The first of two PCRs (Figure 1A) creates a linear insert with plasmid sequences at both ends (see Supplementary Materials for methods and instructions for primer design). These extensions subsequently allow the strands of the PCR product (Figure 1A) to act as a pair of oversized primers on the vector fragment (Figure 1B). After denaturation and annealing, the insert strands hybridize to the vector and extend to form new double-stranded plasmid. Phusion DNA polymerase (Cat. no. F-530; New England BioLabs, Ipswich, MA, USA), crucial for performance of the technique, does not possess strand displacement activity. Therefore, the final product of the reaction is a double stranded fusion plasmid with two nicks (one on each strand). This relaxed double-stranded plasmid is then transformed into competent Escherichia coli cells, which seal the nicks with DNA repair enzymes (Figure 1C). We employ the same thermostable polymerase for both PCRs, so inexperienced users can clone efficiently without mastering the idiosyncrasies of multiple restriction enzymes, polymerases, glycosylases, recombinases, and ligases.