Natural and artificially-engineered nucleic acid aptamers: design, characterization and technological applications

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Background

Nucleic acid biopolymers have the ability to form complex three-dimensional structures using base pairing and self-recognition as the driving force. This unique property confers nucleotide sequences with an enormous degree of conformational diversity to form structures, so-called aptamers, that can bind to virtually any target molecule of interest. Since the first reports in 1990 regarding the isolation of evolutionary optimized aptamers using an iterative in vitro evolution process called Systematic Evolution of Ligands by Exponential enrichment (SELEX), the advances in the combinatorial chemistry of the SELEX methods have been astonishing and high-throughput protocols are now available against an almost infinite set of targets ranging from individual metal ions to whole live cells. Because of their flexibility and relatively simple implementation, SELEX methodologies have gained tremendous attention and their use by many laboratories worldwide in one way or another has rapidly increased over the last decade.
The interest in aptamer-based technologies has expanded even further with the discovery in 2002 that Nature has also explored the concept of evolutionary optimized nucleic acid sequences as recognition elements to regulate gene expression. RNA aptamers constitute the ligand binding element of naturally-occurring riboswitches that control regulation of genes related to the transport or biosynthesis of the metabolite they bind. Since their discovery, the range of RNA binding motifs embedded within riboswitch sequences has growth enormously and nowadays comprises sequences that specifically respond to aminoacids, nucleobases, sugars, coenzymes and a variety of metal ions. Importantly, a variety of riboswitch-like sequences have been discovered whose cognate ligand remains unidentified. A key challenge in this area will involve developing more efficient methods to match these orphan sequences to their corresponding ligands.
From a technological perspective, both natural and artificially-engineered aptamers offer several key features including reproducibility and stability that should facilitate their transition from bench-top techniques to fully automated assays for sensing, diagnostic and therapeutic applications. Since the approval of Macugen by the Food and Drug Administration to treat aged-related macular degeneration almost a decade ago, significant efforts have been directed to expand the role of aptamers in imaging, targeted drug delivery, point-of-care biomedical devices and electrochemical sensing and some aptamers are in advanced stages of clinical trials. Diagnostic methods to detect active thrombin and activated protein C are also now commercially available in ready-to-use kits formats. These applications are just starting to reveal the potential of aptamer-based technologies; however, further improvements in the success rate of high-throughput SELEX methods need to be overcome, for instance by using modified nucleotides or by designing entirely novel building blocks. The present Research Topic aims to cover the state-of-the-art research concerning the design and characterization of natural and artificially-engineered aptamer sequences with an special emphasis on discussing, from a chemical and synthetic biology perspective, the challenges lying ahead to increase and consolidate the application space of this promising technology.

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