Seminar: Accessibility is a significant feature for design of siRNAs targeting structured RNA

2011-12-20: by Hakim Tafer, University of Leipzig, Institute for Bioinformatics. At 14:00, University of Copenhagen, LIFE, Grønnegårdsvej 7 (bldg. 1-04), 1st floor, Library/M106, 1870 Frederiksberg C.

Registration is not necessary. Refreshments will be served.


A long debated topic in the field of siRNA design is the influence of the target structure on the target recognition process and subsequently on the siRNA efficiency. While target site structure was recognized as an important feature in the design of antisense oligonucleotides and ribozymes, conflicting data continue to argue for and against the influence of target site accessibility on the siRNA efficiency.

Based on a hand-curated data set the influence of the accessibility on the RNA was studied. A range of machine leaning approaches were used to include accessibility effects into a new siRNA design tool, metarnai. Although the improvements over a purely sequence-based approach are small, significant improvements can be achieved for highly structured targets.