In Silico Pre-Screening as a Design-Assessment Tool for Gold Nanoparticle-Amplified DNA Displacement Assays: Identifying Sequence-Level Design Limitations Across Electrode and Magnetic-Bead Configurations.
5 affiliations
- 1Department of Science, Technology and Innovation (DSTI)/TIA Innovation Platform, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.
- 2South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville 7535, South Africa.
- 3Sensor Technology Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok 10150, Thailand.
- 4Nanobiotechnology Research Group, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.
- 5Industrial Sensor Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok 10150, Thailand.
Abstract
The growing demand for decentralised and point-of-care (POC) nucleic acid testing has increased interest in label-free, sequence-specific DNA biosensors and computational approaches that can guide their design before extensive experimental optimisation. Here, an in silico workflow was first employed to evaluate a gold nanoparticle (AuNP)-amplified, target-induced DNA displacement assay. Nearest-neighbour duplex thermodynamics, DNA secondary-structure analysis, and High Ambiguity Driven biomolecular DOCKing (HADDOCK) were used to assess sequence complementarity and displacement behaviour. The analyses confirmed Watson-Crick complementarity among the electrode capture, reporter, and target sequences and identified an unintended mismatch in the magnetic bead-capture probe. HADDOCK analyses using default RNA and explicit DNA settings consistently favoured target over non-target displacement, although control poses were more setting-sensitive. Experimental testing subsequently provided supporting evidence for the computational assessment. Electrochemical measurements showed the anticipated signal hierarchy of target > non-target > buffer, although differences were not statistically significant at the replicate numbers tested. The magnetic bead platform produced weak, non-differential responses, consistent with the sequence-level design limitation identified computationally. Together, these findings demonstrate the utility of computational pre-screening for interrogating displacement mechanisms, identifying correctable design errors, and guiding rational experimental optimisation of nucleic acid biosensors. No statistically significant target discrimination was achieved at the replicate numbers tested, and the proposed corrected bead-capture sequence has not been experimentally validated.
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BibTeX
@article{martin2026silico,
title = {{In Silico Pre-Screening as a Design-Assessment Tool for Gold Nanoparticle-Amplified DNA Displacement Assays: Identifying Sequence-Level Design Limitations Across Electrode and Magnetic-Bead Configurations.}},
author = {Darius Riziki Martin and Tatchanun Ngamdee and Ruben Cloete and Abram Madimabe Madiehe and Mervin Meyer and Patsamon Rijiravanich},
journal = {International journal of molecular sciences},
year = {2026},
month = sep,
doi = {10.3390/ijms27198652},
url = {https://europepmc.org/article/MED/42883899},
note = {CC BY},
}
RIS
TY - JOUR
TI - In Silico Pre-Screening as a Design-Assessment Tool for Gold Nanoparticle-Amplified DNA Displacement Assays: Identifying Sequence-Level Design Limitations Across Electrode and Magnetic-Bead Configurations.
AU - Darius Riziki Martin
AU - Tatchanun Ngamdee
AU - Ruben Cloete
AU - Abram Madimabe Madiehe
AU - Mervin Meyer
AU - Patsamon Rijiravanich
PY - 2026
DA - 2026/09/27
JO - International journal of molecular sciences
DO - 10.3390/ijms27198652
UR - https://europepmc.org/article/MED/42883899
AB - The growing demand for decentralised and point-of-care (POC) nucleic acid testing has increased interest in label-free, sequence-specific DNA biosensors and computational approaches that can guide their design before extensive experimental optimisation. Here, an in silico workflow was first employed to evaluate a gold nanoparticle (AuNP)-amplified, target-induced DNA displacement assay. Nearest-neighbour duplex thermodynamics, DNA secondary-structure analysis, and High Ambiguity Driven biomolecular DOCKing (HADDOCK) were used to assess sequence complementarity and displacement behaviour. The analyses confirmed Watson-Crick complementarity among the electrode capture, reporter, and target sequences and identified an unintended mismatch in the magnetic bead-capture probe. HADDOCK analyses using default RNA and explicit DNA settings consistently favoured target over non-target displacement, although control poses were more setting-sensitive. Experimental testing subsequently provided supporting evidence for the computational assessment. Electrochemical measurements showed the anticipated signal hierarchy of target > non-target > buffer, although differences were not statistically significant at the replicate numbers tested. The magnetic bead platform produced weak, non-differential responses, consistent with the sequence-level design limitation identified computationally. Together, these findings demonstrate the utility of computational pre-screening for interrogating displacement mechanisms, identifying correctable design errors, and guiding rational experimental optimisation of nucleic acid biosensors. No statistically significant target discrimination was achieved at the replicate numbers tested, and the proposed corrected bead-capture sequence has not been experimentally validated.
SN - 1422-0067
ER -