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siRNA Design pp 111-134 | Cite as

The Design, Selection, and Evaluation of Highly Specific and Functional siRNA Incorporating Unlocked Nucleobase Analogs

  • Narendra Vaish
  • Pinky Agarwal
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 942)

Abstract

The efficient and specific silencing of genes via RNA interference (RNAi) for functional genomics and therapeutics depends on careful consideration of the factors that affect the functionality of small interfering RNA (siRNA). These factors include (1) the length of sequence available for siRNA targeting of an mRNA, (2) the structural and thermodynamic properties of target and siRNA sequences, (3) the mechanisms of siRNA off-target effects, and (4) the susceptibility of siRNA degradation when exposed to nucleases in serum and inside cells. Incorporation of Unlocked Nucleobase analogs (UNAs) in the siRNA design offers an attractive approach to design highly efficacious siRNAs with dramatically reduced off-target activity. Here, we describe methods and principles pertaining to the design, selection and screening of optimal siRNAs containing UNA.

Key words

RNA interference Gene silencing Small interfering RNA siRNA design Unlocked nucleobase analog Modified nucleotide 

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Vaish Biotech ConsultingKirklandUSA
  2. 2.Evergreen Neuroscience InstituteKirklandUSA

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