Figure 1. PCR amplification of sodium bisulfite treated small RNAs.

Small RNAs were treated with sodium bisulfite and used as a template for cDNA synthesis. A) Primers for cDNA synthesis hybridize to the 3′ end of the tRNA and contain a stem loop. Each primer hybridizes to 7-12 nucleotides at the 3′ end of the tRNA. B) The forward PCR primer binds to the 5′ end of the tRNA. The reverse PCR primer binds to the stem loop. The cDNA primers and forward PCR primers were designed to be complementary to the deaminated cDNA assuming no modified cytosines in the priming region. C) PCRs either lacked template (H₂O), contained mock cDNA made in the absence of reverse transcriptase (-RT), or contained cDNA made in the presence of reverse transcriptase (+RT). Reactions were separated by agarose gel electrophoresis and stained with GelRed.