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CRISPRcruncher: A tool for engineering restriction sites into coding regions.

Samuel F Fay1, David S Fay2, Vikram E Chhatre2,1

  • 1Wyoming INBRE Bioinformatics Core.

Micropublication Biology
|January 25, 2021
PubMed
Summary
This summary is machine-generated.

CRISPR genome editing can be improved with CRISPRcruncher, a new tool that finds ways to add restriction enzyme sites without changing the protein sequence. This aids in detecting and genotyping genetic edits more efficiently.

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Area of Science:

  • Genetics and Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • CRISPR/Cas9 genome editing frequently incorporates restriction endonuclease (RE) sites for detecting genetic modifications.
  • Placing RE sites within coding regions is challenging due to numerous endonuclease choices and the need to preserve amino acid sequences.

Purpose of the Study:

  • To develop a computational tool, CRISPRcruncher, for identifying potential RE sites within coding sequences.
  • To enable the creation of new RE sites without altering the original peptide sequence.

Main Methods:

  • CRISPRcruncher analyzes input coding sequences to list all possible nucleotide changes that generate new RE sites.
  • The tool ensures that the original amino acid sequence is maintained throughout the modification process.

Main Results:

  • CRISPRcruncher identified approximately one new RE site per nucleotide for 4-bp or longer RE motifs.
  • For 6-bp or longer RE motifs, the tool found about 0.5 new RE sites per nucleotide.

Conclusions:

  • CRISPRcruncher is a valuable computational tool for enhancing CRISPR/Cas9 genome editing strategies.
  • The tool facilitates the design of efficient detection and genotyping methods by creating synonymous RE sites.