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cDNA synthesis - (Oct/31/2008 )

Dear colleagues,

I am just wondering what is the difference between using hexamer random primers and oligo dT primers when we are synthesizing cDNA?


any answers please


Oligo dT primers will always produce cDNA that begins at the poly-A tail. If your gene is large, the RT may fall off before getting to the 5' end. Random hexamers (or longer random primers) will anneal at a variety of positions on the mRNA and so will produce a variety of products, some of which may contain the 5' end.


when amplifying RNA that does not have a poliA tail, the only option in random primers. oligo dT is used for total expressed RNA, random primers for other cases, for instance, the case of viral RNAs.