I need to design some anti-miRs to inhibit the micro RNA function first in vitro and then in vivo. Literature describes use of oligos that are anti-sense to the mature micro RNA sequence along with modifications like 2'-O methyl, 2'-Fluoro with partial or complete phosphorothioate backbone. Is there a way to anticipate the binding efficiency, Tm, secondary structure formation etc of these oligos? I will greatly appreciate if you can give some useful hints regarding the design of such oligos.
For 2'-O methyl inhibitors, it is simply the reverse complementary of the mature guide miR sequence. If you use IDT website (https://eu.idtdna.com/site/order/mirna) it will design it for you if you simply input your mature sequence. 2'-O methyl is much cheaper than LNA but not as potent. Good luck!
Thanks Adam. 2' O methyl modified oligos need to be delivered in high doses and it becomes a bottle neck when using these oligos in vivo. LNA is more potent but it also has toxicity issues. In a 21 nucleotide long sequence how many LNA modified nucleotides should be there to keep the toxicity low without compromising potency? Any idea ...?
I'm not sure, but when I use LNAs for sRNA Northern blots, I made 5 out of the 16 bases LNA nucleotides.
- Badges
- Science method