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MicroRNA Detection in Biological Media Using a Split Aptamer Platform

Liming Wang, View ORCID ProfileKern Hast, Tushar Aggarwal, View ORCID ProfileMelih Baci, Jonathan Hong, View ORCID ProfileEnver Cagri Izgu
doi: https://doi.org/10.1101/2022.01.17.476684
Liming Wang
1Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
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Kern Hast
1Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
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Tushar Aggarwal
1Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
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Melih Baci
1Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
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Jonathan Hong
1Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
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Enver Cagri Izgu
1Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
2Cancer Pharmacology Program, Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA
3Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
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  • For correspondence: ec.izgu@rutgers.edu
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ABSTRACT

Intercellular microRNA (miRNA)-based communication has been implicated in a wide array of functional and dysfunctional biological processes. This has raised attention to the potential use of miRNAs as biomarkers for disease diagnosis and prognosis and produced interest in their detection. Though the list of clinically significant miRNA biomarkers is rapidly expanding, it remains challenging to adapt current tools to investigate new targets in biological environments. Systematic approaches for the rapid development of miRNA biosensors are valuable to reduce this disparity. We describe here a methodology for developing aptamer-based fluorescent biosensors that can specifically detect miRNAs in biological environments, including culture medium from HeLa cells, human serum, and human plasma. This methodology includes the semi-rational design of the hybridization between a pair of split DNA aptamer oligonucleotides and the miRNA target to build a pool of potential sensor designs, and the screening of this pool for designs with high signal-to-background ratio and sequence selectivity. The method uses natural oligonucleotides without chemical modification, and is effective in buffer, 10%, and 30% (v/v) biological media. Following this approach, we developed sensors that detect three miRNA targets (miR-19b, miR-21, and miR-92a) at concentrations as low as 5 nM without amplification and are selective against single-nucleotide mutants. This work expands upon the current design principles of nucleic acid-based biosensors and provides a method to rapidly develop diagnostic tools for novel and niche miRNA targets of interest.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 18, 2022.
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MicroRNA Detection in Biological Media Using a Split Aptamer Platform
Liming Wang, Kern Hast, Tushar Aggarwal, Melih Baci, Jonathan Hong, Enver Cagri Izgu
bioRxiv 2022.01.17.476684; doi: https://doi.org/10.1101/2022.01.17.476684
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MicroRNA Detection in Biological Media Using a Split Aptamer Platform
Liming Wang, Kern Hast, Tushar Aggarwal, Melih Baci, Jonathan Hong, Enver Cagri Izgu
bioRxiv 2022.01.17.476684; doi: https://doi.org/10.1101/2022.01.17.476684

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