Molecular flossing
| Molecular flossing | |
|---|---|
| File:Dual nanopore flossing cycle.svg Schematic of one flossing scan: a tagged DNA strand drawn between two pores by opposing voltages | |
| Classification | Resistive pulse sensing with two pores and active control |
| Analytes | Long DNA molecules carrying protein tags |
| Year | 2019 (tug-of-war); 2020 (flossing) |
| Related | Ping-pong sensing, Translocation (nanopore), Solid-state nanopore |
Molecular flossing is a nanopore technique in which one long DNA molecule is held across two pores and pulled back and forth between them by opposing voltages, so that the same stretch of the molecule is read many times. A group working with dual-pore devices gave the method its name in 2020, reporting up to hundreds of back-and-forth electrical scans of a single protein-tagged molecule in a few seconds.[1] Each scan gives a noisy estimate of the distances between tags, and averaging many scans turns the noise down. In 2022 the same group used the method to map a bacterial genome.
Background
A molecule that has crossed a pore is gone unless something brings it back. In 2007 Gershow and Golovchenko showed that reversing the voltage within milliseconds sends a DNA molecule back through a single solid-state pore, the idea behind ping-pong sensing.[2] A second pore adds tension. A molecule caught by both pores at once cannot diffuse away, and each pore has its own voltage and its own current to report.
| Year | Device | Result |
|---|---|---|
| 2016 | Two pores drilled side by side in one solid-state membrane | A DNA molecule captured by both pores was mechanically trapped, and its residence time rose by orders of magnitude[3] |
| 2017 | Two pores 20 nm apart, bridged by a droplet of about a zeptoliter | Molecules were slowed by up to three orders of magnitude[4] |
| 2018 | Double-barrel pores about 20 nm apart | Pore-to-pore transfer at near 100% efficiency, and an increase of more than two orders of magnitude in dwell time for bridging molecules[5] |
| 2019 | Two independently controlled pores near each other | A "tug-of-war" state on 76.8% of captured molecules, with translocation times up to two orders of magnitude longer than through one pore[6] |
| 2020 | The same dual-pore device with trigger logic | Hundreds of scans of one tagged 48.5 kb λ-DNA molecule in seconds[1] |
| 2022 | A dual-pore chip with automated recapture | A bacterial genome mapped electronically[7] |
Method
In the 2022 device the two pores sit in one silicon nitride membrane about 30 nm thick, 20 to 30 nm wide and about 500 nm apart. They open from a shared chamber above into separate channels below, and each has its own electrode, bias and current record. The buffer is 2 M lithium chloride, which slows DNA.[7] A strand is first captured by one pore. Reversing that pore's voltage threads part of the strand back into the shared chamber, where the other pore catches it, and the strand then spans the gap and passes through both pores. The two voltages pull in opposite directions, and the stronger pull decides which way the molecule moves. With the second pore held at 300 mV, a bias of 150 mV at the first pore moves the strand toward the second and 650 mV moves it back.
Protein tags on the DNA, monostreptavidin in the 2019 work, show as spikes in the current of the second pore. A controller counts them against a moving baseline, and when the count reaches the set number it flips the first voltage and the strand runs the other way. After a number of scans in each direction it raises the count, a step called zooming out, to read a longer stretch.[7] Averaging the scans cuts the noise of the distance estimate in proportion to the square root of their number, so a hundred scans improve it tenfold.
The method also straightens the molecule. Folds in a DNA strand corrupt a single-pass measurement of tag spacing. In the 2020 experiments the share of molecules passing the pore fully linearized rose to more than 98% by the second scan, from 35% for a single pass through one pore.[1]
Genome mapping
The 2022 paper put the method to work on Escherichia coli, whose genome has 4.6 million base pairs. The authors tagged DNA at the positions of a sequence motif and measured the spacing of the tags, which yields a map and not the sequence. With 3.1-fold coverage of 2,355 resolvable sites after 5.6 hours of recording, they mapped the genome, resolving tags 150 base pairs apart on engineered λ-DNA and 166 base pairs apart on native fragments of the bacterial genome. The authors worked at Nooma Bio of Santa Cruz, California, a company that holds an exclusive license to the dual-pore patent from the University of California, Santa Cruz, with a physicist at McGill University as partner.[7] The patent, titled "Dual-pore device", was granted in 2015 to the Regents of the University of California.[8]
At Molecular Reality
Kent Kemmish posted about the 2022 paper on March 29, 2026, under the title "Flossing with DNA". The post is one of the shared papers with the founder's comments that the company gathers under Early Releases on Maxine's Quest. He connects the work to Two Pore Guys, the company now called Ontera, whose name he lists with Roswell Biotechnologies and demonpore, inc. as "the three coolest/quirkiest names for a genomic tech startup ever". His description of the method is "just like 'ping-pong', but with tension in the analyte": two pores, a gap, and "a tug of war" that lets a strand be flossed. In the paper the gap is about 500 nm, and in the post it is "a few microns".[9]
His reading of the result is that the authors "didn't sequence the genome" but "were able to map the positions of large tags on the DNA", which he compares to "being able to see the continents of Earth from space, so you know it's Earth and not another very similar planet, where actually sequencing would be like Google Maps." On the relation to the company's own design he asks "why did they almost do what we did, but not quite?" and answers that "They were just a few microns away from it!" The post ends with an invitation to the authors, "if they want to get in touch", and a line of advice: "let the idea floss back and forth in your mind."[9]
In the company's public essay on its machine-learning plans, the controls a molecular instrument might have include "dual-pore flossing" beside voltage, salt and sliding occlusion, and per-molecule control is limited to molecules that are held, "on a tether, between two pores, or in a bridge between them".[10]
See also
References
- ^ a b c Liu, X.; et al. (2020). "Flossing DNA in a dual nanopore device". Small 16 (3): 1905379. doi:10.1002/smll.201905379.
- ^ Gershow, M.; Golovchenko, J. A. (2007). "Recapturing and trapping single molecules with a solid-state nanopore". Nature Nanotechnology 2 (12): 775-779. doi:10.1038/nnano.2007.381.
- ^ Pud, S.; et al. (2016). "Mechanical trapping of DNA in a double-nanopore system". Nano Letters 16 (12): 8021-8028. doi:10.1021/acs.nanolett.6b04642.
- ^ Cadinu, P.; et al. (2017). "Single molecule trapping and sensing using dual nanopores separated by a zeptoliter nanobridge". Nano Letters 17 (10): 6376-6384. doi:10.1021/acs.nanolett.7b03196.
- ^ Cadinu, P.; et al. (2018). "Double barrel nanopores as a new tool for controlling single-molecule transport". Nano Letters 18 (4): 2738-2745. doi:10.1021/acs.nanolett.8b00860.
- ^ Liu, X.; et al. (2019). "Controlling DNA tug-of-war in a dual nanopore device". Small 15 (30): 1901704. doi:10.1002/smll.201901704.
- ^ a b c d Rand, A. C.; et al. (2022). "Electronic mapping of a bacterial genome with dual solid-state nanopores and active single-molecule control". ACS Nano 16 (4): 5258-5273. doi:10.1021/acsnano.1c09575.
- ^ "US8961763B2: Dual-pore device". Google Patents. Retrieved October 25, 2026.
- ^ a b Kemmishtree (March 29, 2026). "Flossing with DNA". EQBio-OS.
- ^ "Keltar's Critique v2: The Nanopore World Model (Hardened)". Molecular Reality Corporation. August 2026.
