RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts

The use of antisense oligodeoxyribonucleotides (ODN) or ribozymes to specif ically suppress gene expression is simple in concept and relies on efficien t binding of the antisense strand to the target RNA. Although the identific ation of target sites accessible to base pairing is gradually being overcom e by different techniques, it remains a major problem in the antisense and ribozyme approaches. In this study we have investigated the potential of a recent experimental and theoretical approach to predict the local accessibi lity of murine DNA-methyltransferase (MTase) mRNA in a comparative way. The accessibility of the native target RNA was probed with antisense ODN in ce llular extracts. The results strongly correlated with the theoretically pre dicted target accessibility. This work suggests an effective two-step proce dure for predicting RNA accessibility: first, computer-aided selection of O DN binding sites defined by an accessibility score followed by a more detai led experimental procedure to derive information about target accessibility at the single nucleotide level.