Choice of reverse transcription primers

Priming affects the size and specificity of the cDNA produced. There are three types of primers that may be used for reverse transcription:

Oligo(dT)12–18, which binds to the endogenous poly(A)⁺ tail at the 3' end of mammalian mRNA. This primer often produces a full-length cDNA.

Random hexanucleotides, which bind to mRNA at a variety of complementary sites and lead to partial length (short) cDNAs. Random hexanucleotides may be ideal for overcoming the difficulties presented by extensive secondary structure in the template. These primers may also transcribe more efficiently 5' regions of the mRNA.

Specific oligonucleotide primers, which selectively prime the mRNA of interest. This type of primer has been used very successfully in diagnostic assays.