Can you describe the different modifications routinely used in antisense experiments ?

Phosphothioate bonds are added to antisense oligos to protect them from nuclease degradation. You can have a full phosphothioate backbone, however, your Tm decreases with each phosphothioate bond you add. You can decrease this effect by 'capping' your oligo. This is accomplished by adding 2-5 bonds to each end of your oligo (most people add 3 to each end.) The 5-Me dC, 2' O-Me RNA bases and C5-Propyne Pyrimidine modifications are sometimes added to increase the nuclease resistance and binding affinity of your oligos, but they are not critical. You can start your experiments without them and add them to subsequent oligos if you need increased stability. Antisense oligos are generally 18-24 bases in length. The concentrations will need to be determined on a case-by-case basis as they vary between organisms. Usually a concentration of 2uMolar (or 10ug/ml) is a good starting point.

If you would like more information on Antisense oligo design and usage, please see our Technical Reports:

Designing Antisense Oligonucleotides

Introducing Antisense Oligonucleotides into Cells

Application Support Topics