Abstract:
:Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA-RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a biophysical model to describe asRNA-RNA hybridization that incorporates in vivo factors using large-scale experimental hybridization data for three model RNAs: a group I intron, CsrB and a tRNA. A unique element of our model is the estimation of the availability of the target region to interact with a given asRNA using a differential entropic consideration of suboptimal structures. We showcase the utility of this model by evaluating its prediction capabilities in four additional RNAs: a group II intron, Spinach II, 2-MS2 binding domain and glgC 5΄ UTR. Additionally, we demonstrate the applicability of this approach to other bacterial species by predicting sRNA-mRNA binding regions in two newly discovered, though uncharacterized, regulatory RNAs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Vazquez-Anderson J,Mihailovic MK,Baldridge KC,Reyes KG,Haning K,Cho SH,Amador P,Powell WB,Contreras LMdoi
10.1093/nar/gkx115subject
Has Abstractpub_date
2017-05-19 00:00:00pages
5523-5538issue
9eissn
0305-1048issn
1362-4962pii
3038235journal_volume
45pub_type
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