Problem:
Your lab is working on characterizing the interactions between viral RNAs and the human genome and identifying a host protein that recognizes viral RNA transcripts. The current hypothesis is that this protein binds and specifically recognizes the 5'-end of the viral RNAs. To test this hypothesis, you have been tasked to design DNA templates for the first 500-nts of the viral genome and purify RNA transcripts in large quantities for biochemical and structural studies.
Q1) Explain in detail your template design strategy and the protocol for RNA purification.
Q2) Explain your strategy to produce RNAs with homogenous 5'- and 3'-ends.
Q3) After purification, you want to check the quality of your RNA prep. Discuss in detail your choice of method to check the quality of the RNA preps.