The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity
Open accessPublished version of a preprint
Abstract
CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing on the basis of its ability to generate targeted, double-stranded DNA breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, nonspecific single-stranded deoxyribonuclease (ssDNase) cleavage is also a property of other type V CRISPR-Cas12 enzymes. By combining Cas12a ssDNase activation with isothermal amplification, we create a method termed DNA endonuclease-targeted CRISPR trans reporter (DETECTR), which achieves attomolar sensitivity for DNA detection. DETECTR enables rapid and specific detection of human papillomavirus in patient samples, thereby providing a simple platform for molecular diagnostics.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Cas12a enzymes are single crRNA-guided endonucleases measuring 3.9 kb”
From Viral Delivery Systems for CRISPR (2019) · cites this paper as [78]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“their distinguishable differences from Cas9 include: a T nucleotide-rich PAM site (5′-TTTV), self-catalysis of crRNA maturation, and a staggered dsDNA cut [76,77,78,79].”
From Viral Delivery Systems for CRISPR (2019) · cites this paper as [78]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Additionally, Cas12a′s trans-nuclease activity is utilized to detect sequence-specific nucleic acid (Chen et al., 2018).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Chen et al., 2018
The cited source says what the claim attributes to it.
In the citing paper
“their distinguishable differences from Cas9 include: a T nucleotide-rich PAM site (5′-TTTV), self-catalysis of crRNA maturation, and a staggered dsDNA cut [76,77,78,79].”
From Viral Delivery Systems for CRISPR (2019) · cites this paper as [78]
The cited source says what the claim attributes to it.
In the citing paper
“their distinguishable differences from Cas9 include: a T nucleotide-rich PAM site (5′-TTTV), self-catalysis of crRNA maturation, and a staggered dsDNA cut [76,77,78,79].”
From Viral Delivery Systems for CRISPR (2019) · cites this paper as [78]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Self-citationThe new frontier of genome engineering with CRISPR-Cas9
Doudna, J. A., & Charpentier, E. (2014) · Science · doi:10.1126/science.1258096 · Cited by 7,062
Self-citationCRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 5,947
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.038 · Cited by 4,761
Nucleic acid detection with CRISPR-Cas13a/C2c2
Gootenberg, J. S., Abudayyeh, O. O., Lee, J. W., Essletzbichler, P., Dy, A. J., Joung, J., Verdine, V. K., Donghia, N. M., Daringer, N. M., Freije, C. A., et al. (2017) · Science · doi:10.1126/science.aam9321 · Cited by 3,887
An updated evolutionary classification of CRISPR–Cas systems
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., et al. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3569 · Cited by 2,480
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
Abudayyeh, O. O., Gootenberg, J. S., Konermann, S., Joung, J., Slaymaker, I. M., Cox, D. B. T., Shmakov, S., Makarova, K. S., Semenova, E., Minakhin, L., et al. (2016) · Science · doi:10.1126/science.aaf5573 · Cited by 2,336
Crystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. A. (2014) · Nature · doi:10.1038/nature13011 · Cited by 1,822
Self-citationCRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA
Marraffini, L. A., & Sontheimer, E. J. (2008) · Science · doi:10.1126/science.1165771 · Cited by 1,642
Diversity, classification and evolution of CRISPR-Cas systems
Koonin, E. V., Makarova, K. S., & Zhang, F. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.05.008 · Cited by 1,423
Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection
East-Seletsky, A., O’Connell, M. R., Knight, S. C., Burstein, D., Cate, J. H. D., Tjian, R., & Doudna, J. A. (2016) · Nature · doi:10.1038/nature19802 · Cited by 1,236
Self-citationStructures of Cas9 endonucleases reveal RNA-mediated conformational activation
Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., et al. (2014) · Science · doi:10.1126/science.1247997 · Cited by 1,230
Self-citationRichardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L., & Corn, J. E. (2016) · Nature Biotechnology · doi:10.1038/nbt.3481 · Cited by 1,098
The natural history of cervical HPV infection: unresolved issues
Woodman, C. B. J., Collins, S. I., & Young, L. S. (2006) · Nature reviews. Cancer · doi:10.1038/nrc2050 · Cited by 1,056
Diversity and evolution of class 2 CRISPR–Cas systems
Shmakov, S., Smargon, A., Scott, D., Cox, D., Pyzocha, N., Yan, W., Abudayyeh, O. O., Gootenberg, J. S., Makarova, K. S., Wolf, Y. I., et al. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.184 · Cited by 1,029
The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA
Fonfara, I., Richter, H., Bratovič, M., Le Rhun, A., & Charpentier, E. (2016) · Nature · doi:10.1038/nature17945 · Cited by 988
Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array
Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., DeGennaro, E. M., Winblad, N., Choudhury, S. R., Abudayyeh, O. O., Gootenberg, J. S., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3737 · Cited by 926
Sorek, R., Kunin, V., & Hugenholtz, P. (2007) · Nature Reviews Microbiology · doi:10.1038/nrmicro1793 · Cited by 909
Fork Reversal and ssDNA Accumulation at Stalled Replication Forks Owing to Checkpoint Defects
Sogo, J. M., Lopes, M., & Foiani, M. (2002) · Science · doi:10.1126/science.1074023 · Cited by 824
Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA
Yamano, T., Nishimasu, H., Zetsche, B., Hirano, H., Slaymaker, I. M., Li, Y., Fedorova, I., Nakane, T., Makarova, K. S., Koonin, E. V., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.003 · Cited by 776
Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells
Kim, D., Kim, J., Hur, J. K., Been, K. W., Yoon, S.-H., & Kim, J.-S. (2016) · Nature Biotechnology · doi:10.1038/nbt.3609 · Cited by 731
Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells
Kleinstiver, B. P., Tsai, S. Q., Prew, M. S., Nguyen, N. T., Welch, M. M., Lopez, J. M., McCaw, Z. R., Aryee, M. J., & Joung, J. K. (2016) · Nature Biotechnology · doi:10.1038/nbt.3620 · Cited by 670
Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a
Swarts, D. C., John van der, O. O. S. T., & Jínek, M. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.03.016 · Cited by 625
A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants
Tang, X. D., Lowder, L. G., Zhang, T., Malzahn, A. A., Zheng, X., Voytas, D. F., Zhong, Z., Chen, Y., Ren, Q., Li, Q., et al. (2017) · Nature Plants · doi:10.1038/nplants.2017.18 · Cited by 619
Smargon, A. A., Cox, D. B. T., Pyzocha, N. K., Zheng, K., Slaymaker, I. M., Gootenberg, J. S., Abudayyeh, O. A., Essletzbichler, P., Shmakov, S., Makarova, K. S., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.023 · Cited by 575
Palefsky, J. M., Holly, E. A., Ralston, M. L., & Jay, N. (1998) · The Journal of Infectious Diseases · doi:10.1086/514194 · Cited by 543
Self-citationThe crystal structure of Cpf1 in complex with CRISPR RNA
Dong, D., Ren, K., Qiu, X., Zheng, J., Guo, M., Guan, X., Liu, H., Li, N., Zhang, B., Yang, D., et al. (2016) · Nature · doi:10.1038/nature17944 · Cited by 430
Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity
Samai, P., Pyenson, N., Jiang, W., Goldberg, G. W., Hatoum-Aslan, A., & Marraffini, L. A. (2015) · Cell · doi:10.1016/j.cell.2015.04.027 · Cited by 426
Structural Basis of Transcription Initiation
Zhang, Y., Feng, Y., Chatterjee, S., Tuske, S., Ho, M. X., Arnold, E., & Ebright, R. H. (2012) · Science · doi:10.1126/science.1227786 · Cited by 398
In vivo high-throughput profiling of CRISPR-Cpf1 activity
Kim, H. K., Song, M., Lee, J., Menon, A. V., Jung, S., Kang, Y.-M., Choi, J. W., Woo, E., Koh, H. C., Nam, J.-W., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4104 · Cited by 383
Application of the Theory of Diffusion-controlled Reactions to Enzyme Kinetics
Alberty, R., & Hammes, G. (1958) · The Journal of Physical Chemistry · doi:10.1021/j150560a005 · Cited by 338
A decade of discovery: CRISPR functions and applications
Barrangou, R., & Horvath, P. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.92 · Cited by 328
Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage
Stella, S., Alcón, P., & Montoya, G. (2017) · Nature · doi:10.1038/nature22398 · Cited by 244
Gao, P., Yang, H., Rajashankar, K. R., Huang, Z., & Patel, D. J. (2016) · Cell Research · doi:10.1038/cr.2016.88 · Cited by 238
Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR–Cas systemPreprint
Elmore, J. R., Sheppard, N. F., Ramia, N. F., Deighan, T., Li, H., Terns, R. M., & Terns, M. P. (2016) · Genes & Development · doi:10.1101/gad.272153.115 · Cited by 214
Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors
Tak, Y. E., Kleinstiver, B. P., Nuñez, J. K., Hsu, J. Y., Horng, J. E., Gong, J., Weissman, J. S., & Joung, J. K. (2017) · Nature Methods · doi:10.1038/nmeth.4483 · Cited by 208
In vivo high-throughput profiling of CRISPR–Cpf1 activity
송명재 (2018) · Cited by 201
Singh, D., Mallon, J. P., Poddar, A., Wang, Y., Tippana, R., Yang, O., Bailey, S., & Ha, T. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1718686115 · Cited by 198
The chemistry of Cas9 and its CRISPR colleagues
Chen, J. S., & Doudna, J. A. (2017) · Nature Reviews Chemistry · doi:10.1038/s41570-017-0078 · Cited by 143
Self-citationSingle-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes
Ma, E., Harrington, L. B., O’Connell, M. R., Zhou, K., & Doudna, J. A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.030 · Cited by 128
Self-citationCRISPR-Cas12a exploits R-loop asymmetry to form double-strand breaks
Cofsky, J. C., Karandur, D., Huang, C. J., Witte, I. P., Kuriyan, J., & Doudna, J. A. (2020) · eLife · doi:10.7554/elife.55143 · Cited by 108
Self-citationDNase H Activity of Neisseria meningitidis Cas9
Zhang, Y., Rajan, R., Seifert, H. S., Mondragón, A., & Sontheimer, E. J. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.020 · Cited by 73
Detection and quantitation of HPV in genital and oral tissues and fluids by real time PCR
Seaman, W. T., Andrews, E., Couch, M. E., Kojic, E. M., Cu‐Uvin, S., Palefsky, J. M., Deal, A. M., & Webster-Cyriaque, J. Y. (2010) · Virology Journal · doi:10.1186/1743-422x-7-194 · Cited by 55
Self-citationThe Role of Replication-Associated Repair Factors on R-Loops
Bhatia, V., Herrera‐Moyano, E., Aguilera, A., & Gómez‐González, B. (2017) · Genes · doi:10.3390/genes8070171 · Cited by 46
Morrison, E. A. B., Goldberg, G. L., Kadish, A. S., & Burk, R. D. (1992) · Journal of Clinical Microbiology · doi:10.1128/jcm.30.10.2539-2543.1992 · Cited by 44
Singh, D., Mallon, J. P., Poddar, A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/205575 · Cited by 7
Inducible, tunable and multiplex human gene regulation using CRISPR-Cpf1-based transcription factorsPreprint
Tak, Y. G., Kleinstiver, B. P., Nuñez, J. K., Hsu, J. Y., Gong, J., Weissman, J. S., & Joung, J. K. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/150656 · Cited by 2
Flagged first, then by citations
Cited by
Sorted by citations
CRISPR–Cas12-based detection of SARS-CoV-2
Broughton, J. P., Deng, X., Yu, G., Fasching, C. L., Servellita, V., Singh, J., Miao, X., Streithorst, J. A., Granados, A. C., Sotomayor-González, A., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0513-4 · Cited by 2,777
Self-citationMultiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6
Gootenberg, J. S., Abudayyeh, O. O., Kellner, M. J., Joung, J., Collins, J. J., & Zhang, F. (2018) · Science · doi:10.1126/science.aaq0179 · Cited by 2,679
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors
Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237
Li, H., Yang, Y., Hong, W., Huang, M., Wu, M., & Zhao, X. (2020) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-019-0089-y · Cited by 1,829
SHERLOCK: nucleic acid detection with CRISPR nucleases
Kellner, M. J., Koob, J. G., Gootenberg, J. S., Abudayyeh, O. O., & Zhang, F. (2019) · Nature Protocols · doi:10.1038/s41596-019-0210-2 · Cited by 1,699
Metadata
- Authors
- Chen, J. S., Ma, E., Harrington, L. B., Da Costa, M., Tian, X., Palefsky, J. M., & Doudna, J. A.
- Affiliations
- University of California, Berkeley (US)
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
- University of California, San Francisco (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Chen, Janice S.
- Ma, Enbo
- Harrington, Lucas B.
- Doudna, Jennifer A.
- ORCID
- Venue
- Science
- Published
- 2018-04-27
- Volume
- 360
- Issue
- 6387
- Pages
- 436-439
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC6628903
- OpenAlex
- W2787024379
- Cited by
- 4,507
- References
- 48
- Citations by year
- 2026: 759 · 2025: 816 · 2024: 736 · 2023: 643 · 2022: 624 · 2021: 452 · 2020: 271 · 2019: 135 · 2018: 67
- FWCI
- 82.27
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (MCB-1244557)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR/Cas12a, single-stranded DNA cleavage, isothermal amplification, DETECTR, DNA detection, HPV testing, molecular diagnosis, genome editing
- MeSH terms
- Clostridiales, Eubacteriales, Bacterial Proteins, DNA, Single-Stranded, Endodeoxyribonucleases, Endonucleases, Kinetics, Substrate Specificity, DNA Cleavage, CRISPR-Cas Systems, CRISPR-Associated Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
