ORCID
https://orcid.org/0009-0003-2761-5769
Date of Award
Summer 2025
Language
English
Embargo Period
1-24-2026
Document Type
Master's Thesis
Degree Name
Master of Science (MS)
College/School/Department
Department of Chemistry
Program
Chemistry
First Advisor
Alan Chen
Committee Members
Alan Chen, Ting Wang, Ken Halvorsen
Keywords
DNA Nanotechnology, DNA Nanoswitches, Aptamers, Thrombin, Biosensing, Nucleic Acids, Biosensor
Subject Categories
Biochemistry | Biochemistry, Biophysics, and Structural Biology | Biotechnology | Life Sciences
Abstract
Bio-transducers are devices capable of converting the binding signals from molecular recognition events into readable signals for analytical detection. There is a need for modular bio-transducers that can specifically detect a wide range of analytes using a unified readout technique, as this approach could dramatically reduce costs of healthcare diagnostics and environmental monitoring.
To create such a modular transducer, the molecular recognition properties of aptamers will be used and integrated with the already established biosensing capabilities of DNA nanoswitches that reconfigure their shape in the presence of their target molecule. In this design, the detector strands of the nanoswitch will be made up of aptamer sequences, and thrombin will be the target molecule. Using this design of the nanoswitch successful binding of thrombin to the aptamer strands on the nanoswitch was observed. Various optimization methods were performed to determine the ideal conditions for aptamer folding and target binding producing a clear distinct signal on the agarose gel. To retrieve a clear signal on the agarose gel it was determined that it was important to include NaCl2, KCl, MgCl2, and CaCl2 into the sample prep, running conditions, and gel construction. Thrombin concentrations as low as 0.0187nM were detected using the developed nanoswitch. The specificity of the nanoswitch to thrombin was also tested by introducing 0.1mg/mL BSA, which proved that the nanoswitch only formed its looped conformation when thrombin was present.
This work will broaden the diversity of molecules that can be sensed with DNA nanoswitches and provide valuable information on the limit of detection of the aptamers used in the nanoswitch since aptamers are known to be weak binders compared to a DNA structure.
License
This work is licensed under the University at Albany Standard Author Agreement.
Recommended Citation
Beckles, Camryn A., "Development of DNA Nanoswitches with Aptamer Based Detection for Thrombin" (2025). Electronic Theses & Dissertations (2024 - present). 263.
https://scholarsarchive.library.albany.edu/etd/263