Factors limiting the sensitivity of DNA-conjugated quantum dot molecular beacons

Colloidal quantum dots are desirable for a broad range of applications from biosensing to in vivo imaging due to their high luminosity and large surface areas available for bioconjugation. QDs are highly effective as fluorescent donors for Forster resonance energy transfer (FRET) and can be conjugated with multiple acceptors to enhance FRET efficiency and increase on/off ratios for sensing applications. We have demonstrated an efficient method for conjugating nucleic acids to QDs using chimeric peptide-peptide nucleic acids (peptide-PNA), and here we have characterized QD-FRET reporters assembled with this technique for use in CRISPR/Cas nuclease assays to identify factors which could limit the sensitivity of such reporters in practice.