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Use of an RNA folding algorithm to choose regions for amplification by the polymerase chain reaction
L Pallansch1, H Beswick, J Talian
1Laboratory of Molecular and Developmental Biology, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892.
Analytical Biochemistry
|February 15, 1990
Abstract:
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.