Author: Prywes, Noam ; Pollard, Katherine S ; Desmarais, John J ; Stephens, Stephanie I ; Tan, Ming X ; Liu, Tina Y ; Savage, David F ; Kumar, G Renuka ; Harris, Andrew R ; Mok, Amanda ; Zhao, Chunyu ; Smock, Dylan C J ; Charles, Emeric J ; Armstrong, Maxim ; Switz, Neil A ; Dugan, Eli J ; Doudna, Jennifer A ; Thornton, Brittney W ; Jakhanwal, Shrutee ; Iavarone, Anthony T ; Fozouni, Parinaz ; Agrawal, Shreeya ; Escajeda, Arturo M ; Son, Sungmin ; Hsu, Patrick D ; Lareau, Liana F ; Bhuiya, Abdul ; Kim, Shineui ; McIntosh, Roger ; Knott, Gavin J ; Fletcher, Daniel A ; Ott, Melanie ; Díaz de León Derby, María ; Shu, Jeffrey

01 Sep 2021·Nature Chemical Biology

Accelerated RNA detection using tandem CRISPR nucleases

Article

Author: Prywes, Noam ; Pollard, Katherine S ; Desmarais, John J ; Stephens, Stephanie I ; Tan, Ming X ; Liu, Tina Y ; Savage, David F ; Kumar, G Renuka ; Harris, Andrew R ; Mok, Amanda ; Zhao, Chunyu ; Smock, Dylan C J ; Charles, Emeric J ; Switz, Neil A ; Dugan, Eli J ; Armstrong, Maxim ; Doudna, Jennifer A ; Thornton, Brittney W ; Fozouni, Parinaz ; Iavarone, Anthony T ; Agrawal, Shreeya ; Jakhanwal, Shrutee ; Escajeda, Arturo M ; Son, Sungmin ; Hsu, Patrick D ; Lareau, Liana F ; Bhuiya, Abdul ; Kim, Shineui ; McIntosh, Roger ; Knott, Gavin J ; Fletcher, Daniel A ; Díaz de León Derby, María ; Ott, Melanie ; Shu, Jeffrey

Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided RNA recognition that triggers cleavage and release of a fluorescent reporter molecule, but long reaction times hamper their detection sensitivity and speed. Here, we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 molecules per µl of RNA in 20 min. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA extracted from respiratory swab samples with quantitative reverse transcriptase PCR (qRT-PCR)-derived cycle threshold (C_t) values up to 33, using a compact detector. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables sensitive, direct RNA detection in a format that is amenable to point-of-care infection diagnosis as well as to a wide range of other diagnostic or research applications.

Accelerated RNA detection using tandem CRISPR nucleases

Author: Prywes, Noam ; Pollard, Katherine S ; Desmarais, John J ; Kim, Shin E ; Doudna, Jennifer A ; Stephens, Stephanie I ; de León Derby, María Díaz ; Tan, Ming X ; Liu, Tina Y ; Savage, David F ; Hsu, Patrick D ; Kumar, G Renuka ; Harris, Andrew R ; Mok, Amanda ; Zhao, Chunyu ; Smock, Dylan C J ; Charles, Emeric J ; Switz, Neil A ; Armstrong, Maxim ; Dugan, Eli J ; Thornton, Brittney W ; Fozouni, Parinaz ; Fletcher, Daniel A ; Iavarone, Anthony T ; Agrawal, Shreeya ; Jakhanwal, Shrutee ; Escajeda, Arturo M ; Son, Sungmin ; Lareau, Liana F ; Bhuiya, Abdul ; McIntosh, Roger ; Knott, Gavin J ; Ott, Melanie ; Shu, Jeffrey

Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule1,2, but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ∼30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.

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