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Anal Biochem. 1990 Feb 15;185(1):57-62.

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

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  • 1Laboratory of Molecular and Developmental Biology, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892.


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.

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