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

  • Oleksandr Zavoiura
  • Ute Resch-Genger
  • Oliver SeitzEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2105)


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.

Key words

RNA-templated reactions Click chemistry Peptide nucleic acid Quantum dots RNA detection Fluorescence spectroscopy 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Oleksandr Zavoiura
    • 1
    • 2
  • Ute Resch-Genger
    • 1
  • Oliver Seitz
    • 2
    Email author
  1. 1.Division BiophotonicsFederal Institute for Materials Research and Testing (BAM)BerlinGermany
  2. 2.Department of ChemistryHumboldt University of BerlinBerlinGermany

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