Knot sequencing
| Knot sequencing | |
|---|---|
| Classification | Resistive pulse sensing (macroscale demonstration) |
| Analytes | Knots in a nylon filament |
| Inventor | demonpore, inc. |
| Year | 2020 or 2021 |
| Related | Nanopore sequencing; Coulter counter; Quipu |
Knot sequencing is the name later used in company materials for a demonstration made by demonpore, inc., now Molecular Reality Corporation, in 2020 or 2021. Knots tied in a nylon filament were drawn through a hole about 2 mm wide in a wall between two chambers of salt solution, and each knot registered as a short downward spike in the electric current through the hole.[1][2] The recording was made while the company was testing the prototype of its demonpore 64 reader, and the spikes became the targets of the first game the company wrote, Spyke Hunter.
The hole was about a million times wider than the 2 nm pores that pass single strands of DNA in nanopore sequencing. The physics of the signal is the same at both scales.
Demonstration
Kent Kemmish described the experiment in a post to members on March 29, 2026, titled "Sequencing a string". He did not remember whether the idea had been his or that of the outside electronics designer who built the demonpore 64's core electronics in 2020 and 2021 and had written about tabletop Coulter-counter experiments of his own; when the two discussed it, he wrote, the designer called it "a brilliant idea" and wished he had thought of it, "though I think he actually did think of it. Great minds, and all that".[1]
Kemmish ran the experiment with the colleague who led the design of the demonpore 64's enclosure and flow cells. The post gives "at least three reasons" for it: "we wanted to just see if it would work, we were testing the prototype anyway, and because there could be real non-just-educational-value in doing this with smaller and smaller 'strings' as we 'Journey to the Nanoscale', until we're actually sequencing DNA." He added that this was not his plan for sequencing DNA with a solid-state nanopore, only "a useful way to conceptualize the challenge".[1]
The recording shows, in the post's words, "downward (resistive) spikes as the knots we tied in a nylon filament are drawn through a ~2 mm macropore". Kemmish described the hole as not much fancier than the melted one in the designer's own demonstration. Company materials of July 2026 list the result as "macro-scale 'knot sequencing' of a nylon strand".[2]
Physics
When an insulating wall with one hole separates two chambers of salt water and a voltage is applied across it, ions can cross only through the hole, so the current measures how much of the hole is open. A filament threaded through the hole fills part of its cross-section and lowers the current by a fixed amount. A knot carries several crossings of the filament into the hole at once, so while it passes, more of the conducting liquid is pushed aside and the current dips further. For a long hole of diameter D containing a filament of diameter d, the filament fills a fraction (d/D)2 of the cross-section: a filament one tenth as wide as the hole fills one percent of it.
Because the resistance of a hole full of salt water depends on the ratios of the sizes involved, the same geometry gives the same fractional dip at any scale while the liquid behaves as a uniform conductor. The relation between the size of a particle and the depth of its pulse was worked out for particles smaller than a micrometer in 1970.[3] In a nanopore the analogy weakens. The charged walls of the pore gather a layer of counter-ions about a nanometer thick (the Debye length), the current is limited partly by the access resistance at the pore's mouths, and in dilute salt a DNA molecule entering the pore can raise the current instead of lowering it, because of the ions it carries with it, a conductive pulse.[4] A knotted string also crosses its hole slowly enough for each knot to be seen, while DNA crosses a nanopore faster than its bases can be resolved, the difficulty the company calls the speeding bullet problem.
Knots in DNA
Knots form in real DNA, and nanopores can see them. In 2016 a group at Delft University of Technology reported knots in single DNA molecules up to 166,000 bases long, which appeared as short spikes of extra blockade within the dip made by the molecule as a whole, the same signature as in the nylon demonstration. The share of molecules carrying a knot rose with their length, and most of the knots were tight, smaller than 100 nm.[5] A study published in 2019 reported that nanopores could map knots without pulling them tight, found loose knots as well as tight ones, and detected rare composite knots made of more than one simple knot.[6]
For other nanopore work the knot is a nuisance. The paper that introduced QuipuNet, a neural network for reading DNA molecules built with barcodes of hairpin loops, lists "DNA knots" among the common causes of errors in finding the extra current drops that carry the code.[7] The same paper compares those drops to "the knots on a string used in the Inca Quipu system". A quipu is an Andean record of knotted cords; in 1912 the mathematics historian L. Leland Locke showed that the type and position of the knots on many quipus recorded numbers in base ten.[8]
Spyke Hunter
The same post introduced what Kemmish called the first "molecular game" the company coded, "the unfortunately named 'Spyke Hunter'", which turned the spikes from the string into targets. He explained the name as a pun on the 1983 arcade game Spy Hunter and asked: "Maybe I don't always give things the best names?"[1]
He expected more of the same from the company's players. In the early phases of its quest, "traversing the macro to the micro scale", he wrote, they would "come up with a lot of things similar to this that will exist at the border between fun and interesting and maybe just educational but maybe more".[1]
From the string to the nanopore
The company's holes since the string demonstration span five orders of magnitude:
| Hole | Width | Use |
|---|---|---|
| Knot sequencing | about 2 mm | nylon filament, 2020 or 2021[1] |
| 200-micron laser-drilled pore | 200 µm | live streams, 2026[9] |
| Molecular Aquarium arrays | under 10 µm | sliding pore arrays made in 2020[10] |
| Silicon underpore | 200 nm | the company's best early data, 2018[11] |
| Target juxtapore | below 15 nm | a goal not yet reached[12] |
See also
References
- ^ a b c d e f Kemmishtree (March 29, 2026). "Sequencing a string". EQBio-OS.
- ^ a b "Company records". Molecular Reality Corporation. October 2026.
- ^ "Counting and sizing of submicron particles by the resistive pulse technique". Review of Scientific Instruments 41 (7): 909. 1970. doi:10.1063/1.1684724.
- ^ "Salt Dependence of Ion Transport and DNA Translocation through Solid-State Nanopores". Nano Letters 6 (1): 89-95. 2006. doi:10.1021/nl052107w.
- ^ "Direct observation of DNA knots using a solid-state nanopore". Nature Nanotechnology 11 (12): 1093-1097. 2016. doi:10.1038/nnano.2016.153.
- ^ "Complex DNA knots detected with a nanopore sensor". Nature Communications 10: 4473. 2019. doi:10.1038/s41467-019-12358-4.
- ^ "QuipuNet: Convolutional Neural Network for Single-Molecule Nanopore Sensing". Nano Letters 18 (6): 4040-4045. 2018. doi:10.1021/acs.nanolett.8b01709.
- ^ "The Ancient Quipu, a Peruvian Knot Record". American Anthropologist 14 (2): 325-332. 1912. doi:10.1525/aa.1912.14.2.02a00070.
- ^ Lenora Ashgrove (July 29, 2026). "Nineteen Billion Ions a Second, Live on the Internet". Signal & Noise.
- ^ Quartermaster (March 29, 2026). "The Line". EQBio-OS.
- ^ Kemmishtree (March 29, 2026). "Focused Ion Beam pore". EQBio-OS.
- ^ Lenora Ashgrove (October 8, 2026). "Can a Hole That Slides Read a Molecule?" Signal & Noise.