ArticleNature nanotechnology2016
Direct observation of DNA knots using a solid-state nanopore.
Article in Nature nanotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed.
- Trefoil polymers from a knotted synthon.Nature chemistry · 2026Article
- Nanopore-Based Profiling of PEGylation in Nucleic Acid Therapeutics.Journal of the American Chemical Society · 2026Article
- Orthogonal nanopores cross-validation for multiplex single-molecule profiling.Chemical science · 2026Article
- Pressure-Modulated, Electroosmotic Flow-Driven DNA Translocations Determine DNA Super-Structure.Small methods · 2026Article
- Generating knotted polymer and protein structures by machine learning.Communications chemistry · 2026Article
- Hybrid Microtubule-Solid-State Nanopores for Single-Molecule Analysis.Electrophoresis · 2026Article
- Geometric Confinement in Solid-State Nanopores Enables Single-Molecule Discrimination of Ferritin Subunits and Translocation Bias.Nano letters · 2026Article
- Uncovering Hidden Protein Conformations with High Bandwidth Nanopore Measurements.Nano letters · 2026Article
- Nanopore Label-Free Monitoring of B-DNA and Z-DNA Conformational Transition in Real Time.ACS nano · 2026Article
- Single-molecule magnetic tweezers reveal distinct dynamics and enhanced mechanical stability of ssDNA 31 and 52 knots.Nucleic acids research · 2026Article
- P.O.R.E.: A Programmable Ohmic Research Engine for Low-Cost Solid-State Nanopore Fabrication.IEEE access : practical innovations, open solutions · 2026Article
- Metrology of Nanoscale Objects Using Nanopores.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Single-molecule sensing with an anthrax nanopore enabled by pH-asymmetric ionic liquids.Journal of nanobiotechnology · 2025Article
- Supramolecular Interactions Modulate RNA:DNA Folding Observed via Nanopore Sensing.Angewandte Chemie (International ed. in English) · 2025Article
- Effects of Knotting on the Collapse of Active Ring Polymers.Macromolecules · 2025Article
- Decoding information stored in DNAs through single-molecule electrical detection platforms.Innovation (Cambridge (Mass.)) · 2025Review
- Chemical Composition and Backbone Modifications Define Deformability of Nucleic Acid Nanoparticles.ACS nano · 2025Article
- Generation and characteristics analysis of the overhand knot using co-screw as gene.Scientific reports · 2025Article
- Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.Nature communications · 2025Article
- Controlled Sensing of User-Defined Aptamer-Based Targets Using Scanning Ionic Conductance Spectroscopy.ACS nano · 2025Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCl buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation-based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.