Spacer sequences for targeting lactate dehydrogenase (ldhA) in Escherichia coli K-12 through CRISPR-Cas9 genome editing

Cluster regularly interspersed short palindromic repeats (CRISPR)-Cas9 is the dominant genome editing technique in contemporary biological research. The approach requires a guide RNA encoding a spacer sequence to target a specific location in the genome for editing; thereby, necessitating design for the spacer sequence. Typically, the spacer sequence is immediately adjacent to the protospacer adjacent motif (PAM). This work illustrates the approach by using an in-house MATLAB software to design the spacer sequence that would target the lactate dehydrogenase gene (ldhA) in Escherichia coli K-12 for editing. Specifically, the 20 nucleotide spacer sequences could be either on the sense and antisense DNA strands for the gene. Overall, this dataset should find use in biotechnology or metabolic engineering applications where the objective is to delete the ldhA gene to help redirect metabolic flux away from mixed acid fermentation during anaerobic growth of E. coli K-12 in glucose-based medium.