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Identifying Accessible Sites in RNA: The First Step in Designing Antisense Reagents

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There is continued interest in development of antisense reagents (ASRs), including especially antisense oligonucleotides and small interfering RNAs, for experimental as well as therapeutic purposes. Optimization of ASRs begins with target site selection. Here we review protocols which have been developed to empirically determine effective target sites in RNAs. Such library selection technologies have demonstrated clear utility, and in vitro identification of sites has generally proven effective for cellular applications. A few groups are developing large combinatorial libraries and approaches to adapt use of such libraries to individual target RNAs, as well as learning algorithms to help with the optimization of target sites, particularly with respect to small interfering RNAs.

Keywords: DNAzymes; RNA-folding; accessible-site; antisense oligonucleotides; library selection; ribozymes; siRNAs

Document Type: Research Article


Affiliations: Gittlen Cancer Research Foundation, H059, Hershey Medical Center, Pennsylvania State University, 500 University Drive, Hershey, PA 17033, USA.

Publication date: October 1, 2006

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  • Current Medicinal Chemistry covers all the latest and outstanding developments in medicinal chemistry and rational drug design. Each issue contains a series of timely in-depth reviews written by leaders in the field covering a range of the current topics in medicinal chemistry. Current Medicinal Chemistry is an essential journal for every medicinal chemist who wishes to be kept informed and up-to-date with the latest and most important developments.

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