shRNA loop length - (Mar/10/2006 )

Hi everybody

i would know if possible what do you think about loop length in shRNA...this is because invitrogen website (on line tools) suggests 4 nt loop, while ambion (for example) or sigma indicate a 6 or 8 nt loops...
do you know if this loop length is closely related to efficiency of breakdown of my shRNA or not?
thanks a lot

-asan-

hi
general published sequences shows longer loops. I use 8nt... i think 4nt is too short for proper folding of the hairpin.

-fred_33-

QUOTE (fred_33 @ Mar 13 2006, 06:09 PM)

hi
general published sequences shows longer loops. I use 8nt... i think 4nt is too short for proper folding of the hairpin.

ok very thanks...i was just thinking to use longer loops than 4 nt, i had doubts about.
i will design longer loops! hoping good work....

-asan-