title: Volatility in mRNA secondary structure as a design principle for antisense.
abstract: Designing effective antisense sequences is a formidable problem. A method for predicting efficacious antisense holds the potential to provide fundamental insight into this biophysical process. More practically, such an understanding increases the chance of successful antisense design as well as saving considerable time, money and labor. The secondary structure of an mRNA molecule is believed to be in a constant state of flux, sampling several different suboptimal states. We hypothesized that particularly volatile regions might provide better accessibility for antisense targeting. A computational framework, GenAVERT was developed to evaluate this hypothesis. GenAVERT used UNAFold and RNAforester to generate and compare the predicted suboptimal structures of mRNA sequences. Subsequent analysis revealed regions that were particularly volatile in terms of intramolecular hydrogen bonding, and thus potentially superior antisense targets due to their high accessibility. Several mRNA sequences with known natural antisense target sites as well as artificial antisense target sites were evaluated. Upon comparison, antisense sequences predicted based upon the volatility hypothesis closely matched those of the naturally occurring antisense, as well as those artificial target sites that provided efficient down-regulation. These results suggest that this strategy may provide a powerful new approach to antisense design.
authors.affiliation: Department of Chemical, Materials and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA.
authors.forename: Erik
authors.initials: E
authors.lastname: Johnson
authors.forename: Ranjan
authors.initials: R
authors.lastname: Srivastava
mesh_terms: D016375:Antisense Elements (Genetics) / Q000737:chemistry*; D001427:Bacterial Toxins / Q000235:genetics; D001483:Base Sequence; D002262:Carboxy-Lyases / Q000235:genetics; D046969:Clostridium acetobutylicum / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D015536:Down-Regulation; D029968:Escherichia coli Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D006360:Heat-Shock Proteins / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010709:Phosphate Acetyltransferase / Q000235:genetics; D017851:Phosphotransferases (Carboxyl Group Acceptor) / Q000235:genetics; D016372:RNA, Antisense / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry*; D012808:Sigma Factor / Q000235:genetics; D012984:Software
chemical_list: D016375:Antisense Elements (Genetics); D001427:Bacterial Toxins; D029968:Escherichia coli Proteins; D006360:Heat-Shock Proteins; C087025:Hok protein, E coli; D008565:Membrane Proteins; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012808:Sigma Factor; C087026:Sok antisense RNA, E coli; C069774:heat-shock sigma factor 32; C087023:pndA protein, E coli; C071524:HokC protein, E coli; D010709:Phosphate Acetyltransferase; D017851:Phosphotransferases (Carboxyl Group Acceptor); C019285:butyrate kinase; D002262:Carboxy-Lyases; C023743:acetoacetate decarboxylase