MultiCRISPR-EGA: Optimizing Guide RNA Array Design for Multiplexed CRISPR Using the Elitist Genetic Algorithm

Multiplexed CRISPR design, which allows for the concurrent
and
efficient editing of multiple genomic sites, is a powerful tool for
complex genetic modifications. However, designing effective multiplexed
guide RNA (gRNA) arrays remains challenging due to the exponential
increase in potential gRNA array candidates and the significant impact
of different target site selections on efficiency and specificity.
Recognizing that more stable gRNAs, characterized by lower minimum
free energy (MFE), have prolonged activity and thus higher efficacy,
we developed MultiCRISPR-EGA, a graphical user interface (GUI)-based
tool that employs the Elitist Genetic Algorithm (EGA) to design optimized
single-promoter-driven multiplexed gRNA arrays. Computational experiments
on Escherichia coli gene targets demonstrate
that the EGA can rapidly optimize multiplexed gRNA arrays, outperforming
other intelligent optimization algorithms in CRISPR interference (CRISPRi)
applications, while the GUI provides real-time design progress control
and compatibility with various CRISPR-Cas systems. This tool aims
to advance the multiplexed gRNA array design process, enabling more
efficient and cost-effective genome editing for synthetic biology.