The proper selection of target sites and the correct design of specific ribozymes are decisive initial steps in any attempt to perform ribozyme-mediated gene silencing. Combinatorial methodologies can be used to improve ribozyme targeting and design. The in vitro selection strategy described in this chapter uses a combinatorial library of potentially self-cleaving RNA molecules. The hairpin ribozyme is attached to the target mRNA, and is adequately randomized to generate a population representing all possible substrate specificities. The selection procedure yields information on the best target sites, and provides information about optimal ribozyme sequences. Thus, this method helps in the rational design of efficient hairpin ribozymes for targeting purposes, and avoids trial-and-error assays usually associated with theoretical ribozyme design.
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