Design of Antisense Oligonucleotides

Alistair M. Chalk¹, Erik L.L. Sonnhammer²
¹alistair.chalk@cgb.ki.se, CGB, Karolinska Institute; ²esr@algol.cgb.ki.se, CGB, Karolinska Institute

Antisense oligonucleotides (AOs) are sequences of 10-20 nucleotide bases that are complementary to a specific sub-sequence of a mRNA. They are synthetic, and are designed to bind to mRNA by standard Watson-Crick base pairing rules. This bound duplex stops the mRNA from being translated, thus inhibiting protein expression in a specific and reversible manner, hence the term “Gene knockdown”. A key issue in AO design is the question of which regions of the RNA to target. At present there are a number of methods for selecting these regions, some using current RNA structure prediction methods. However each method has generally been tested on a single gene. Here we present a comparison of different RNA accessibility prediction methods in terms of their ability to predict antisense efficacy. We use a set of over 400 AOs from 16 genes with known efficacy compiled from the literature (AOdb) for the analysis. In addition we present a set of tools for use in AO and/or siRNA design that are available online at http://sonnhammer.cgb.ki.se.

 AOsearch
   Check the specificity of your AO.

 OligoControlDesigner
   Design controls for your AO experiment.

 siSearch
   Identify siRNA target sites in sequence.

 2sfs
   Generate (or display) structure prediction results    
   together with other information used in AO design.