The text details the methodology for "Sidewinder," a DNA assembly approach that utilizes oligo-derived heteroduplex fragments, barcode sequences, and toehold-mediated ligation. The process relies on computational design (NUPACK), specific thermal cycling protocols, and rigorous sequencing validation to assemble and screen complex DNA constructs.
Fragment and Barcode Design
Sidewinder fragments are composed of DNA oligos. The design process relies on calculating the length of a construct and a barcode to determine the maximum bases of coding information.
Toeholds: Standardized to 10 bases. Ligation is effective at ≥±6 bases from the Sidewinder helix; 10 bases allow sufficient distance for ligase docking.
Barcodes: Designed to be compatible with toeholds using a "guess-check" method or NUPACK Python scripts. Barcodes are screened for secondary structure and crosstalk at 50°C.
Ligase Selection: Taq ligase and HiFi Taq ligase were selected for their stability at high temperatures and efficiency at the 3-way junction (3WJ).
Oligo Preparation and Annealing
Sourcing: Oligos were synthesized by Millipore-Sigma. Standard desalt purification was generally sufficient, though PAGE purification was used for specific characterization steps.
Heteroduplex Formation: Coding oligos (phosphorylated via T4PNK) and barcode oligos are annealed in a PCR tube. The mixture is heated to 98°C and ramped down to 25°C to form stable heteroduplexes.
Purification: Annealed heteroduplexes are purified via PAGE gel extraction.
Assembly Protocols
The authors describe two primary assembly conditions using HiFi Taq ligase with fragments at equimolar concentrations (~1 nM):
Cycling Protocol: Cycles between 85°C (1 min) and 50°C (2 min) for 100 cycles, followed by a 1-hour hold at 50°C.
Ramp Protocol (e.g., h-fibroin): Heats to 85°C, slowly cools to 50°C, and incubates overnight at 50°C.
These methods were benchmarked against conventional 2-way junction (2WJ) and Gibson assembly methods.
Movies that come to mind that involve genetic building at this level are Gremlins 2, The Clone Wars, and some in the Alien franchise.
Yes, someone has attempted in the last to breed or alter for specific traits, we’ve cloned many kinds of life, and if there was extraterrestrial life here, someone probably mixed it with humans and animals.
But the pace of this is not going to increase anytime soon, if history is a judge. CRISPR was scaring people years ago when publicized, but those worries were unfounded and so shall these be. Life is much harder than coding apps.
The article mentions AI multiple times even though the invention appears to have nothing to do with AI. I guess it’s important to have it as a marketing buzzword.
Sidewinder itself sounds neat.
Has anyone dabbled in hobbyist genome editing and DNA synthesis or is this something that requires a huge pile of capital?
Probably AI in the sense of what Google DeepMind has been up to with the protein folding and other biological simulations, instead of the LLM variant of AI.
This is probably the only way "humans" are going to colonize any planets other than Earth. And probably lots of new places on Earth too.
Just include the genes for extreme-cold or extreme-arid climates. Or the genes for low oxygen environments, or even for metabolizing useful things from eating rocks. Or from spending 24 hours a day in salt water.
The same scientists who cry about ethics, have happily experimented on mice and guinea pigs in their labs, even if it causes the deaths or distress of those little sentient beings.
Mutations/mutatives like Halo's Master Chief and Marvel's Super Soldier serum won't remain sci-fi for much longer, methinks.
That page numbers in books were only invented 50 years after the printing press is a fun snippet from the article
The text details the methodology for "Sidewinder," a DNA assembly approach that utilizes oligo-derived heteroduplex fragments, barcode sequences, and toehold-mediated ligation. The process relies on computational design (NUPACK), specific thermal cycling protocols, and rigorous sequencing validation to assemble and screen complex DNA constructs.
Fragment and Barcode Design
Sidewinder fragments are composed of DNA oligos. The design process relies on calculating the length of a construct and a barcode to determine the maximum bases of coding information.
Toeholds: Standardized to 10 bases. Ligation is effective at ≥±6 bases from the Sidewinder helix; 10 bases allow sufficient distance for ligase docking.
Barcodes: Designed to be compatible with toeholds using a "guess-check" method or NUPACK Python scripts. Barcodes are screened for secondary structure and crosstalk at 50°C.
Ligase Selection: Taq ligase and HiFi Taq ligase were selected for their stability at high temperatures and efficiency at the 3-way junction (3WJ).
Oligo Preparation and Annealing
Sourcing: Oligos were synthesized by Millipore-Sigma. Standard desalt purification was generally sufficient, though PAGE purification was used for specific characterization steps.
Heteroduplex Formation: Coding oligos (phosphorylated via T4PNK) and barcode oligos are annealed in a PCR tube. The mixture is heated to 98°C and ramped down to 25°C to form stable heteroduplexes.
Purification: Annealed heteroduplexes are purified via PAGE gel extraction.
Assembly Protocols
The authors describe two primary assembly conditions using HiFi Taq ligase with fragments at equimolar concentrations (~1 nM):
Cycling Protocol: Cycles between 85°C (1 min) and 50°C (2 min) for 100 cycles, followed by a 1-hour hold at 50°C.
Ramp Protocol (e.g., h-fibroin): Heats to 85°C, slowly cools to 50°C, and incubates overnight at 50°C.
These methods were benchmarked against conventional 2-way junction (2WJ) and Gibson assembly methods.
What's the source of the text? It seems to be either a copypasta from a journal article or LLM-generated (and not your own text).
LLM–generated summary. A human summary wouldn't specify the temperature used because it's irrelevant.
Movies that come to mind that involve genetic building at this level are Gremlins 2, The Clone Wars, and some in the Alien franchise.
Yes, someone has attempted in the last to breed or alter for specific traits, we’ve cloned many kinds of life, and if there was extraterrestrial life here, someone probably mixed it with humans and animals.
But the pace of this is not going to increase anytime soon, if history is a judge. CRISPR was scaring people years ago when publicized, but those worries were unfounded and so shall these be. Life is much harder than coding apps.
Ok that’s it for me. Selective breeding via BLUP at least had a speed limit, this is going to end with cronenburg brundlefly creations.
Paper: https://www.nature.com/articles/s41586-025-10006-0
Such a simple concept took this long to discover? Now we just need a way of packing the DNA strings into blank cells reliably.
Cool. I wonder how long until we are able to steal anti-cancer genes from whales.
The article mentions AI multiple times even though the invention appears to have nothing to do with AI. I guess it’s important to have it as a marketing buzzword.
Sidewinder itself sounds neat.
Has anyone dabbled in hobbyist genome editing and DNA synthesis or is this something that requires a huge pile of capital?
Probably AI in the sense of what Google DeepMind has been up to with the protein folding and other biological simulations, instead of the LLM variant of AI.
This is probably the only way "humans" are going to colonize any planets other than Earth. And probably lots of new places on Earth too.
Just include the genes for extreme-cold or extreme-arid climates. Or the genes for low oxygen environments, or even for metabolizing useful things from eating rocks. Or from spending 24 hours a day in salt water.
The ease of this "just" is the most concerning thing in the context of humankind's survival.
Then I recommend you don't find out what "Project Molecule" intends to do.
Is there a gene to avoid getting addicted to doomscrolling? ;-)
There is no way it is just "just". And we should start from simpler stuff like vitamin B12, C and D.
Everything is “just” eventually.
Just tell your car to drive you to the airport. On the way just tell it to play that song you like.
Imagine if we could turn our bodies into perfect spheres, and then adjust genetic beauty preferences to match it.
Oh if only science was not constrained by ethics.
I can already see the people protesting against the creation of space marines.
Science has never been constrained by ethics.
The same scientists who cry about ethics, have happily experimented on mice and guinea pigs in their labs, even if it causes the deaths or distress of those little sentient beings.
Mutations/mutatives like Halo's Master Chief and Marvel's Super Soldier serum won't remain sci-fi for much longer, methinks.
And save human life at the same time? Experiments are not just about torturing animals; people spend a lot of time optimizing for experiment design.
No laws on mars