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Title: Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface

Abstract

Detection of single-base mismatches with respect to a probe strand has been a predominant pursuit in electrochemical biosensor efforts, due to links found between single nucleotide polymorphisms (SNPs) and the predisposition to various diseases. We report an osmium tetroxide bipyridine-based, thermally-controlled, competitive-strand electrochemical assay to allow amplified detection of single-base mismatches. Optimally designed competitive-strand displacement and hybridization temperature allows us to distinguish the single-mismatched-target from the fully complementary sequence with unambiguous, highly reproducible, robust signal differences of over 90%. Furthermore, we find a complex interplay between the position of the redox label, variations in strand displacement kinetics due to mismatches incorporated into the competitive strand, and alterations in the melting temperature of DNA duplexes tethered on the gold surface, when probed by square-wave voltammetry. Furthermore, these insights will apply to any surface-tethered DNA-based electrochemical biosensor, and can help with understanding complex phenomena involved in these types of assays.

Authors:
 [1]; ORCiD logo [2];  [3];  [3];  [4];  [4];  [5]
  1. Univ. Rostock (Germany); Univ. at Albany, State Univ. of New York, Albany, NY (United States)
  2. Univ. at Albany, State Univ. of New York, Albany, NY (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Univ. Rostock (Germany)
  4. Masaryk Univ., Brno (Czech Republic); Institute for Biophysics of the CAS, Brno (Czech Republic)
  5. Univ. at Albany, State Univ. of New York, Albany, NY (United States); Gensoric GmbH, Rostock (Germany)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)
OSTI Identifier:
1464009
Alternate Identifier(s):
OSTI ID: 1702302
Grant/Contract Number:  
AC05-00OR22725; AC05-00OR227525; RVO 68081707
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Electrochimica Acta
Additional Journal Information:
Journal Volume: 285; Journal Issue: C; Journal ID: ISSN 0013-4686
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Single-base mismatch detection; Osmium tetroxide bipyridine labeling; Melting temperature; Surface-immobilized DNA

Citation Formats

Biala, Katarzyna, Sedova, Ada A., Mix, Maren, Bar, Katharina, Orsag, Petr, Fojta, Miroslav, and Flechsig, Gerd -Uwe. Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface. United States: N. p., 2018. Web. doi:10.1016/j.electacta.2018.07.188.
Biala, Katarzyna, Sedova, Ada A., Mix, Maren, Bar, Katharina, Orsag, Petr, Fojta, Miroslav, & Flechsig, Gerd -Uwe. Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface. United States. https://doi.org/10.1016/j.electacta.2018.07.188
Biala, Katarzyna, Sedova, Ada A., Mix, Maren, Bar, Katharina, Orsag, Petr, Fojta, Miroslav, and Flechsig, Gerd -Uwe. 2018. "Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface". United States. https://doi.org/10.1016/j.electacta.2018.07.188. https://www.osti.gov/servlets/purl/1464009.
@article{osti_1464009,
title = {Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface},
author = {Biala, Katarzyna and Sedova, Ada A. and Mix, Maren and Bar, Katharina and Orsag, Petr and Fojta, Miroslav and Flechsig, Gerd -Uwe},
abstractNote = {Detection of single-base mismatches with respect to a probe strand has been a predominant pursuit in electrochemical biosensor efforts, due to links found between single nucleotide polymorphisms (SNPs) and the predisposition to various diseases. We report an osmium tetroxide bipyridine-based, thermally-controlled, competitive-strand electrochemical assay to allow amplified detection of single-base mismatches. Optimally designed competitive-strand displacement and hybridization temperature allows us to distinguish the single-mismatched-target from the fully complementary sequence with unambiguous, highly reproducible, robust signal differences of over 90%. Furthermore, we find a complex interplay between the position of the redox label, variations in strand displacement kinetics due to mismatches incorporated into the competitive strand, and alterations in the melting temperature of DNA duplexes tethered on the gold surface, when probed by square-wave voltammetry. Furthermore, these insights will apply to any surface-tethered DNA-based electrochemical biosensor, and can help with understanding complex phenomena involved in these types of assays.},
doi = {10.1016/j.electacta.2018.07.188},
url = {https://www.osti.gov/biblio/1464009}, journal = {Electrochimica Acta},
issn = {0013-4686},
number = C,
volume = 285,
place = {United States},
year = {Mon Jul 30 00:00:00 EDT 2018},
month = {Mon Jul 30 00:00:00 EDT 2018}
}

Journal Article:

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Cited by: 2 works
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