Figure 1

CODEHOP description and PCR strategy. (A) A conserved DNA polymerase sequence motif in LOGOS representation [31] and a sense-strand CODEHOP (HNLCA) derived from that motif is shown. The 3' degenerate core contains all possible codons encoding four conserved amino acids and has a degeneracy of 32. The 5' clamp contains a consensus sequence derived from the most frequently used codons for 5 upstream amino acids within the motif. (B) Schematic description of the CODEHOP PCR strategy illustrating regions of mismatch in primer-to-template annealing during the early PCR cycles and primer-to-product annealing during subsequent cycles. Vertical lines indicate matches between primer (arrow) and template or amplified PCR product. The overall degeneracy of the 3' degenerate core is the product of the degeneracies at each nucleotide position so that the fraction of primers with sequences identical to the targeted template across the degenerate core = 1/degeneracy.