Showing papers by "Cristina Romero-López published in 2004"

Design and optimization of sequence-specific hairpin ribozymes.

Abstract: The hairpin ribozyme belongs to a group of small catalytic RNAs that have been extensively used to trans-cleave RNA molecules. Many efforts have been made to elucidate its reaction mechanism, and there is great interest in designing hairpin ribozymes with improved catalytic activity for use in the development of agents that specifically inactivate RNA molecules. This chapter summarizes the general principles in the design of hairpin ribozymes for targeting purposes, and provides a brief overview of the well-characterized modifications of the ribozyme sequences and structural domains that are necessary for optimal activity. The main features of the target sequence are also examined and other procedures or modifications of interest are also discussed.

An experimental method for selecting effective target sites and designing hairpin ribozymes.

Abstract: 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