Scheme of error correction using coupled methods of site directed mutagenesis and homologous recombination. Assembled synthetic gene fragments subcloned into a plasmid vector are subjected initially to sequence analysis of the synthesized product to detect nucleotide errors. Error correction can be conducted in two ways using oligonucleotide primers (30–35 nucleotides long) that are designed to include the correcting nucleotide (when needed) at the midpoint. First, mutagenic primers are targeted exclusively against the assembled synthetic gene (route A). Two, three and four pairs of primers are required to correct one, two and three point mutation (ptm) sites respectively. DNA fragments are amplified by two or all primer pairs F1-R1, F2-R2, F3-R3 and F1-R4 in separate reactions. The terminal primers have overlapping homologous regions with that of the targeted plasmid vector. Reaction products are mixed for transformation into an appropriate cell host. The second approach involves the amplification of the plasmid vector (routes B-D). To remove 3 point mutations, two correcting primers, reverse-complement of each other, are designed at each mutation site, with the correcting nucleotide being at the midpoint of each primer. DNA fragments are amplified by PCR using primer pairs F1-R1, F2-R2 and F3-R3 respectively in 3 separate reactions (D). Two pairs of primers are similarly used for 2 point mutations involving only 2 separate reactions (C). Single site error correction requires a non-mutagenic primer pair corresponding to a sequence in the vector backbone in addition to the correcting primer set such that 2 fragments are generated (as if 2 corrections were being made). Products of the correcting reactions are retransformed into competent cells for plasmid isolation and sequencing. Upon verification of error free clones, the plasmids are then transformed into an appropriate host cell for protein expression.
Marsic et al. BMC Biotechnology 2008 8:44 doi:10.1186/1472-6750-8-44