Assuming that by termination signal you mean transcription termination signal (and not a stop codon), you would have one shorter RNA molecule. You can have two shorter RNA molecules if there is another transcription start site after the termination signal, but there is no reason to assume this will be the case.
In some cases the RNA polymerase will skip a ...
Without the sequence information I can only give very general advice.
1) Pick a different location — primers generally work best when they have something close to 50% GC content.
2) Make sure the 3' ends of your primers aren't complementary.
There is detailed advice on how to design effective primers available online including:
Dieffenbach, C. ...
Here is a good explanation of the theory and chemistry behind DMS footprinting, from chapter 11 of Probing RNA structure within living cells :
In vivo chemical probing assay using dimethyl sulfate (DMS). (A) DMS methylates the N1 atom of adenosines and the N3 atom of cytosines. Both of these positions are located on the Watson–Crick face of the respective ...