Isolation of Natural DNA Aptamers for Challenging Small-Molecule Targets, Cannabinoids

Overview

Journal Anal Chem

Specialty Chemistry

Date 2021 Feb 2

PMID 33528997

Citations 11

Authors

Haixiang Yu

Yingping Luo

Obtin Alkhamis

Juan Canoura

Boyang Yu

Yi Xiao

Affiliations

Soon will be listed here.

Abstract

Aptamers are nucleic acid-based affinity reagents that are isolated via an process known as systematic evolution of ligands by exponential enrichment (SELEX). Despite their great potential for a wide range of analytical applications, there are relatively few high-quality small-molecule binding aptamers, especially for "challenging" targets that have low water solubility and/or limited moieties for aptamer recognition. The use of libraries containing chemically modified bases may improve the outcome of some SELEX experiments, but this approach is costly and yields inconsistent results. Here, we demonstrate that a thoughtfully designed SELEX procedure with natural DNA libraries can isolate aptamers with high affinity and specificity for challenging small molecules, including targets for which such selections have previously failed. We first isolate a DNA aptamer with nanomolar affinity and high specificity for (-)--Δ-tetrahydrocannabinol (THC), a target previously thought to be unsuitable for SELEX with natural DNA libraries. We subsequently isolate aptamers that exhibit high affinity and cross-reactivity to two other challenging targets, synthetic cannabinoids UR-144 and XLR-11, while maintaining excellent specificity against a wide range of non-target interferents. Our findings demonstrate that natural nucleic acid libraries can yield high-quality aptamers for small-molecule targets, and we outline a robust workflow for isolating other such aptamers in future selection efforts.

Citing Articles

A Label-Free Colorimetric Aptasensor for Flavokavain B Detection.

Ke S, Wang N, Chen X, Tian J, Li J, Yu B Sensors (Basel). 2025; 25(2).

PMID: 39860936 PMC: 11768667. DOI: 10.3390/s25020569.

Examining the Relationship between Aptamer Complexity and Molecular Discrimination of a Low-Epitope Target.

Wang L, Canoura J, Byrd C, Nguyen T, Alkhamis O, Ly P ACS Cent Sci. 2024; 10(12):2213-2228.

PMID: 39735321 PMC: 11672540. DOI: 10.1021/acscentsci.4c01377.

Systematic bio-fabrication of aptamers and their applications in engineering biology.

Cai R, Chen X, Zhang Y, Wang X, Zhou N Syst Microbiol Biomanuf. 2023; 3(2):223-245.

PMID: 38013802 PMC: 9550155. DOI: 10.1007/s43393-022-00140-5.

High-Performance Cannabinoid Sensor Empowered by Plant Hormone Receptors and Antifouling Magnetic Nanorods.

Li Z, Shen Y, Beltran J, Tian H, Bedewitz M, Wheeldon I ACS Sens. 2023; 8(10):3914-3922.

PMID: 37737572 PMC: 11288662. DOI: 10.1021/acssensors.3c01488.

Capture-SELEX for Chloramphenicol Binding Aptamers for Labeled and Label-Free Fluorescence Sensing.

Zhao Y, Li A, Liu J Environ Health (Wash). 2023; 1(2):102-109.

PMID: 37614296 PMC: 10442912. DOI: 10.1021/envhealth.3c00017.

References

Stojanovic M, De Prada P, Landry D . Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc. 2001; 123(21):4928-31. DOI: 10.1021/ja0038171. View

Rosenthal M, Pfeiffer F, Mayer G . A Receptor-Guided Design Strategy for Ligand Identification. Angew Chem Int Ed Engl. 2019; 58(31):10752-10755. DOI: 10.1002/anie.201903479. View

Yang K, Pei R, Stefanovic D, Stojanovic M . Optimizing cross-reactivity with evolutionary search for sensors. J Am Chem Soc. 2011; 134(3):1642-7. DOI: 10.1021/ja2084256. View

Langer N, Lindigkeit R, Schiebel H, Ernst L, Beuerle T . Identification and quantification of synthetic cannabinoids in 'spice-like' herbal mixtures: a snapshot of the German situation in the autumn of 2012. Drug Test Anal. 2013; 6(1-2):59-71. DOI: 10.1002/dta.1499. View

Huestis M . Human cannabinoid pharmacokinetics. Chem Biodivers. 2007; 4(8):1770-804. PMC: 2689518. DOI: 10.1002/cbdv.200790152. View

Han Y, Diao D, Lu Z, Li X, Guo Q, Huo Y . Selection of Group-Specific Phthalic Acid Esters Binding DNA Aptamers via Rationally Designed Target Immobilization and Applications for Ultrasensitive and Highly Selective Detection of Phthalic Acid Esters. Anal Chem. 2017; 89(10):5270-5277. DOI: 10.1021/acs.analchem.6b04808. View

Villar-Guerra R, Trent J, Chaires J . G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy. Angew Chem Int Ed Engl. 2017; 57(24):7171-7175. PMC: 5920796. DOI: 10.1002/anie.201709184. View

Rohloff J, Gelinas A, Jarvis T, Ochsner U, Schneider D, Gold L . Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. Mol Ther Nucleic Acids. 2014; 3:e201. PMC: 4217074. DOI: 10.1038/mtna.2014.49. View

Ruscito A, McConnell E, Koudrina A, Velu R, Mattice C, Hunt V . In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target. Curr Protoc Chem Biol. 2017; 9(4):233-268. DOI: 10.1002/cpch.28. View

10.

Zhou J, Rossi J . Aptamers as targeted therapeutics: current potential and challenges. Nat Rev Drug Discov. 2016; 16(3):181-202. PMC: 5700751. DOI: 10.1038/nrd.2016.199. View

11.

Yang Q, Xiang J, Yang S, Li Q, Zhou Q, Guan A . Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism. Nucleic Acids Res. 2009; 38(3):1022-33. PMC: 2817466. DOI: 10.1093/nar/gkp1045. View

12.

Hili R, Niu J, Liu D . DNA ligase-mediated translation of DNA into densely functionalized nucleic acid polymers. J Am Chem Soc. 2012; 135(1):98-101. PMC: 3544274. DOI: 10.1021/ja311331m. View

13.

Masud M, Kuwahara M, Ozaki H, Sawai H . Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX. Bioorg Med Chem. 2004; 12(5):1111-20. DOI: 10.1016/j.bmc.2003.12.009. View

14.

Imaizumi Y, Kasahara Y, Fujita H, Kitadume S, Ozaki H, Endoh T . Efficacy of base-modification on target binding of small molecule DNA aptamers. J Am Chem Soc. 2013; 135(25):9412-9. DOI: 10.1021/ja4012222. View

15.

Sefah K, Yang Z, Bradley K, Hoshika S, Jimenez E, Zhang L . In vitro selection with artificial expanded genetic information systems. Proc Natl Acad Sci U S A. 2014; 111(4):1449-54. PMC: 3910645. DOI: 10.1073/pnas.1311778111. View

16.

White R, Rusconi C, Scardino E, Wolberg A, Lawson J, Hoffman M . Generation of species cross-reactive aptamers using "toggle" SELEX. Mol Ther. 2001; 4(6):567-73. DOI: 10.1006/mthe.2001.0495. View

17.

Frost J, Dart M, Tietje K, Garrison T, Grayson G, Daza A . Indol-3-ylcycloalkyl ketones: effects of N1 substituted indole side chain variations on CB(2) cannabinoid receptor activity. J Med Chem. 2009; 53(1):295-315. DOI: 10.1021/jm901214q. View

18.

Shoji A, Kuwahara M, Ozaki H, Sawai H . Modified DNA aptamer that binds the (R)-isomer of a thalidomide derivative with high enantioselectivity. J Am Chem Soc. 2007; 129(5):1456-64. DOI: 10.1021/ja067098n. View

19.

Nakatsuka N, Yang K, Abendroth J, Cheung K, Xu X, Yang H . Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing. Science. 2018; 362(6412):319-324. PMC: 6663484. DOI: 10.1126/science.aao6750. View

20.

Yang K, Pei R, Stojanovic M . In vitro selection and amplification protocols for isolation of aptameric sensors for small molecules. Methods. 2016; 106:58-65. PMC: 4981533. DOI: 10.1016/j.ymeth.2016.04.032. View