Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies

Overview

Journal Molecules

Publisher MDPI

Specialty Biology

Date 2021 Sep 10

PMID 34500620

Citations 9

Authors

Dong-Min Kim

Myeong-June Go

Jingyu Lee

Dokyun Na

Seung-Min Yoo

Affiliations

Soon will be listed here.

Abstract

Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.

Citing Articles

Recent Advances of Strategies and Applications in Aptamer-Combined Metal Nanocluster Biosensing Systems.

Kim K, Kim S, Yoo S Biosensors (Basel). 2024; 14(12).

PMID: 39727889 PMC: 11675020. DOI: 10.3390/bios14120625.

Urmi R, Banerjee P, Singh M, Singh R, Chhillar S, Sharma N Biotechnol Rep (Amst). 2024; 42:e00843.

PMID: 38881649 PMC: 11179248. DOI: 10.1016/j.btre.2024.e00843.

Aptamer-modified metal organic frameworks for measurement of food contaminants: a review.

Tavassoli M, Khezerlou A, Khalilzadeh B, Ehsani A, Kazemian H Mikrochim Acta. 2023; 190(9):371.

PMID: 37646854 DOI: 10.1007/s00604-023-05937-2.

Recent advances in immunoassay-based mycotoxin analysis and toxicogenomic technologies.

Liew W, Sabran M J Food Drug Anal. 2023; 30(4):549-561.

PMID: 36753365 PMC: 9910299. DOI: 10.38212/2224-6614.3430.

Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens.

Wang J, Davidson J, Kaur S, Dextre A, Ranjbaran M, Kamel M Biosensors (Basel). 2022; 12(12).

PMID: 36551061 PMC: 9776365. DOI: 10.3390/bios12121094.

References

Li J, Ma X, Li X, Gu J . PPAI: a web server for predicting protein-aptamer interactions. BMC Bioinformatics. 2020; 21(1):236. PMC: 7285591. DOI: 10.1186/s12859-020-03574-7. View

Bing T, Zheng W, Zhang X, Shen L, Liu X, Wang F . Triplex-quadruplex structural scaffold: a new binding structure of aptamer. Sci Rep. 2017; 7(1):15467. PMC: 5684193. DOI: 10.1038/s41598-017-15797-5. View

Yu H, Luo Y, Alkhamis O, Canoura J, Yu B, Xiao Y . Isolation of Natural DNA Aptamers for Challenging Small-Molecule Targets, Cannabinoids. Anal Chem. 2021; 93(6):3172-3180. PMC: 7895305. DOI: 10.1021/acs.analchem.0c04592. View

Chatterjee B, Kalyani N, Anand A, Khan E, Das S, Bansal V . GOLD SELEX: a novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity. Mikrochim Acta. 2020; 187(11):618. DOI: 10.1007/s00604-020-04577-0. View

Roxo C, Kotkowiak W, Pasternak A . G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives. Molecules. 2019; 24(20). PMC: 6832456. DOI: 10.3390/molecules24203781. View

Morihiro K, Kasahara Y, Obika S . Biological applications of xeno nucleic acids. Mol Biosyst. 2016; 13(2):235-245. DOI: 10.1039/c6mb00538a. View

Higuchi R, Ochman H . Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction. Nucleic Acids Res. 1989; 17(14):5865. PMC: 318226. DOI: 10.1093/nar/17.14.5865. View

Kaur H . Recent developments in cell-SELEX technology for aptamer selection. Biochim Biophys Acta Gen Subj. 2018; 1862(10):2323-2329. DOI: 10.1016/j.bbagen.2018.07.029. View

Hong S, Wan Y, Tang M, Pang D, Zhang Z . Multifunctional Screening Platform for the Highly Efficient Discovery of Aptamers with High Affinity and Specificity. Anal Chem. 2017; 89(12):6535-6542. DOI: 10.1021/acs.analchem.7b00684. View

10.

Gatto B, Palumbo M, Sissi C . Nucleic acid aptamers based on the G-quadruplex structure: therapeutic and diagnostic potential. Curr Med Chem. 2009; 16(10):1248-65. DOI: 10.2174/092986709787846640. View

11.

Zhang H, Li X, Huang A, Yan Z, Chen Y, Bie Z . PEI-assisted boronate affinity magnetic nanoparticle-based SELEX for efficient evolution of saponin-binding aptamers. RSC Adv. 2022; 11(15):8775-8781. PMC: 8695300. DOI: 10.1039/d1ra00889g. View

12.

Guo K, Ziemer G, Paul A, Wendel H . CELL-SELEX: Novel perspectives of aptamer-based therapeutics. Int J Mol Sci. 2009; 9(4):668-678. PMC: 2635693. DOI: 10.3390/ijms9040668. View

13.

Lyu C, Khan I, Wang Z . Capture-SELEX for aptamer selection: A short review. Talanta. 2021; 229:122274. DOI: 10.1016/j.talanta.2021.122274. View

14.

Song S, Wang X, Xu K, Li Q, Ning L, Yang X . Selection of highly specific aptamers to Vibrio parahaemolyticus using cell-SELEX powered by functionalized graphene oxide and rolling circle amplification. Anal Chim Acta. 2019; 1052:153-162. DOI: 10.1016/j.aca.2018.11.047. View

15.

Gopinathan P, Hung L, Wang C, Chiang N, Wang Y, Shan Y . Automated selection of aptamers against cholangiocarcinoma cells on an integrated microfluidic platform. Biomicrofluidics. 2017; 11(4):044101. PMC: 5498186. DOI: 10.1063/1.4991005. View

16.

Ma Y, Li W, Xing R, Li P, Liu Z . Epitope-Imprinted Magnetic Nanoparticles as a General Platform for Efficient Evolution of Protein-Binding Aptamers. ACS Sens. 2020; 5(8):2537-2544. DOI: 10.1021/acssensors.0c00846. View

17.

Martin J, Chavez J, Chushak Y, Chapleau R, Hagen J, Kelley-Loughnane N . Tunable stringency aptamer selection and gold nanoparticle assay for detection of cortisol. Anal Bioanal Chem. 2014; 406(19):4637-47. DOI: 10.1007/s00216-014-7883-8. View

18.

Huang S, Zou X . MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins. 2010; 78(15):3096-103. PMC: 2952710. DOI: 10.1002/prot.22797. View

19.

Gu H, Duan N, Xia Y, Hun X, Wang H, Wang Z . Magnetic Separation-Based Multiple SELEX for Effectively Selecting Aptamers against Saxitoxin, Domoic Acid, and Tetrodotoxin. J Agric Food Chem. 2018; 66(37):9801-9809. DOI: 10.1021/acs.jafc.8b02771. View

20.

Ranganathan S, Halvorsen K, Myers C, Robertson N, Yigit M, Chen A . Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces. Langmuir. 2016; 32(24):6028-34. DOI: 10.1021/acs.langmuir.6b00456. View