresce upon Hybridization, Nat. Biotechnol., 1996, 14, 303–308
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
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
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
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.
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
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.
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.
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
S. Tyagi, S. A. E. Marras and F. R. Kramer, Wavelength-shifting molecular beacons, Nat. Biotechnol., 2000, 18, 1191–1196
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.
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
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.
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
I. Trkulja and R. Häner, Monomeric and Heterodimeric Triple Helical DNA Mimics, J. Am. Chem. Soc., 2007, 129, 7982–7989
V. L. Malinovskii, F. Samain and R. Häner, Monomeric and Heterodimeric Triple Helical DNA Mimics, Angew. Chem., Int. Ed., 2007, 46, 4464–4467
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.
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.
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
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.
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
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
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
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
N. Dave and J. Liu, Fast Molecular Beacon Hybridization in Organic Solvents with Improved Target Specificity, J. Phys. Chem. B, 2010, 114, 15694–15699.
Author information
Authors and Affiliations
Corresponding author
Additional information
Electronic supplementary information (ESI) available. See DOI: 10.1039/c1pp05091e
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1039/c1pp05091e