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Updated: Jul 16, 2026

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

Craspase Protease Activation Is Sensitive to Oncogenic Single-Nucleotide RNA Mismatches

Dani Feldmann1,2, Sam P B van Beljouw1,2, Anna C Haagsma1,2

  • 1Department of Bionanoscience, Delft University of Technology, 2629HZ, Delft, The Netherlands.

ACS Chemical Biology
|July 15, 2026
PubMed

Insights

This study introduces a novel CRISPR-based system, Craspase, for precisely targeting cancer-driving mutations. The system selectively activates against specific single-nucleotide variants in oncogenic RNA, paving the way for new diagnostics and therapeutics.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Type III-E CRISPR-controlled protease Craspase offers a unique platform for bioengineering due to its single-subunit RNA-guided complex and direct RNA recognition to protease activation.
  • This system bypasses second messenger signaling, enhancing its potential for therapeutic applications.

Purpose of the Study:

  • To identify specific positions within the CRISPR RNA (crRNA) of Craspase sensitive to single-nucleotide mismatches.
  • To engineer crRNAs for selective targeting of clinically relevant single-nucleotide variants (SNVs) in oncogenic RNA transcripts.
  • To demonstrate selective activation of Craspase by the KRAS G12D SNV.

Main Methods:

  • Identification of five single-nucleotide sensitive positions in the crRNA of *Candidatus* "Scalindua brodae" (Sb-Craspase).
  • Design of crRNAs leveraging these positions to target specific SNVs in oncogenic RNA.
  • Testing of Sb-Craspase activation against KRAS G12D SNV and wild-type transcripts.

Main Results:

  • Five crRNA positions sensitive to single-nucleotide mismatches were identified in Sb-Craspase.
  • Engineered crRNAs demonstrated selective targeting of clinically relevant SNVs in oncogenic RNA.
  • Sb-Craspase was selectively activated by the KRAS G12D SNV, with no activation by the wild-type transcript.

Conclusions:

  • A framework for designing crRNAs to target clinically relevant SNVs was established.
  • This approach lays the groundwork for developing Craspase-based diagnostics and therapeutics for intractable oncogenic mutations.
  • The study highlights the potential of Craspase for precision medicine targeting specific genetic variants.

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