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Complex DNA knots detected with a nanopore sensor
- Source :
- Nature Communications, Vol 10, Iss 1, Pp 1-9 (2019), Nature Communications
- Publication Year :
- 2019
- Publisher :
- Nature Publishing Group, 2019.
-
Abstract
- Equilibrium knots are common in biological polymers—their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.<br />Nanopore microscopy is capable of detecting knots in DNA polymers, a common structural feature. Here the authors show nanopore sensors can map the equilibrium structure of these knots between tight and loose states.
- Subjects :
- Models, Molecular
Polymers
Science
General Physics and Astronomy
02 engineering and technology
010402 general chemistry
01 natural sciences
General Biochemistry, Genetics and Molecular Biology
Article
Quantitative Biology::Subcellular Processes
chemistry.chemical_compound
Nanopores
Knot (unit)
Single-molecule biophysics
Nanotechnology
Statistical physics
lcsh:Science
Physics
Physics::Biological Physics
Quantitative Biology::Biomolecules
Multidisciplinary
Nanoscale biophysics
General Chemistry
DNA
021001 nanoscience & nanotechnology
Mathematics::Geometric Topology
0104 chemical sciences
Nanostructures
Nanopore
Kinetics
chemistry
Nucleic Acid Conformation
lcsh:Q
0210 nano-technology
Biological physics
Monte Carlo Method
Algorithms
Subjects
Details
- Language :
- English
- ISSN :
- 20411723
- Volume :
- 10
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Nature Communications
- Accession number :
- edsair.doi.dedup.....3c4880e9be8e011b75c61366e4fba02d