I am working on an (expensive) synthetic construct, which happens to have many "repetitive" sequences within it that are integral to its function. Primarily, the two sequences that are worrying me are:
- A long polyA (about 15 nucleotides).
- A consecutive sequence of two nucleotides: GGGUUUGGUUGU, etc.
I've heard from many some of the transcription horrors they've been through because of similar sequences with similar nucleotides. However, some advise that transcribing it shouldn't be a problem.
How predictably can RNA polymerase transcribe these sorts of sequences in E.coli?