Identification of Hybridization Accessible Sequence in Messenger RNA

A major obstacle to employing short complementary nucleic acid strands for modulating gene expression is the apparent randomness with which target mRNAs are inhibited (1). We have hypothesized that the inability to predict mRNA structure in vivo is a significant component of this problem because it is not known which regions of an mRNA molecule are accessible for basepairing or other recognition processes. A number of strategies have been developed to ask if a region of mRNA is single-stranded and free of bound protein, but all have their limitations. Accordingly, we have attempted to develop a different approach to this problem.