oligodT

Oligo-dT, also written oligodT, is a short synthetic DNA oligonucleotide composed of consecutive deoxythymidine residues. Common forms include oligo-dT15 and oligo-dT20, referring to 15 or 20 thymidine residues, though longer variants are used. The primer binds to the polyadenylated tail of eukaryotic mRNA through complementary base pairing and is widely used to initiate first-strand cDNA synthesis in reverse transcription-based techniques.

In reverse transcription, oligo-dT primers are used to generate complementary DNA from poly(A)+ RNA, enabling downstream RT-PCR, RT-qPCR, and related assays. In some protocols, an anchored variant with a non-T base at the 3' end (for example oligo-dT18VN) reduces non-specific priming and improves 5' coverage. The annealing temperature depends on the primer length and enzyme and is typically around 42-50 C.

Oligo-dT is also used to isolate mRNA from total RNA by binding the poly(A) tail to oligo-dT-coated beads or columns, enabling poly(A)+ RNA purification before downstream analyses.

Limitations include selection for polyadenylated transcripts only, potential bias toward 3' ends, and susceptibility to internal priming at A-rich regions. It does not capture non-polyadenylated RNAs such as many noncoding RNAs. Alternatives or complements include random hexamer primers and gene-specific primers, which can broaden transcript coverage or improve specificity depending on the experimental goal.