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Sensors 2015, 15(4), 7754-7767; doi:10.3390/s150407754

Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance

Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
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Author to whom correspondence should be addressed.
Academic Editor: Ashutosh Tiwari
Received: 21 January 2015 / Revised: 23 March 2015 / Accepted: 24 March 2015 / Published: 31 March 2015
(This article belongs to the Special Issue Smart Materials for Switchable Sensors)
View Full-Text   |   Download PDF [1146 KB, uploaded 31 March 2015]   |  

Abstract

The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM). Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes. View Full-Text
Keywords: aptamer; electrochemical; sensors; aminoglycoside; therapeutic window; binding affinity aptamer; electrochemical; sensors; aminoglycoside; therapeutic window; binding affinity
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Schoukroun-Barnes, L.R.; White, R.J. Rationally Designing Aptamer Sequences with Reduced Affinity for Controlled Sensor Performance. Sensors 2015, 15, 7754-7767.

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