Abstract: This work is to explore that effect of hairpin structure formed by inverted repeats on template amplification. We investigated the factors affecting PCR amplification efficiency of DNA with hairpin structure，including ring size，stem length and the stem position as to the primer’s hybridization，and discussed how to achieve efficient amplification of DNA with hairpin structure by designing primers and changing the annealing temperature. The results showed that if the position of the primers completely or partly complemented to the 5'-sequence of the hairpin stem，the formation of hairpin structure hindered the binding of primer and template，therefore the inhibition to PCR amplification occurred；moreover，the inhibition increased with the stem length increasing. The inhibition decreased significantly when，the loop portion was longer than 50 nt. Higher annealing temperature and primer concentration were favorable for primers to compete with the formation of hairpin structure within molecule，therefore leading PCR amplification to be more efficient.

Key words: hairpin structure, PCR amplification, inverted repeat sequence