Abstract
Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications. Herein, we introduce a DNA equalizer gate (DEG) approach, a class of simulation-guided nucleic acid hybridization probes that drastically expand detection windows for discriminating single nucleotide variants in double-stranded DNA (dsDNA) via the user-definable transformation of the quantitative relationship between the detection signal and target concentrations. A thermodynamic-driven theoretical model was also developed, which quantitatively simulates and predicts the performance of DEG. The effectiveness of DEG for expanding detection windows and improving sequence selectivity was demonstrated both in silico and experimentally. As DEG acts directly on dsDNA, it is readily adaptable to nucleic acid amplification techniques, such as polymerase chain reaction (PCR). The practical usefulness of DEG was demonstrated through the simultaneous detection of infections and the screening of drug-resistance in clinical parasitic worm samples collected from rural areas of Honduras.
Highlights
Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications
To quantitatively describe the detection window, we introduce a Robustness Factor (RF) that is defined as the ratio of concentrations between a spurious and a correct target generating the same level of detection signal, RF = [T]spurious/[T]correct (Fig. 2b)
We have introduced DNA equalizer gate (DEG), a class of nucleic acid hybridization probes for the direct analysis of double-stranded DNA (dsDNA) with the user-definable expansion of detection windows and improved sequence selectivity
Summary
Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications. We introduce a DNA equalizer gate (DEG) approach, a class of simulation-guided nucleic acid hybridization probes that drastically expand detection windows for discriminating single nucleotide variants in double-stranded DNA (dsDNA) via the user-definable transformation of the quantitative relationship between the detection signal and target concentrations. We describe a class of simulation-guided nucleic acid hybridization approach, termed DNA equalizer gate (DEG), which drastically expands detection windows for discriminating single nucleotide variants (SNVs) in double-stranded DNA (dsDNA). Different from existing approaches, DEG offers a paradigm to expand the detection window without compromising sensitivity at lower concentration range by transforming the quantitative relationship between the detection signal and target concentrations from a monotonic sigmoidal function to an asymmetric unimodal function (Fig. 1c). The practical usefulness of DEG was established through the integration of polymerase chain reaction (PCR) for the simultaneous infection detection and drug-resistance screen in clinical parasitic worm samples collected from school-age children residing in endemic rural areas of Honduras
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