Use of an RNA folding algorithm to choose regions for amplification by the polymerase chain reaction

We have used the program FOLD, which employs the Zuker folding algorithm, to identify regions of stable secondary structure in three chicken proto-oncogene mRNAs: c-src, c-myc, and c-fos. We have found that use of reverse transcriptase to synthesize a cDNA template for amplification by the polymerase chain reaction is successful only if the region chosen for amplification does not contain stem structures with calculated free energies less than −14 kcal/mol.