CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis
Abstract
:1. Introduction
1.1. The Mechanism of the CRISPR/Cas9 System
1.2. The Mechanism of the CRISPR/Cas12 System
1.3. The Mechanism of CRISPR/Cas13 System
2. Application of CRISPR in Live-Cell Imaging
Application | Imaging System | Cas Protein | Effector Molecule(s) | Advantage(s) | Limitation(s) | Ref. |
---|---|---|---|---|---|---|
Chromatin/genomic loci imaging | FP-based | dCas 9 | dCas9-EGPF | Simple and versatile tool for imaging | Low SNR, poor labeling efficiency | [31] |
dCas 9 | dSaCas9-EGFP dSpCas9-mCherry | Achieved two-color CRISPR imaging | Relatively weak fluorescence signal and low signal-to-noise ratio | [34] | ||
dCas 9 | sgRNA-aptamer-FP | Simultaneous labeling of six genetic loci | Complex sgRNA engineering, efficient delivery system needed | [35] | ||
dCas 9 | dCas9-Suntag-scFv-GCN 4-sfGFP | Amplification of fluorescence signal intensity to improve signal-to-noise ratio enables labeling of low-repeat motifs | Large array size affects Cas9 functionality | [36] | ||
dCas 9 | dCas9-SuTag10×-sfGFP-LEXY | Simultaneous labeling of nine duplicate genomic loci with a significantly improved signal-to-noise ratio | Large array size affects Cas9 functionality | [37] | ||
Organic dye-based | dCas 9 | dCas9-HaloTag | Economical, efficient | Altered cell physiology | [38] | |
dCas 9 | sgRNA-MTS-MB | Different combinations of fluorophore/bursting agent pairs and MB/MTS sequences can be flexibly selected | MBs are expensive | [39] | ||
dCas 9 | 3sgMUC4-dual-MTS-MB | Dynamic imaging of non-repetitive genomic motifs with only three unique sgRNAs Higher sensitivity | MBs are expensive No simultaneous visualization of multiple genomic motifs | [40] | ||
Quantum dot (QD)-based imaging | dCas 9 | dCas9-QD | Enables tracking of individual viruses | Large size, difficult cell delivery | [41] | |
dCas 9 | SA-QDs | Efficient labeling of internal viruses without altering the virus envelope and capsid | Large size, difficult cell delivery | [42] | ||
RNA imaging | FP-based | Rcas9 | dCas9-FP | Imaging of RNA | Limit to imaging of low-abundance mRNA | [43] |
FP-based | RCas9 | dCas9-EGFP | Imaging of RNA | Limit to imaging of low-abundance mRNA | [44] | |
FP-based | dCas9 | dCas9-EGFP | Allow efficient imaging of low-abundance mRNA | Large array size | [45] | |
Organic dye-based | dCas9 | sgRNA-Pepper530 | High fluorescence intensity and turn-on rate | Detailed structure-activity of Pepper to be analyzed | [46] | |
FP-based | dCas13a | dCas13-EGFP | Imaging of RNA | No current guidelines to design efficient gRNAs targeting an RNA of interest | [47] | |
FP-based | dCas13a | dCas13a-msfGFP-ZF-KRAB | Optimized S/N ratio | Imaging of intranuclear RNA is not possible | [48] | |
Organic dye-based | dCas13b | CRISPR-TRA-tag | Modular design flexibility Smaller and more accurate fluorescent signals | Large array size | [49] |
2.1. CRISPR/Cas for Imaging of Chromatin/Genomic Loci
2.1.1. FP-Based CRISPR/dCas9 Systems
2.1.2. Organic Dye-Based CRISPR/dCas9 Systems
2.1.3. Quantum-Dots-Based CRISPR/dCas9 Systems
2.2. CRISPR/Cas for RNA Imaging
2.2.1. CRISPR/Cas9-Based RNA Imaging System
2.2.2. CRISPR/Cas13-Based RNA Imaging System
2.2.3. RNA Imaging Based on other Cas Platforms
2.3. CRISPR/Cas for Protein Imaging
2.3.1. Fluorescent Protein Labeling
2.3.2. Near-Infrared Imaging
2.4. Deficiencies and Shortcomings of CRISPR/Cas for Live-Cell Imaging
3. Research Progress of CRISPR/Cas for Bioanalysis
3.1. Nucleic Acid Analysis
3.1.1. Cas9-Based Nucleic Acid Detection System
3.1.2. Cas12-Based Nucleic Acid Detection System
3.1.3. Cas13-Based Nucleic Acid Detection System
3.1.4. Other Cas-Based Nucleic Acid Detection Systems
3.2. Protein Analysis
3.3. Small Molecule Analysis
3.4. Flaws and Shortcomings of CRISPR/Cas Systems for Bioanalysis
4. Outlook
Author Contributions
Funding
Conflicts of Interest
Abbreviations
ACTB | Actin beta |
aM | Artificial microorganisms |
AMP | Adenosine monophosphate |
APC | Antigen-presenting cell |
ASD | Activating sequence discriminator |
ATP | Adenosine-5′-triphosphate |
BA-CASLFA | Bivalent aptamer-assisted CRISPR/Cas12a-mediated transversal flow assay |
BPE-ECL | bipolar electrode-electrochemiluminescence |
CAS-EXPER | CRISPR/Cas9-triggered isothermal exponential amplification reaction |
C2c2 | Class 2 type VI-A CRISPR/Cas effector |
Cas | CRISPR-associated proteins |
CFU | Colony-forming units |
CLISA | CRISPR/Cas signal amplification linked immunosorbent assay |
CRISPR | Clustered regularly interspaced short palindromic repeats |
CREST | Cas13-based robust, equitable, scalable testing |
crRNA | CRISPR RNA |
dCas | Deactivated CRISPR-associated proteins |
DENV | Dengue virus |
DETECTR | DNA endonuclease-targeted CRISPR transporter |
DNA | Deoxyribonucleic acid |
DNase | Deoxyribonuclease I |
dSaCas9 | Deactivated Staphylococcus aureus Cas9 |
dsDNA | Double-stranded DNA |
dSpCas9 | Deactivated Streptococcus pyogenes Cas9 |
ECL | enhanced chemiluminescence |
E-CRISPR | Electrochemical CRISPR |
E-DNA | Electrochemical DNA |
EGFP | Enhanced green fluorescent protein |
ELISA | Enzyme-linked immunosorbent assay |
EXPAR | Exponential amplification reaction |
Fc-ssDNA | Fragment crystallizable region ssDNA |
FPs | Farnesyl diphosphate synthase |
F-Q | Fluorophore quencher |
GCN | General control noninducible |
GFP | Green fluorescence protein |
HA | Humic acid |
HARRY | Highly sensitive aptamer-regulated Cas12f R-loop for bioanalysis |
HDR | Homology-directed repair |
HIV | Human immunodeficiency virus |
HNH | His-Asn-His |
HOLMES | One-hour low-cost multipurpose highly efficient system |
HUDSON | Heating unextracted diagnostic samples to obliterate nucleases |
KRAB | KRAB-containing zinc finger proteins |
LAMP | Loop-mediated isothermal amplification |
LbCas12a | Lachnospiraceae bacterium Cas12a |
lncRNAs | Long non-coding RNAs |
LRET | Luminescence resonance energy transfer |
LwaCas13a | Leptotrichia wadei Cas13a |
MB | Molecular beacon |
MCP | MS2 coat protein |
miRNAs | MicroRNAs |
MNPs | Magnetic nanoparticles |
MS | Methylation-sensitive |
MTS | MB target sequence |
MUC | Mucin |
mRNA | Messenger RNA |
NASBA | Nucleic acid sequence-based amplification |
NASBACC | Nucleic acid sequence-based amplification—CRISPR cleavage |
NIR | Near-infrared |
NLS | Nuclear localization signal |
PAM | Protospacer-adjacent motif |
PAMmer | PAM-presenting DNA oligonucleotide |
PCR | Polymerase chain reaction |
POCT | Point-of-care testing |
PM | Peritrophic matrix |
PNK | Polynucleotide kinase |
PRV | Pseudorabies virus |
QD | Quantum dot |
RACE | Rapid amplification of cDNA end |
RCA | Rolling circle amplification |
RNA | Ribonucleic acid |
RN | Ribonucleic |
RPA | Recombinase polymerase amplification |
RT | Reverse transcription |
SaCas9 | Staphylococcus aureus Cas9 |
SA | Streptavidin |
scFv | Single-chain antibody fragment |
SDA | Strand displacement amplification |
sfGFP | Superfolder GFP |
SgRNA | Single guide RNA |
sgMUC | Small guide mucin |
SHERLOCK | Specific high-sensitivity enzymatic reporter unlocking |
SNPs | Single-nucleotide polymorphisms |
SNR | Signal-to-noise ratio |
SpCas9 | Streptococcus pyogenes Cas9 |
ssDNA | Single-stranded DNA |
ssRNA | Single-stranded RNA |
SunTag | Supernova tagging system |
SVT | Single-virus tracking |
T4 PNK | T4 polynucleotide kinase |
TdT | Terminal deoxynucleotidyl transferase |
TFRC | Transferrin receptor protein 1 |
TGF-β1 | Transforming growth factor beta 1 |
tracrRNA | Transactivating CRISPR RNA |
UCNP | Upconversion nanoparticle |
UDG | Uracil-DNA glycosylase |
UV | Ultraviolet radiation |
VEGF | Vascular endothelial growth factor |
ZIF | Zeolite imidazolate framework |
ZIKV | Zika virus |
ZF | Zinc finger |
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Classification | Method | Cas Protein Based | Amplification | Analysis | Readout | Sensitivity | Quantification | Time | Portability | Ref. |
---|---|---|---|---|---|---|---|---|---|---|
nucleic acid analysis | NASBACC | Cas9 | NASBA | DNA | Fluorescence | aM | N | ~3 h | N | [92] |
CAS-EXPAR | Cas9 | EXPAR | IncRNA | Fluorescence | aM | N | ~1 h | N | [102] | |
RACE | Cas9 | RCA | RNA | colorimetric | fM | Y | ~4 h | N | [103] | |
E-CRISPR | Cas9/Cas12a | N | DNA | electrochemistry | pM | Y | ~1 h | N | [104] | |
HOLMES | Cas12a | PCR; RT-PCR | DNA/RNA | Fluorescence | aM | N | ~1 h | N | [90] | |
HOLMESv2 | Cas12b | LAMP | DNA/RNA | Fluorescence | aM | Y | ~1 h | Y | [105] | |
DETECTR | Cas12a | RPA | DNA | Fluorescence | aM | N | ~2 h | N | [24] | |
Ultrafast visual detection platform | Cas12a | PCR | DNA | Fluorescence | 1.28 copies | N | ~10 min | Y | [97] | |
CRISPR/hybrid Cas | Cas12a, Cas13a | N | DNA/RNA | Fluorescence | 10 viral copies/μL | Y | <2 h | N | [106] | |
SHERLOCK | LwCas13a | RPA | DNA/RNA | Fluorescence | aM | N | 2–5 h | Y | [30] | |
HUDSON + SHERLOCK | LwCas13a | RPA | RNA/DNA | Fluorescence | aM | N | ~2 h | Y | [91] | |
DETECTR-Cas12f | Cas12f | RPA | DNA | Fluorescence | aM | N | ~2 h | N | [107] | |
protein analysis | TdT-combined CRISPR/Cas12a amplification | Cas12 | N | UDG | Fluorescence | uM | Y | ~4 h | N | [108] |
CLISA | Cas13 | N | IL-6, VEGF | Fluorescence | ng/Ml | Y | - | N | [109] | |
E-CRISPR | Cas12a | LAMP | Protein | electrochemistry | nM | Y | ~1 h | Y | [110] | |
ATP analysis | CRISPR-LbCas12a biosensor | LbCas12a | N | ATP | Fluorescence | μM | Y | 40 min | Y | [100] |
ASD-Cas12a | LbCas12a | SDA | ATP | Fluorescence | μM | Y | ~20 min | N | [101] | |
Molecular Radar | Cas12a | N | ATP | Fluorescence | nM | Y | ~25 min | Y | [99] | |
BPE-ECL | Cas12a | N | ATP | electrochemistry | nM | Y | ~2 h | N | [111] | |
BA-CASLFA | Cas12a | N | ATP | Fluorescence | μM | Y | ~26 min | N | [112] | |
dsDNA-ZIF-90@Ag3AuS2@Fe3O4 nanoplatform | Cas12a | N | ATP, ADP | Fluorescence | nM | Y | ~30 min | N | [113] |
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Huang, S.; Dai, R.; Zhang, Z.; Zhang, H.; Zhang, M.; Li, Z.; Zhao, K.; Xiong, W.; Cheng, S.; Wang, B.; et al. CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis. Int. J. Mol. Sci. 2023, 24, 13447. https://doi.org/10.3390/ijms241713447
Huang S, Dai R, Zhang Z, Zhang H, Zhang M, Li Z, Zhao K, Xiong W, Cheng S, Wang B, et al. CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis. International Journal of Molecular Sciences. 2023; 24(17):13447. https://doi.org/10.3390/ijms241713447
Chicago/Turabian StyleHuang, Shuo, Rui Dai, Zhiqi Zhang, Han Zhang, Meng Zhang, Zhangjun Li, Kangrui Zhao, Wenjun Xiong, Siyu Cheng, Buhua Wang, and et al. 2023. "CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis" International Journal of Molecular Sciences 24, no. 17: 13447. https://doi.org/10.3390/ijms241713447