In this screen, you select the nucleotide spacer between the sense and antisense sequences that will generate the loop structure of each shRNA oligo.
Select one of the predesigned 4-nucleotide loop sequences from the Default Loop Sequence pulldown list, or enter a custom loop sequence of 4–11 nucleotides in the Custom Loop Sequence field. Note that short loop sequences (4–7 nucleotides) are usually more efficient. Avoid using a loop sequence containing thymidines (T’s) as they may cause early termination. This is particularly true if the target sequence ends in a T residue.
When you have specified a loop sequence for each target, click on the Design button to generate the final shRNA designs. See shRNA Final Designs for more information.