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

Abstract

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.

Fast and Accurate Pneumocystis Pneumonia Diagnosis in Human Samples Using a Label-Free Plasmonic Biosensor

“…They are formed by the addition of a third strand to a duplex, containing tracks of polypurine-polypyrimidine sequences [19]. The design, synthesis and use of hairpins for the formation of triplexes in biosensing and gene inhibition have been recently reviewed [20,21]. A marked enhancement for the detection when using the triplex structure configuration compared with the conventional duplex approach has been reported, for example, for the detection of miRNAs for cancer diagnosis [22] or RNAs from Listeria innocua with predicted secondary structures [23,24].…”

Advanced Evanescent-Wave Optical Biosensors for the Detection of Nucleic Acids: An Analytic Perspective

“…Phosphorodiamidate morpholino oligos (PMO) are also synthetic DNA analogs that possess a neutral backbone of morpholine rings, which not only provides higher solubility in aqueous solutions than PNAs, but also more flexibility in length (Liao et al, 2017). Probes based on triplex-affinity capture are gaining much interest for the detection of NAs in biosensing platforms (Aviñó et al, 2019a). NA triplexes can be induced by the interaction of DNA or RNA molecules with a hairpin-like polypurine-polypyrimidine-rich sequence.…”

“…In particular, evanescent-wave biosensors have achieved great progress for NA analyses (Carrascosa et al, 2016). They have been benefited from improvements in biosensor fabrication and production quality (Fernández Gavela et al, 2016; Soler et al, 2019), the availability of new surface chemistry methods (Escorihuela et al, 2015; Escorihuela and Zuilhof, 2017; Bañuls et al, 2019), the availability of highly efficient probes for NA detection (Shi et al, 2015; Nafa et al, 2016; Aviñó et al, 2019a), and new approaches for the enhancement of the detected signal (Guo et al, 2015). Also, the biosensor integration with microfluidics permits the incorporation of different modules, including fluidic transportation, sorting, mixing or separation methods for liquid samples, and the automation of the complete analysis, which pave the way for the full development of the so-called lab-on-a-chip (LoC) platforms (Jung et al, 2015; Szydzik et al, 2015, 2017).…”

Chemical Modifications in Nucleic Acids for Therapeutic and Diagnostic Applications

“…Triple helices can be found in polypurine‐polypyrimidine tracks through the interaction of a single‐stranded triplex‐forming oligonucleotide which binds to the major groove of the Watson‐Crick double helix [17,18] . The precise knowledge of these structures has generated a large number of applications in gene analysis and in the development of biosensors [19–21] …”

“…[17,18] The precise knowledge of these structures has generated a large number of applications in gene analysis and in the development of biosensors. [19][20][21] In this paper, we will describe some of the most important advances in the chemical modification of nucleic acids made by our group during the last decade, with the aim to improve the therapeutic and diagnostic applications of oligonucleotides. Specifically, we will first describe our contributions in the design of novel modified siRNAs for therapeutic use.…”