Abstract
Combinatorial fluorescence energy transfer (CFET) tags, constructed by exploiting fluorescence energy transfer and combinatorial synthesis to generate a large number of unique fluorescence emission signatures from a limited number of fluorophores, allow multiple biological targets to be identified simultaneously. All of the CFET tags can be excited by a single wavelength of 488 nm and analyzed by a simple optical system. In genetic analysis, the CFET tags are coupled with solid phase capture for multiplex singlenucleotide polymorphism (SNP) detection. The design, synthesis, purification of CFET tags, and the methods to use the CFET tags and molecular affinity for SNP detection in the retinoblastoma tumor suppressor gene are described.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ju, J., Li, Z., Tong, A., and Russo, J. J. (2003) Combinatorial fluorescence energy transfer tags and their applications for multiplex genetic analyses. US Patent 6,627,748.
Ju, J., Ruan, C., Fuller, C. W., Glazer, A. N., and Mathies, R. A. (1995) Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. Proc. Natl. Acad. Sci. USA 92, 4347–4351.
Marra, M., Weinstock, L. A., and Mardis, E. R. (1996) End sequence determination from large insert clones using energy transfer fluorescent primers. Genome Res. 6, 1118–1122.
Rosenblum, B. B., Lee, L. G., Spurgeon, S. L., et al. (1997) New dye-labeled terminators for improved DNA sequencing patterns. Nucleic Acids Res. 25, 4500–4504.
Heiner, C. R., Hunkapiller, K. L., Chen, S. M., Glass, J. I., and Chen, E. Y. (1998) Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res. 8, 557–561.
International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.
Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.
Berti, L., Medintz, I. L., Tom, J., and Mathies, R. A. (2001) Energy-transfer cassette labeling for capillary array electrophoresis short tandem repeat DNA fragment sizing. Bioconjugate Chem. 12, 493–500.
Chen, X., Zehnbauer, B., Gnirke, A., and Kwok, P.-Y. (1997) Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc. Natl. Acad. Sci. USA 94, 10,756–10,761.
Scheibner, K. A., Zhang, Z., and Cole, P. A. (2003) Merging fluorescence resonance energy transfer and expressed protein ligation to analyze protein-protein interactions. Anal. Biochem. 317, 226–232.
Medintz, I. L., Clapp, A. R., Mattoussi, H., Goldman, E. R., Fisher, B., and Mauro, J. M. (2003) Self-assembled nanoscale biosensors based on quantum dot FRET donors. Nat. Mater. 2, 630–638.
Chen, C. T., Wagner, H., and Still, W. C. (1998) Fluorescent, sequence-selective peptide detection by synthetic small molecules. Science 279, 851–853.
Tong, A. K., Li, Z., Jones, G. S., Russo, J. J., and Ju, J. (2001) Combinatorial fluorescence energy transfer tags for multiplex biological assays. Nature Biotech. 19, 756–759.
Ju, J., Glazer, A. N., and Mathies, R. A. (1996) Cassette labeling for facile construction of energy transfer fluorescent primers. Nucleic Acids Res. 24, 1144–1148.
Tong, A. K. and Ju, J. (2002) Single nucleotide polymorphism detection by combinatorial fluorescence energy transfer tags and biotinylated dideoxynucleotides. Nucleic Acids Res. 30, e19.
Tong, A. K., Li, Z., and Ju, J. (2002) Combinatorial fluorescence energy transfer tags: New molecular tools for genomics Applications. IEEE J. Quantum Electron. 38, 110–121.
Tong, A. K., Jockusch, S., Li, Z., et al. (2001) Triple fluorescence energy transfer in covalently trichromophore-labeled DNA. J. Am. Chem. Soc. 123, 12,923–12,924.
Watrob, H. M., Pan, C.-P., and Barkley, M. D. (2003) Two-step FRET as a structural tool. J. Am. Chem. Soc. 125, 7336–7343.
Ju, J. (2002) DNA sequencing with solid-phase-capturable dideoxynucleotides and energy transfer primers. Anal. Biochem. 309, 35–39.
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Tong, A.K., Ju, J. (2006). Multiplex Single-Nucleotide Polymorphism Detection by Combinatorial Fluorescence Energy Transfer Tags and Molecular Affinity. In: Didenko, V.V. (eds) Fluorescent Energy Transfer Nucleic Acid Probes. Methods in Molecular Biology™, vol 335. Humana Press. https://doi.org/10.1385/1-59745-069-3:201
Download citation
DOI: https://doi.org/10.1385/1-59745-069-3:201
Publisher Name: Humana Press
Print ISBN: 978-1-58829-380-0
Online ISBN: 978-1-59745-069-0
eBook Packages: Springer Protocols