CRISPR-induced DNA reorganization for multiplexed nucleic acid detection

Margot Karlikow*, Evan Amalfitano, Xiaolong Yang, Jennifer Doucet, Abigail Chapman, Peivand Sadat Mousavi, Paige Homme, Polina Sutyrina, Winston Chan, Sofia Lemak, Alexander F. Yakunin, Adam G. Dolezal, Shana Kelley, Leonard J. Foster, Brock A. Harpur, Keith Pardee*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Nucleic acid sensing powered by the sequence recognition of CRIPSR technologies has enabled major advancement toward rapid, accurate and deployable diagnostics. While exciting, there are still many challenges facing their practical implementation, such as the widespread need for a PAM sequence in the targeted nucleic acid, labile RNA inputs, and limited multiplexing. Here we report FACT (Functionalized Amplification CRISPR Tracing), a CRISPR-based nucleic acid barcoding technology compatible with Cas12a and Cas13a, enabling diagnostic outputs based on cis- and trans-cleavage from any sequence. Furthermore, we link the activation of CRISPR-Cas12a to the expression of proteins through a Reprogrammable PAIRing system (RePAIR). We then combine FACT and RePAIR to create FACTOR (FACT on RePAIR), a CRISPR-based diagnostic, that we use to detect infectious disease in an agricultural use case: honey bee viral infection. With high specificity and accuracy, we demonstrate the potential of FACTOR to be applied to the sensing of any nucleic acid of interest.

Original languageEnglish (US)
Article number1505
JournalNature communications
Issue number1
StatePublished - Dec 2023

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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