RPA Primer Design

For each of the gene targets (5 S. Typhi and 3 S. Paratyphi) 4 sets of RPA Primers were designed using Primer 3 and manually on the Benchling platform. Primer parameters were set using the Twistdx guideline for RPA primer design.  Primers specificities were checked using the BLAST link on the Benchling platform. All primers were synthesized by Twistdx.

Guide RNA Design

Guide RNA sequences were designed for each gene target for both S. typhi and S. paratyphi using the CRISPR guide design on the Benchling platform. Guides were selected based on their off-target scores (100%). Guide RNA parameters were set for cpf1/Cas12.
RPA primers and guide RNA sequences for S. typhi and S. paratyphi are represented on the table below