What is the reason for using oligo(dT) primer in cDNA synthesis?
Eukaryotic messenger RNAs possess a post-transcriptional poly(A) tail of 100-250 adenine residues at the 3' end, essential for stability, nuclear export, and efficient translation. Oligo(dT) primers consisting of 12-18 thymidylates anneal specifically to this poly(A) stretch through A-T base pairing, providing a free 3' hydroxyl for reverse transcriptase to initiate complementary DNA synthesis. This ensures selective reverse transcription of mRNA rather than abundant rRNA or tRNA contaminants. Random hexamers prime throughout transcripts, while oligo(dT) yields full-length, 3'-biased cDNA libraries enriched for eukaryotic coding sequences.
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.