I want to design a template for in vitro transcription of RNA Pol II and have a questions regarding the construction of the DNA:RNA hybrid.
I have an approximately 80-200 nt long ssDNA (template DNA) with an 8 nt long RNA annealed to it. If I now add a second 80-200 nt long ssDNA (non-template DNA) complementary to the first ssDNA, will it displace the RNA, or will it anneal to the DNA only outside the RNA-bound area?
Thank you so much for your advise!