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casmini-tool: a comprehensive database for efficient and specific guide RNA design using dCasMINI

Spencer Lopp, Robin W. Yeo, Nishant Jha, Xiao Yang, Gabriella Alvarez, Courtney Klappenbach, Daniel O. Hart, View ORCID ProfileLei S. Qi, Timothy P. Daley
doi: https://doi.org/10.1101/2023.09.17.558168
Spencer Lopp
1Epicrispr Biotechnologies
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Robin W. Yeo
1Epicrispr Biotechnologies
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Nishant Jha
2Nitro Bio
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Xiao Yang
1Epicrispr Biotechnologies
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Gabriella Alvarez
1Epicrispr Biotechnologies
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Courtney Klappenbach
1Epicrispr Biotechnologies
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Daniel O. Hart
1Epicrispr Biotechnologies
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Lei S. Qi
3Department of Bioengineering, Sarafan ChEM-H, Stanford University
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  • ORCID record for Lei S. Qi
Timothy P. Daley
1Epicrispr Biotechnologies
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  • For correspondence: timy.pdaley@gmail.com
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Abstract

The dCasMINI protein is a hyper-compact, nuclease-inactivated CRISPR-Cas system engineered for transcriptional modulation and epigenetic editing [Xu et al., 2021]. The small size of dCas-Mini (529 amino acids), less than half the size of comparable Cas9 molecules, makes it ideal for AAV-based therapies which are frequently limited by AAV’s small cargo capacity. Unlike Cas9 or Cas12a, there is no available computational tools for designing CasMINI guides. To facilitate and accelerate the development of dCasMINI-based applications, we synthesized knowledge regarding CasMINI guide design and built a website to assist researchers in designing optimal guides for dCasMINI-based experiments for transcriptional inhibition (CRISPRi) and activation (CRISPRa), which covers 99.7% of genes for CRISPRi and 99.9% of genes for CRISPRa. We experimentally characterized the importance of each nucleotide position on the guide RNA for determining its activity. Based on this information,, our tool offers more sensitively mapping off-targets and provides information about alignment mismatches in the spacer seed region, which we have experimentally determined to be critical for true binding events. The tool is freely available at casmini-tool.com.

Competing Interest Statement

L.S.Q. is the founder of Epicrispr Biotechnologies, and also serves as a scientific advisor for Laboratory of Genomics Research and Kytopen. S.L., R.W.Y., X.Y., D.O.H., L.S.Q., and T.P.D. hold provisional patents relating to this work, are employees of and acknowledge outside interest in Epicrispr Biotechnologies.

Footnotes

  • spencer.lopp{at}epic-bio.com

  • robin.yeo{at}epic-bio.com

  • me{at}nishantjha.org

  • xiao.yang{at}epic-bio.com

  • dan.hart{at}epic-bio.com

  • slqi{at}stanford.edu

  • tim.daley{at}epic-bio.com

  • https://www.casmini-tool.com/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted September 18, 2023.
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casmini-tool: a comprehensive database for efficient and specific guide RNA design using dCasMINI
Spencer Lopp, Robin W. Yeo, Nishant Jha, Xiao Yang, Gabriella Alvarez, Courtney Klappenbach, Daniel O. Hart, Lei S. Qi, Timothy P. Daley
bioRxiv 2023.09.17.558168; doi: https://doi.org/10.1101/2023.09.17.558168
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casmini-tool: a comprehensive database for efficient and specific guide RNA design using dCasMINI
Spencer Lopp, Robin W. Yeo, Nishant Jha, Xiao Yang, Gabriella Alvarez, Courtney Klappenbach, Daniel O. Hart, Lei S. Qi, Timothy P. Daley
bioRxiv 2023.09.17.558168; doi: https://doi.org/10.1101/2023.09.17.558168

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