The Effect of Hairpin Structure on PCR Amplification Efficiency

Design of primers for efficient DNA amplification using polymerase chain reaction is critical. Therefore, evaluation of hairpin structures while designing position dependent primers needs special attention. Here, we present the data on the effect of hairpins on DNA amplification using polymerase chain reaction. X-antigen of Hepatitis B Virus has been used as a model. Studies showed that hairpin loop with less than three complementary nucleotides did not have any effect whereas primer length is directly proportional to the hairpin size. Most important characteristic of hairpin structure affecting the amplification is loop size. There should be no complementarity among the primers at their 3' end because this greatly increases the possibility of spurious products by amplifying themselves, thereby, decreasing the amplification efficiency. Hairpin structures greatly affect the primer designing theory having direct relation to amplification.