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Optimization of nucleic acid scaffold design using fluorescence measurements

Published online by Cambridge University Press:  28 January 2019

Jessica Anderson
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
McKenze Moss
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Nancy Nguyen
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Natalie Hughes
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Amira Gee
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
Mehnaaz F. Ali
Affiliation:
Department of Chemistry, Xavier University of Louisiana, 1, Drexel Drive, New Orleans LA70125
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Abstract

The current work focuses on optimizing aptamer scaffolds that are tailored to allow for the formation of binding pockets for both a redox active signaling molecule and the target miR-92a. These newly designed allosteric nucleic acid systems are studied for efficacy to undergo a target based conformational switch. Two hairpin scaffolds were designed with differing stem stabilities and were explored using fluorescence quenching measurements. The dose dependent data for the detection of miR-92a shows the importance of scaffold design where the stability of the intra-molecular hairpin structure has to be optimized for target binding. Additional experiments explored the selectivity of the aptamer scaffolds in the presence of competing miR’s and mismatched sequences. These results provide an important precursor to constructing nucleic acid scaffolds for the detection of miR’s using label-free redox signaling.

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Copyright
Copyright © Materials Research Society 2019 

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