PrimeDesign software for rapid and simplified design of prime editing guide RNAs

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Prime editing (PE) is a powerful genome editing technology.
• Designing guide RNAs for PE is more complex than for standard CRISPR or base editors.
• Efficient design tools are needed to facilitate PE applications.

Purpose of the Study:

• To introduce PrimeDesign, a user-friendly tool for designing prime editing experiments.
• To develop PrimeVar, a database of prime editing guide RNAs for pathogenic variants.
• To demonstrate the utility of PrimeDesign in designing and executing PE experiments.

Main Methods:

• Development of a web application and command-line tool (PrimeDesign) for PE guide RNA design.
• Creation of PrimeVar, a database containing pegRNA and ngRNA combinations for >68,500 human variants from ClinVar.
• Experimental validation of PrimeDesign by designing and implementing PE experiments in human cells.

Main Results:

• PrimeDesign offers a streamlined approach for designing single and combination PE experiments.
• PrimeVar provides a comprehensive resource for targeting pathogenic human genetic variants.
• Successful installation of human pathogenic variants in cells using PrimeDesign-generated guide RNAs.

Conclusions:

• PrimeDesign significantly simplifies the design process for prime editing experiments.
• PrimeVar serves as a valuable resource for researchers studying genetic variants.
• Prime editing, facilitated by tools like PrimeDesign, holds great promise for therapeutic applications.