Figure 1.

Annealing of primers tel 1 and tel 2 to genomic DNA and to each other in the first round of PCR. (A) Annealing of primers to genomic DNA. The tel 1 primer can hybridize to any available partially complementary 31 bp stretch along the strand of telomeric DNA oriented 5′→3′ toward the centromere. The tel 2 primer can hybridize to any partially complementary 33 bp stretch along the strand oriented 5′→3′ toward the end of the chromosome. In both of these primer–template hybridizations, every sixth base is mismatched, however, the last five bases at the 3′-end of the primers are perfectly matched to complementary bases in the template. Addition of bases by DNA polymerase begins at the 3′-ends of the annealed primers and proceeds in the direction of the large arrows. (B) Annealing of primers to each other. The strongest possible hybridizations of the primers to each other involve a repeated pattern of six bases containing four consecutive paired bases followed by two mismatched bases, an example of which is shown here. Note that the 3′-terminal base of each primer cannot form a stable base pair with the base opposite it, thereby blocking addition of bases by DNA polymerase.