INTERFERENCE BY COMPLEX STRUCTURES OF TARGET DNA WITH SPECIFIC PCR AMPLIFICATION

It has been considered that target DNA is a forgiving component for PC R amplification. Herein we present evidence to demonstrate that second ary structure located at the end of a template may interfere with the specificity of amplification. Experiments indicate that nonspecific am plification results from a long stretch of stem and loop structures at the 3' end of prochymosin cDNA. Based on the sequence of mRNA coding for prochymosin, it is argued that the sequence responsible for the fo rmation of the complex structure described here is most likely generat ed during synthesis of the second cDNA strand.