CRISPR/Cas Systems towards Next-Generation Biosensing.

Beyond its remarkable genome editing ability, the CRISPR/Cas9 effector has also been utilized in biosensing applications. The recent discovery of the collateral RNA cleavage activity of the Cas13a effector has sparked even greater interest in developing novel biosensing technologies for nucleic acid detection and promised significant advances in CRISPR diagnostics. Now, along with the discovery of Cas12 collateral cleavage activities on single-stranded DNA (ssDNA), several CRISPR/Cas systems have been established for detecting various targets, including bacteria, viruses, cancer mutations, and others. Based on key Cas effectors, we provide a detailed classification of CRISPR/Cas biosensing systems and propose their future utility. As the field continues to mature, CRISPR/Cas systems have the potential to become promising candidates for next-generation diagnostic biosensing platforms.

[1]  Frank Schwede,et al.  Type III CRISPR–Cas systems produce cyclic oligoadenylate second messengers , 2017, Nature.

[2]  G. K. Rasineni,et al.  Diagnosis and therapy with CRISPR advanced CRISPR based tools for point of care diagnostics and early therapies. , 2018, Gene.

[3]  Kira S. Makarova,et al.  Diversity and evolution of class 2 CRISPR–Cas systems , 2017, Nature Reviews Microbiology.

[4]  Daniel S. Chertow,et al.  Next-generation diagnostics with CRISPR , 2018, Science.

[5]  Xiaoshu Xu,et al.  A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology. , 2019, Journal of molecular biology.

[6]  Qiu-Xiang Cheng,et al.  CRISPR-Cas12a-assisted nucleic acid detection , 2018, Cell Discovery.

[7]  Ronald D. Vale,et al.  A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging , 2014, Cell.

[8]  Takashi Yamamoto,et al.  Magic wands of CRISPR—lots of choices for gene knock-in , 2017, Cell Biology and Toxicology.

[9]  D. Grunwald,et al.  CRISPR-Sirius: RNA Scaffolds for Signal Amplification in Genome Imaging , 2018, Nature Methods.

[10]  Jennifer A. Doudna,et al.  Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection , 2016, Nature.

[11]  Guillaume Lambert,et al.  Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components , 2016, Cell.

[12]  Jane Ru Choi,et al.  An integrated paper-based sample-to-answer biosensor for nucleic acid testing at the point of care. , 2016, Lab on a chip.

[13]  Sita J. Saunders,et al.  An updated evolutionary classification of CRISPR–Cas systems , 2015, Nature Reviews Microbiology.

[14]  R. A. Mumford,et al.  The role and challenges of new diagnostic technology in plant biosecurity , 2015, Food Security.

[15]  Česlovas Venclovas,et al.  A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems , 2017, Science.

[16]  Jennifer A. Doudna,et al.  CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity , 2018, Science.

[17]  Qiu-Xiang Cheng,et al.  CRISPR-Cas12a has both cis- and trans-cleavage activities on single-stranded DNA , 2018, Cell Research.

[18]  Jennifer A. Doudna,et al.  Programmed DNA destruction by miniature CRISPR-Cas14 enzymes , 2018, Science.

[19]  Da Xing,et al.  Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection. , 2018, Analytical chemistry.

[20]  Eugene V Koonin,et al.  Diversity, classification and evolution of CRISPR-Cas systems. , 2017, Current opinion in microbiology.

[21]  George M. Church,et al.  Developmental barcoding of whole mouse via homing CRISPR , 2018, Science.

[22]  Lv-yun Zhu,et al.  Highly Effective and Low-Cost MicroRNA Detection with CRISPR-Cas9. , 2018, ACS synthetic biology.

[23]  Chunhai Fan,et al.  Biosensing: CRISPR-powered diagnostics , 2017, Nature Biomedical Engineering.

[24]  J. Doudna,et al.  Applications of CRISPR-Cas Enzymes in Cancer Therapeutics and Detection. , 2018, Trends in cancer.

[25]  Shaojie Zhang,et al.  Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow , 2016, Nature Biotechnology.

[26]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[27]  Stan J. J. Brouns,et al.  Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.

[28]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[29]  Randall J. Platt,et al.  Transcriptional recording by CRISPR spacer acquisition from RNA , 2018, Nature.

[30]  James J. Collins,et al.  Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6 , 2018, Science.

[31]  A. Regev,et al.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System , 2015, Cell.

[32]  Esteban O. Mazzoni,et al.  CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci , 2016, Nature Communications.

[33]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[34]  Anthony M. Zador,et al.  Cellular barcoding: lineage tracing, screening and beyond , 2018, Nature Methods.

[35]  Hayden C. Metsky,et al.  Field-deployable viral diagnostics using CRISPR-Cas13 , 2018, Science.

[36]  L. G. Pacheco,et al.  Detecting pathogens with Zinc-Finger, TALE and CRISPR- based programmable nucleic acid binding proteins. , 2018, Journal of microbiological methods.

[37]  M. S. Mukhtar,et al.  Genome Editing: Targeting Susceptibility Genes for Plant Disease Resistance. , 2018, Trends in biotechnology.

[38]  Lei S. Qi,et al.  CRISPR/Cas9 in Genome Editing and Beyond. , 2016, Annual review of biochemistry.

[39]  T. Lu,et al.  Emerging applications for DNA writers and molecular recorders , 2018, Science.

[40]  Eric S. Lander,et al.  C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector , 2016, Science.

[41]  David R. Liu,et al.  Rewritable multi-event analog recording in bacterial and mammalian cells , 2018, Science.

[42]  R. Bhattacharyya,et al.  Harnessing CRISPR Effectors for Infectious Disease Diagnostics. , 2018, ACS infectious diseases.

[43]  Shiyuan Li,et al.  CRISPR-Cas12b-assisted nucleic acid detection platform , 2018, bioRxiv.

[44]  Kira S. Makarova,et al.  SnapShot: Class 2 CRISPR-Cas Systems , 2017, Cell.

[45]  C. Chiu.  Cutting-Edge Infectious Disease Diagnostics with CRISPR , 2018, Cell Host & Microbe.

[46]  C. Fan,et al.  Isothermal Amplification of Nucleic Acids. , 2015, Chemical reviews.

[47]  Eugene V Koonin,et al.  Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. , 2015, Molecular cell.

[48]  Jennifer A. Doudna,et al.  Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering , 2016, Cell.

[49]  Aviv Regev,et al.  RNA targeting with CRISPR–Cas13 , 2017, Nature.

[50]  Aviv Regev,et al.  Nucleic acid detection with CRISPR-Cas13a/C2c2 , 2017, Science.

[51]  Q. Ouyang,et al.  Paired Design of dCas9 as a Systematic Platform for the Detection of Featured Nucleic Acid Sequences in Pathogenic Strains. , 2017, ACS synthetic biology.

[52]  Dipali G Sashital.  Pathogen detection in the CRISPR–Cas era , 2018, Genome Medicine.

[53]  Shaojie Zhang,et al.  Multicolor CRISPR labeling of chromosomal loci in human cells , 2015, Proceedings of the National Academy of Sciences.

[54]  A. Kurg,et al.  Nucleic acid detection technologies and marker molecules in bacterial diagnostics , 2014, Expert review of molecular diagnostics.