I know already the oligos length is about 30 bp but I do not know of which part of the undesirable gene in the bacterial genome?
If I understand your question correctly you are trying to design an oligo sequence to be your guide RNA. If that is the case, you want to meet certain criteria when designing the oligo. You want to 1)make sure the sequence is present in all transcript variants. 2) Make sure the sequence is followed by an NGG (PAM) motif, and 3) Make sure the sequence has as few off-targets as possible.
Julies is very right! Just to add, if you want to design the sequence for your guided RNA, it should be in this format GN(19)NGG that is within your target sequence. There are online web based tools for designing the guided RNA. I would recommend this one ( http://www.e-crisp.org/E-CRISP/) it is user-friendly, easy to use and can show the off targets. Hope it helps.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides