Antisense/PTOs/2‘ OMe RNA

Antisense oligonucleotides represent an excellent tool to inhibit gene expression levels both in vitro and in vivo. Their discovery introduced a new approach to the development of drug therapeutics, since antisense drugs are designed to inhibit the production of disease-causing proteins. This offer the potential to develop highly selective and less toxic drugs.

Modifying antisense oligonucleotides, either as synthetic DNA or RNA, is key to prevent their nuclease-based degradation in cells and to increase their affinity to specific target mRNAs. Phosphorothioate (S-oligos/PTO) is the simplest and most widely used nuclease-resistant chemistry available for antisense applications. It consists in a sulfur atom replacing a non-bridging oxygen in the oligo phosphate backbone.

At high concentrations, phosphorothioates can cause toxicity or other artifacts, due to their greater non-specific protein binding, compared to unmodified phosphodiester oligos. These problems can be solved, in part or completely, by using chimeric designs.

Metabion offers:

  • Phosphorothioate (PTOs)/phosphodiester chimera, which typically have a central core of unmodified DNA and one to four S-modified internucleoside linkages at both 5’ and 3’ end. At least 3 PTO bonds at the 5’ and at the 3’-end of an oligonucleotide are generally recommended to prevent degradation by exonucleases. Adding PTO linkages in the central core of your oligonucleotide (thus making a full-PTO oligonucleotide) will additionally prevent endonucleases-related degradation. However, this might also lead to cytotoxicity effects.
  • DNA/ 2'-O-Methyl RNA chimera. The presence of 2'-O-Methyl RNA increases both the affinity of the antisense oligo to the target mRNA (by increasing the Tm), and its nuclease resistance. However, 2'-O-Methyl RNA bases do not activate RNase H cleavage, which can compromise the action of the antisense oligo. Therefore, preferred designs incorporate 2'-O-modified RNA in chimeric antisense oligos that retain an RNase H activating domain of DNA (or phosphorothioate DNA).
  • Replacement of dC with 5-Methyl-dC, which is particularly useful in the context of CpG motives, since 5-Methyl dC reduces adverse immune responses in vivo, along with moderately increasing the Tm. 

An alternative to DNA antisense is RNA interference (RNAi). To order siRNA click here.

metabion recommends that all antisense oligos receive HPLC purification and that oligos undergo a Na+ salt exchange before use in cells or live animals to ensure that salts used in purification are removed. This way, metabion's antisense oligos are ready-to-use for in vivo applications.

metabion’s antisense oligonucleotides have been successfully applied for the splice correction of a deep intronic mutation (1)

(1) Bonifert T., Gonzalez Menendez I., Battke F., Theurer Y., Synofzik M., Schöls L., and Wissinger B.. Antisense Oligonucleotide Mediated Splice Correction of a Deep Intronic Mutation in OPA1. Molecular Therapy Nucleic Acids. 5, 2016, Vol. e390.

We are very happy to offer our customers Phosphorothioates (PTO), 2'O-Methyl RNA, and 5-Me-dC as modifications to DNA oligonucleotides. For synthesis scale and final yield, please refer to the table below. For larger synthesis scales, please inquire.

Scale (µmol)Final Yield (OD)
0,2 5
1 15
10 100

In order to minimize cytotoxicity issues, we recommend using our SEC Cartridge purification service, which is to be intended as an add-on service.


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