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Design, Rationalization, and Automation of a Catalytic Sensing Mechanism for Homogeneous SERS Biosensors
Steven M Quarin1, Amanda C Macke1, Lyndsay N Kissell1
1Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States.
ACS Sensors
|April 20, 2023
Summary
We developed a new homogeneous Surface-Enhanced Raman Scattering (SERS) sensor using DNA self-assembly for improved diagnostic sensitivity. This catalytic amplification approach enhances detection limits for infectious disease biomarkers like SARS-CoV-2 and malaria.
Area of Science:
- Biotechnology and Biomedical Engineering
- Nanotechnology and Nanosensors
- Molecular Diagnostics
Background:
- Current pandemic highlights the need for sensitive, deployable diagnostic technologies.
- Surface-Enhanced Raman Scattering (SERS) sensors offer potential for point-of-need (PON) diagnostics.
- Existing homogeneous SERS sensors lack sufficient sensitivity for viral biomarkers, despite advances in DNA-based catalytic amplification.
Purpose of the Study:
- To develop and investigate a homogeneous SERS sensing mechanism utilizing catalytic amplification via DNA self-assembly.
- To systematically analyze the role of fuel strand domains in driving the catalytic mechanism.
- To create an algorithm for automated design of catalytic SERS sensors applicable to diverse targets.
Main Methods:
- Development of a novel homogeneous SERS sensing mechanism based on DNA self-assembly and catalytic amplification.
- Systematic investigation of fuel strand domains (internal loop, stem, toehold) influencing the catalytic process.
- Thermodynamic parameter determination to build an algorithm for automated sensor design.
- Validation of the algorithm on target sequences for malaria and SARS-CoV-2 strains.
Main Results:
- Achieved a 20-fold amplification with conventional DNA and a 36-fold amplification using locked nucleic acids (LNAs).
- Demonstrated significant improvements in sensor limit of detection (LOD) corresponding to amplification levels.
- Showcased single-base sequence specificity for a sensor targeting the Omicron variant against the Delta variant.
Conclusions:
- The developed catalytic amplification mechanism enhances the sensitivity of homogeneous SERS sensors.
- The automated design algorithm facilitates the translation of this sensing strategy to various targets and applications.
- This approach holds potential for infectious disease surveillance by improving LOD while maintaining the homogeneous sensor character.
