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Peptide Nucleic Acids pp 187–198Cite as

Reactive Quantum Dot-Based FRET Systems for Target-Catalyzed Detection of RNA

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2105))

Abstract

Oligonucleotide-templated reactions (OTRs) between two reactive hybridization probes allow for the detection of a DNA or RNA of interest by exploiting the target molecule as a catalyst of chemical reactions. The product of such a reaction commonly exhibits distinct fluorescence properties and can be detected by the means of fluorescence spectroscopy. The vast majority of OTR systems utilize organic dyes as fluorescent reporters. However, the use of brighter emitters, such as semiconductor quantum dots (QDs), has potential to improve the sensitivity of detection by providing brighter signals and permitting the use of probes at very low concentrations. Here we report an RNA-templated reaction between two fluorescently labeled peptide nucleic acid (PNA)-based probes, which proceeds on the surface of a QD. The QD-bound PNA probe bears a cysteine functionality, while the other PNA is functionalized with an organic dye as a thioester. OTR between these probes proceeds through a transfer of the organic dye to the QD and can be conveniently monitored via fluorescence resonance energy transfer (FRET) from the QD to the Cy5. The reaction was performed in a conventional fluorescence microplate reader and permits the detection of RNA in the picomolar range.

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Authors and Affiliations

  1. Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany

    Oleksandr Zavoiura & Ute Resch-Genger

  2. Department of Chemistry, Humboldt University of Berlin, Berlin, Germany

    Oleksandr Zavoiura & Oliver Seitz

Authors
  1. Oleksandr Zavoiura
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  2. Ute Resch-Genger
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  3. Oliver Seitz
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Corresponding author

Correspondence to Oliver Seitz .

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Editors and Affiliations

  1. Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Peter E. Nielsen

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Zavoiura, O., Resch-Genger, U., Seitz, O. (2020). Reactive Quantum Dot-Based FRET Systems for Target-Catalyzed Detection of RNA. In: Nielsen, P. (eds) Peptide Nucleic Acids. Methods in Molecular Biology, vol 2105. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0243-0_11

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  • DOI: https://doi.org/10.1007/978-1-0716-0243-0_11

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0242-3

  • Online ISBN: 978-1-0716-0243-0

  • eBook Packages: Springer Protocols

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