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Updated: Feb 4, 2026

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
Published on: May 8, 2015
Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single
Yongya Li1, Guan A Wang1, Sean D Mason1
1Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
Abstract:
Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity. We also introduced an auxiliary probe, a molecular fuel capable of tuning the device in solution via noncovalent catalysis. Collectively, our device produced discrimination factors comparable with commonly used molecular probes but improved the assay sensitivity by ∼100 times. Our results also demonstrate that rationally designed DNA probes through computer simulation can be used to quantitatively improve the design and operation of complexed molecular devices and sensors.
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