10.2.2. Chemical blocking of RNA 3’ ends
The free 3’ ends of the RNA can be blocked with borohydride, so that the RNA cannot serve as a primer for cDNA synthesis by self-priming or random priming with small cellular RNAs. This means that only RNA primed with the strand-specific cDNA primers can be elongated by the reverse transcriptase (Gunji et al., 1994). The protocol involves oxidation of the RNA free ends with sodium periodate (NaIO4) followed by reduction with sodium tetrahydroborate (NaBH4).