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Related Concept Videos

CRISPR01:59

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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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CasGen: A Regularized Generative Model for CRISPR Cas Protein Design with Classification and Margin-Based

Bharani Nammi1, Vindi M Jayasinghe-Arachchige2, Sita Sirisha Madugula2

  • 1Department of Industrial, Manufacturing and Systems Engineering, University of Texas at Arlington, Arlington, Texas, United States.

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|March 10, 2025
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Summary
This summary is machine-generated.

CasGen, a new AI model, designs novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) proteins for genome editing. This expands the toolkit for synthetic biology and therapeutic applications with precise and versatile Cas variants.

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Area of Science:

  • Biotechnology
  • Genomics
  • Protein Engineering

Background:

  • Current genome editing relies on a limited set of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) proteins, primarily Cas9 and Cas12 variants.
  • This limitation restricts the scope and versatility of genome engineering applications.

Purpose of the Study:

  • To develop a novel deep generative model, CasGen, for designing new Cas9 and Cas12 proteins.
  • To enhance the quality and functional integrity of generated Cas proteins for broader genome editing applications.

Main Methods:

  • Utilized a transformer-based deep generative model (CasGen) with margin-based latent space regularization.
  • Integrated classification for non-Cas sequence filtering, Bayesian optimization for guided design, and AlphaFold-based structural validation.
  • Compiled a dataset of 3,021 Cas9, 597 Cas12, and 597 Non-Cas protein sequences from InterPro and PDB.

Main Results:

  • Generated Cas9 and Cas12 proteins showed high structural similarity to known variants (TM-scores 0.70-0.85, RMSD < 2.00 Å) via AlphaFold2/3.
  • Sequence identity analysis revealed novel Cas9 orthologs (28-55% identity) and Cas12a variants (up to 48% identity).
  • BLAST analysis confirmed the novelty of generated sequences, filtering out highly similar existing Cas proteins.

Conclusions:

  • The CasGen model successfully designs diverse and functionally sound Cas proteins, significantly expanding the genome editing toolkit.
  • This deep generative approach holds promise for advancing synthetic biology and developing more precise, versatile Cas-based therapeutic tools.