Perspective on the Future Role of Aptamers in Analytical Chemistry

Abstract

It has been almost 30 years since the invention of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology and the description of the first aptamers. In retrospect over the past 30 years, advances in aptamer development and application have demonstrated that aptamers are potentially useful reagents that can be employed in diverse areas within analytical chemistry, biotechnology, biomedicine, and molecular biology. While often touted as artificial antibodies with an ability to be selected for any target, aptamer development, unfortunately, lags behind development of analytical methodologies that employ aptamers, hindering deeper integration into the application of analytical tool development. This perspective covers recent advances in SELEX methodology for improving efficiency of the SELEX procedure and enhancing affinity and specificity of the selected aptamers, what we view as a critical barrier in the future role of aptamers in analytical chemistry. We discuss postselection modifications that can be used for enhancing performance of the selected aptamers in an analytical device by including understanding intermolecular interaction forces in the binding domain. While highlighting promising properties of aptamers that enable several analytical advances, we provide discussion on the challenges of penetration of aptamers in the analytical field.

Figure 1.

(a). Schematic representation of a structure-switchable aptamer (SW-Apt), achieved by conjugating pH-responsive i-motifs with tyrosine kinase-7 (PTK7)-binding aptamer sgc8. At acidic pH 6.5 (red), the i-motifs of the SW-Apt fold into quadruplex structures, enabling the recognition loops to bind receptors; whereas at physiological pH 7.3 (black), the i-motifs of the SW-Apt is unstructured, preventing the recognition loops from binding to receptors. Reproduced with permission from Ref . Copyright (2018) American Chemical Society. (b). Shown are the electrochemical structure-switching aptamer-based sensors for the detection of aminoglycoside antibiotics, low signal gain sensor and high signal gain sensor are shown on the left and right, respectively. High gain sensor was achieved by rationally engineering the secondary structure of the aptamer to create large conformation changes upon target binding. Reproduced with permission from Ref . Copyright (2014) American Chemical Society.

Figure 2.

(a). Schematic representation of real-time measurement of doxorubicin and kanamycin in whole blood. The microfluidic electrochemical detector for in vivo continuous monitoring was developed by including an electrochemical aptamer-based sensor for the measurement and a continuous-flow diffusion filter to protect the aptamer probes from fouling. To minimize current drift and enhance signal-to-noise ratios, the kinetic differential measurement (KDM) was conduct for improving accuracy of real-time measurements. Reproduced with permission from Ref . Copyright (2013) The American Association for the Advancement of Science. (b). Schematic representation of real-time, continuous measurement of drugs in the bloodstream of awake, ambulatory animals. To protect the sensor from fouling, a biocompatible polysulfone membrane with 0.2-μm pores was used to encase the sensor. The resultant device was emplaced in one of the external jugulars of a rat using an 18-gauge catheter. Two serial injections of the antibiotic tobramycin in the blood of an anesthetized rat was demonstrated. Reproduced with permission from Ref . Copyright (2017) The National Academy of Sciences.

Figure 3.

(a). Schematic representation of formation of the 24–2–DFHBI (3,5- difluoro-4-hydroxybenzylidene imidazolinone) complex, termed Spinach. Photobleaching curves for 24–2–DFHBI, enhanced green fluorescent protein (EGFP), and fluorescein demonstrates that Spi nach displays fluorescence emission comparable to fluorescent proteins. Reproduced with permission from Ref . Copyright (2011) The American Association for the Advancement of Science. (b). Schematic representation of secondary structure of Spinach and Spinach2. Systematic mutagenesis was conducted on Spinach stem 1 and stem-loop 3 (boxed) to generate Spinach2. Reproduced with permission from Ref . Copyright (2013) Springer Nature. (c). Shown is fluorescence-activated cell sorting (FACS)-based directed evolution approach for generating the Broccoli aptamer that displays highly efficient cellular performance. Reproduced with permission from Ref . Copyright (2014) American Chemical Society.