Hi!
Novel sequencing technology (eg. single-cell seq) suggest to use poly dT to capture mRNA. However such technology emphasize to decompose unused single strand poly T primer with exonuclease after reverse transcription and before PCR amplification. Yet why is it necessary? as unused single strand poly T primer do not have TSO at 3' end, they will not get amplification in PCR and is very little likely to get read in sequencing. Is it just to remove background noise in sequencing, or keeping the unused poly T primer will result in low PCR amplification efficiency?
Thanks!
Presumably oligodT can still function perfectly adequately as a PCR primer, so presence of these additional, less-specific primers in the mix will interfere with downstream library amplification.