Eisen JS, Smith JC. Controlling morpholino experiments: don’t stop making antisense. Development 2008;135:1735-43.
http://dev.biologists.org/cgi/content/abstract/dev.001115v1?maxtoshow=&HITS=20&hits=20&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&displaysectionid=Review+Article&resourcetype=HWCIT

Eisen and Smith have written an excellent review of Morpholino control strategies, including discussions of the three common Morpholino targeting techniques (against translation, splicing or miRNA maturation). They discuss how to recognize, control for and minimize interactions of Morpholino oligos with off-target RNA.

I strongly recommend this review to anyone working with Morpholino oligos, especially in in vivo systems.