RACE problems - 5-terminal amplication (Nov/27/2006 )

My wife was dedicated in cloning of the whole genome of virus. the 5-terminal can not be acquired, because it is full of secondary structure. through her hard work, the secondary structure has been broken.
PROBLEM:she use terminal transferase which add poly(T) to the 5-terminal, then poly(A) and a specific antisense is used to amplify the 5-terminal. it does not work.

guys,
the protocol is ok? or you have a better protocol to get the 5-terminal of a fragment.

You might consider the SMART technique

http://www.clontech.com/products/detail.as...394&tabno=2