Selection of antisense oligonucleotides based on multiple predicted target mRNA structures

Background: Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties in RNA secondary structure prediction. If all the predicted structures of a given mRNA within a certain energy limit could be used simultaneously, target site selection would obviously be improved in both reliability and efficiency. In this study, some key problems in ODN target selection on the basis of multiple predicted target mRNA structures are systematically discussed. Results: Two methods were considered for merging topologically different RNA structures into integrated representations. Several parameters were derived to characterize local target site structures. Statistical analysis on a dataset with 448 ODNs against 28 different mRNAs revealed 9 features quantitatively associated with efficacy. Features of structural consistency seemed to be more highly corre...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Xiaochen Bo, Shaoke Lou, Daochun Sun, Wenjie Shu, Jing Yang, Shengqi Wang
• Keywords: BMCBI 2006, Target Mrna, Target MRNA Structures, Target Site