Problem:

I'm going to undertake an siRNA experiment soon, but I have only read about them. I want to address the role an enzyme plays in processing a protein.

From what I understand, I will need to pick two specific siRNA's from a screen of multiple siRNA candidates. As a negative control, I should also make a non-sense scramble siRNA. Of course the specific siRNA should show a significant knock-down of the enzyme; the control should not affect expression. As well, there should also be a validated positive control (such as GAPDH) and a mock treated control.

Required:

Question 1: Is this experimental design sufficient?

Question 2: What are some common things to keep in mind, or pitfalls to avoid when doing siRNA studies?

Please explain the things which should be kept in mind during siRNA studies.