A warning on the use of synthetic DNA primers for initiation of reverse transcription on RNA templates: unexpected initiation at a mismatched nucleotide.

A synthetic 13-mer oligodeoxynucleotide designed to specifically initiate on lactic dehydrogenase (LDH) mRNA was shown to prime with high efficiency the synthesis of DNA complementary to the last 133 nucleotides of mitochondrial 16S ribosomal RNA on a mouse liver total poly(A)+ RNA template. One especially interesting feature of this reaction was that reverse transcriptase has been able to initiate at the 3' terminal C residue of the primer despite the fact that it was facing an A. This observation therefore establishes the ability of reverse transcriptase to initiate directly on a mismatched nucleotide.