Figures (3)  Tables (2)
    • Figure 1. 

      The classification of CRISPR/Cas systems. Representative operons for each type are shown here. Gray represents Cas systems employing multi-subunit protein complexes to cut target DNA or RNA; blue represents Cas employing a single multidomain protein in complex for sequence cleavage.

    • Figure 2. 

      Composition of CRISPR/Cas system. CRISPR/Cas9, the Cas9 system is composed of a Cas9 protein and a sgRNA. The yellow arrow represents DNA double-strand break (DSB) induced by RuvC and HNH domains. CBE, a base editor is a fusion of catalytically deactivated Cas9 domain and deaminase domain. CBE deaminates cytosine to generate uracil (C-U), then converts the uracil into thymine (U-T) by DNA repair response, eventually effecting a C-T (or G-A) substitution. ABE deaminates adenosine to generate inosine (A-I), which is read as guanosine (G) by polymerase enzymes, eventually effecting a A-G (or T-C) substitution through DNA repair or replication. PE, Prime editor consist of two simple operational components, a fusion protein made by the fusion nickase Cas9 protein (nCas9) and reverse transcriptase (RT) and a pegRNA contains sgRNA, primer binding site and reverse transcription template.

    • Figure 3. 

      Application of CRISPR/Cas12 and CRISPR/Cas13 in nucleic acid detection. Cas12 collateral cleaves a reporter nucleic acid, which is composed of a single stranded DNA (ssDNA) bearing a fluorophore, and the fluorophore is released and leads to the emission of a fluorescent signal. Cas13 : crRNA complexes activate and cleave fluorescent RNA sensors for RNA target detection.

    • Cas9Cas12Cas13
      Class222
      TypeIIVVI
      SubtypesII-A,B,CV-A(Cas12a); V-B(Cas12b); V-C(C2c3)VI-A(Cas13a/C2c2); VI-B(Cas13b); VI-C(Cas13c);
      VI-D (Cas13d)
      TargetsdsDNAssDNARNA
      Nuclease domain(s)RuvC and HNHRuvCTwo HEPN
      Guide RNAcrRNA and tracrRNAcrRNAcrRNA
      Cleavage typeBlunt ended dsDNA break5′ overhang dsDNA breakssRNA
      Size1000−1600aa1100−1300aa900−1300aa
      Guide spacer18−24nt18−25nt~64nt
      PAMNGG (SpCas9)TTTN (FnCas12a)3′ non-G PFS (LasCas13a)
      NGN (SpCas9-NG)TYCV (LbCas12a-RR)D-(PS)-NAN/NNA (BzCas13b)
      NNG (ScCas9)TATV (LbCas12a-RVR)
      NNGRRT (SaCas9)
      NNNNGATT (NmCas9)
      NNNVRYM (CjCas9)
      NNAGAAW (StCas9)
      PAM-less (SpRY)
      Repair mechanismNHEJ and HDRNHEJ and HDRNo
      ApplicationsMost widely usedMajorly used in epigenetic editingMajorly used in disease detection and diagnostics

      Table 1. 

      Comparative analysis between Cas9, Cas12, and Cas13.

    • NameAdvantageWeb address
      BE-DesignerProvide all possible base editor target sequencehttp://www.rgenome.net/be-designer/
      BEtargetDesign guide RNAs for base editing in plantshttp://skl.scau.edu.cn/betarget/
      Breaking-CasDesign gRNAs for CRISPR/Cas experimentshttp://bioinfogp.cnb.csic.es/tools/breakingcas
      Cas-AnalyzerAnalyze next generation sequencing datahttp://www.rgenome.net/cas-analyzer/
      Cas-DesignerDesign CRISPR targetshttp://www.rgenome.net/cas-designer/
      Cas-OFFinderSearch for potential off-target siteshttp://www.rgenome.net/cas-offinder
      CCTopPredict CRISPR/Cas9 targethttp://crispr.cos.uni-heidelberg.de
      CGDPredict the efficacy of gRNAshttp://big.hanyang.ac.kr:2195/CGD
      CHOPCHOP v3Identify CRISPR–Cas sgRNA targetshttps://chopchop.cbu.uib.no/
      COSMIDSearches genomes for potential off-target siteshttp://crispr.bme.gatech.edu
      CrisPamDetect PAMs for allele-specific targetinghttps://www.danioffenlab.com/crispam
      CRISPORFind guide RNAs and evaluate potential off-targetshttp://crispor.org
      CRISPRdirectSelect rational CRISPR/Cas targetshttp://crispr.dbcls.jp/.
      CRISPRscanDesign sgRNAs for CRISPR/Cas9 targeting in vivohttps://www.crisprscan.org/
      CRISPy-webDesign sgRNAs for microbial genomehttp://crispy.secondarymetabolites.org/
      CRISPR-ERADesign sgRNAs for gene regulationhttp://CRISPR-ERA.stanford.edu
      CRISPR-P 2.0Improved CRISPR-Cas9 tool for genome editing in plantshttp://cbi.hzau.edu.cn/CRISPR2/
      E-CRISPRDesign sgRNAs in a gene-by-gene fashionhttp://www.e-crisp.org/E-CRISP
      MMEJ-KODesign gRNAs for MMEJ-mediated fragment deletionhttp://skl.scau.edu.cn/mmejko/
      Off-SpotterIdentify all potential off-target siteshttps://cm.jefferson.edu/Off-Spotter/
      PhytoCRISP-ExOffer Cas9 target prediction using phytoplankton genomeshttp://www.phytocrispex.biologie.ens.fr/CRISP-Ex/
      The addresses of some web tools could not be resolved, this could be a temporarily unable service so they were not included.

      Table 2. 

      List of available web tools for designing CRISPR/Cas systems.