Title:
ENGINEERED CRISPR-CAS SYSTEMS AND METHODS FOR SENSITIVE AND SPECIFIC DIAGNOSTICS
Document Type and Number:
WIPO Patent Application WO/2021/222130
Kind Code:
A3
Abstract:
The disclosure relates to an engineered type III CRISPR-Cas system for sensitive and sequence specific detection of nucleic acid in a sample. For example, the engineered type III CRISPR-Cas system may be implemented as an assay for testing SARS-CoV-2 virus (or other target nucleic acid in the sample) that can be performed quickly, such as in one hour or less. Nucleic acid recognition by type III systems may trigger Cas10-mediated nuclease activity and/or polymerase activity, which may generate pyrophosphates, protons and cyclic oligonucleotides. The nuclease activity and/or the one or more products of the Cas10-polymerase are detected using colorimetric, visible fluorometric, and/or instrumented fluorometric detection.
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Inventors:
WIEDENHEFT BLAKE A (US)
SANTIAGO-FRANGOS ANDREW (US)
NEMUDRAIA ANNA A (US)
NEMUDRYI ARTEM A (US)
SANTIAGO-FRANGOS ANDREW (US)
NEMUDRAIA ANNA A (US)
NEMUDRYI ARTEM A (US)
Application Number:
PCT/US2021/029219
Publication Date:
December 02, 2021
Filing Date:
April 26, 2021
Export Citation:
Assignee:
UNIV MONTANA STATE (US)
International Classes:
C12N9/22; A61K48/00; C12N15/113; C12N15/32; C12N15/62; C12N15/63; C12N15/79
Foreign References:
| CN110982945A | 2020-04-10 |
Other References:
MIGLE KAZLAUSKIENE, GEORGIJ KOSTIUK, ČESLOVAS VENCLOVAS, GINTAUTAS TAMULAITIS, VIRGINIJUS SIKSNYS: "A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE, US, vol. 357, no. 6351, 11 August 2017 (2017-08-11), US , pages 605 - 609, XP055495134, ISSN: 0036-8075, DOI: 10.1126/science.aao0100
EAST-SELETSKY, A ET AL.: "Two Distinct RNase Activities of CRISPR-C2c2 Enable Guide RNA Processing and RNA Detection", NATURE, vol. 538, no. 7624, 13 October 2016 (2016-10-13), pages 270 - 273, XP055719305, DOI: 10.1038/ nature 19802
BROUGHTON, JP ET AL.: "CRISPR-Cas12-based detection of SARS-CoV-2", NATURE BIOTECHNOLOGY, vol. 38, 16 April 2020 (2020-04-16), pages 870 - 874, XP037187541, DOI: 10.1038/s41587-020-0513-4
TIMOTHY R ABBOTT, DHAMDHERE GIRIJA, LIU YANXIA, LIN XUEQIU, GOUDY LAINE, ZENG LEIPING, CHEMPARATHY AUGUSTINE, CHMURA STEPHEN, HEAT: "Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza", BIORXIV, 14 March 2020 (2020-03-14), XP055733410, DOI: 10.1101/2020.03.13.991307
CHEN, JS ET AL.: "CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity", SCIENCE, vol. 360, no. 6387, 27 April 2018 (2018-04-27), pages 436 - 439, XP055615609, DOI: 10.1126/ science .aar6245
JIA NING; JONES ROGER; SUKENICK GEORGE; PATEL DINSHAW J.: "Second Messenger cA4 Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path", MOLECULAR CELL, ELSEVIER, AMSTERDAM, NL, vol. 75, no. 5, 17 July 2019 (2019-07-17), AMSTERDAM, NL, pages 933, XP085802928, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2019.06.013
ROUILLON, C ET AL.: "Control of cyclic oligoadenylate synthesis in a type III CRISPR system", ELIFE, vol. 7, 2018, pages 1 - 22, XP055729022, DOI: 10.7554/eLife.36734
NORIHIRO TOMITA, YASUYOSHI MORI, HIDETOSHI KANDA, TSUGUNORI NOTOMI: "Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products", NATURE PROTOCOLS, NATURE PUBLISHING GROUP, GB, vol. 3, no. 5, 1 April 2008 (2008-04-01), GB , pages 877 - 882, XP055221080, ISSN: 1754-2189, DOI: 10.1038/nprot.2008.57
FISCHBACH JENS, LOH QIUTING, BIER FRANK F., LIM THEAM SOON, FROHME MARCUS, GLÖKLER JÖRN: "Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method", SCIENTIFIC REPORTS, vol. 7, no. 1, 1 April 2017 (2017-04-01), XP055880466, DOI: 10.1038/srep45085
SANTIAGO-FRANGOS, A ET AL.: "Intrinsic signal amplification by type III CRISPR-Cas systems provides a sequence-specific SARS-CoV-2 diagnostic", CELL REPORTS MEDICINE, vol. 2, no. 6, 15 June 2021 (2021-06-15), pages 100319, XP055872507, DOI: 10.1016/j.xcrm.2021.100319
EAST-SELETSKY, A ET AL.: "Two Distinct RNase Activities of CRISPR-C2c2 Enable Guide RNA Processing and RNA Detection", NATURE, vol. 538, no. 7624, 13 October 2016 (2016-10-13), pages 270 - 273, XP055719305, DOI: 10.1038/ nature 19802
BROUGHTON, JP ET AL.: "CRISPR-Cas12-based detection of SARS-CoV-2", NATURE BIOTECHNOLOGY, vol. 38, 16 April 2020 (2020-04-16), pages 870 - 874, XP037187541, DOI: 10.1038/s41587-020-0513-4
TIMOTHY R ABBOTT, DHAMDHERE GIRIJA, LIU YANXIA, LIN XUEQIU, GOUDY LAINE, ZENG LEIPING, CHEMPARATHY AUGUSTINE, CHMURA STEPHEN, HEAT: "Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza", BIORXIV, 14 March 2020 (2020-03-14), XP055733410, DOI: 10.1101/2020.03.13.991307
CHEN, JS ET AL.: "CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity", SCIENCE, vol. 360, no. 6387, 27 April 2018 (2018-04-27), pages 436 - 439, XP055615609, DOI: 10.1126/ science .aar6245
JIA NING; JONES ROGER; SUKENICK GEORGE; PATEL DINSHAW J.: "Second Messenger cA4 Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path", MOLECULAR CELL, ELSEVIER, AMSTERDAM, NL, vol. 75, no. 5, 17 July 2019 (2019-07-17), AMSTERDAM, NL, pages 933, XP085802928, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2019.06.013
ROUILLON, C ET AL.: "Control of cyclic oligoadenylate synthesis in a type III CRISPR system", ELIFE, vol. 7, 2018, pages 1 - 22, XP055729022, DOI: 10.7554/eLife.36734
NORIHIRO TOMITA, YASUYOSHI MORI, HIDETOSHI KANDA, TSUGUNORI NOTOMI: "Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products", NATURE PROTOCOLS, NATURE PUBLISHING GROUP, GB, vol. 3, no. 5, 1 April 2008 (2008-04-01), GB , pages 877 - 882, XP055221080, ISSN: 1754-2189, DOI: 10.1038/nprot.2008.57
FISCHBACH JENS, LOH QIUTING, BIER FRANK F., LIM THEAM SOON, FROHME MARCUS, GLÖKLER JÖRN: "Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method", SCIENTIFIC REPORTS, vol. 7, no. 1, 1 April 2017 (2017-04-01), XP055880466, DOI: 10.1038/srep45085
SANTIAGO-FRANGOS, A ET AL.: "Intrinsic signal amplification by type III CRISPR-Cas systems provides a sequence-specific SARS-CoV-2 diagnostic", CELL REPORTS MEDICINE, vol. 2, no. 6, 15 June 2021 (2021-06-15), pages 100319, XP055872507, DOI: 10.1016/j.xcrm.2021.100319
Attorney, Agent or Firm:
KOO, Hean L. (US)
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