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Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores
Published on: October 31, 2013
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Direct observation of DNA knots using a solid-state nanopore.
Calin Plesa1, Daniel Verschueren1, Sergii Pud1
1Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
Nature Nanotechnology
|November 8, 2016
Summary
Solid-state nanopores enable direct observation of individual DNA knots in long molecules. Knotting probability increases with DNA length, and knots are found to be small and tight.
Area of Science:
- Biophysics
- Nanotechnology
- Molecular Biology
Background:
- Long DNA molecules can form knots, but current observation methods are limited.
- Gel electrophoresis is restricted to bulk measurements and short, circular DNA.
Purpose of the Study:
- To develop and validate a novel method for observing individual DNA knots.
- To investigate the relationship between DNA length and knot formation.
- To characterize the size and properties of DNA knots.
Main Methods:
- Utilizing solid-state nanopores for direct observation of single DNA molecules.
- Employing high-concentration lithium chloride (LiCl) buffers to enhance measurement resolution.
- Analyzing nanopore current traces to detect knot-induced signal spikes.
Main Results:
- Demonstrated direct observation of individual knots in linear and circular DNA of arbitrary length.
- Observed a rise in knot occurrence with increasing DNA length (up to 166 kbp).
- Estimated knot sizes to be predominantly tight and below 100 nm, consistent with polymer simulations.
- Showed that knots in linear DNA can slide under high voltage.
Conclusions:
- Solid-state nanopores offer a powerful tool for studying DNA knotting in individual molecules.
- DNA knotting probability scales with molecular length, supporting a constant per-unit-length probability.
- Nanopore measurements provide insights into knot tightness and dynamics, complementing theoretical predictions.
