In order to increase the efficiency of knockdown of my protein in cells, I am thinking of using TALEN (transcription activator-like effector nucleases) over shRNA. With the former I get around 75% knockdown (as shown by microarray). I want to improve it. There is an interesting paper published in Science in Dec 2012 - http://www.sciencemag.org/content/338/6113/1411.summary that talks about these technologies. If anyone has any interest, please let me know.