I cloned a 210bp DNA sequence into vector pGEM-4z using BamHI and HindIII restriction sites. Then carried out invitro transcription after doing a single digestion at BamHI site. But on running a 6% denaturing polyacrylamide gel in 8M urea, the RNA transcript shows a 600bp band. I am guessing that there is a strong dimer formation.
Could you help me with finding out as to how to avoid dimer formation and also is there any software or prediction program to detect RNA dimers
any help is appreciated
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