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Parallel Clamps and Polypurine Hairpins (PPRH) for Gene Silencing and Triplex‐Affinity Capture: Design, Synthesis, and Use

Nucleic acid triplexes are formed when a DNA or RNA oligonucleotide binds to a polypurine‐polypyrimidine‐rich sequence. Triplexes have wide therapeutic applications such as gene silencing or site‐specific mutagenesis. In addition, protocols based on triplex‐affinity capture have been used for detecting nucleic acids in biosensing platforms. In this article, the design, synthesis, and use of parallel clamps and polypurine‐reversed hairpins (PPRH) to bind to target polypyrimidine targets are described. The combination of the polypurine Watson‐Crick strand with the triplex‐forming strand in a single molecule produces highly stable triplexes allowing targeting of single‐ and double‐stranded nucleic acid sequences. On the other hand, PPRHs are easily prepared and work at nanomolar range, like siRNAs, and at a lower concentration than that needed for antisense ODNs or TFOs. However, the stability of PPRHs is higher than that of siRNAs. In addition, PPRHs circumvent off‐target effects and are non‐immunogenic. © 2019 by John Wiley & Sons, Inc.