alt Hacker NewsInvention of DNA "Page Numbers" Opens Up Possibilities for the Bioeconomy
Comments
For someone in Software what is a good way to learn the fundamentals of this?
That page numbers in books were only invented 50 years after the printing press is a fun snippet from the article
Chemical modifications of DNA are so amazing, and underpin so much DNA related research and engineering. Illumina and Moderna would not exist without DNA mods. It’s very cool that the set of tools is expanding further!
“ Guided by the removable DNA page numbers, Sidewinder achieves an incredibly high fidelity in DNA construction with a measured misconnection rate of just one in one million, a four to five magnitude improvement over all prior techniques whose misconnection rates range from 1-in-10 to 1-in-30.”
I wonder if this is even a problem, since you could amplify the correct sequence with PCR afterward.
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.
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.
Could we better not?
Very cool, but may have some unexpected consequences. E.g., someone can probably use this to synthesize a bacterial genome containing every known drug resistance gene, and this is just the first thing that comes to mind. Possibilities for bioeconomy indeed.
Saw the headline and thought we were coming full circle on GEB -- a discovery of page number mechanisms in DNA functioning like GOTOs in code.
It's instead a way to stitch together longer sequences of DNA. Still very cool
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?
Cool. I wonder how long until we are able to steal anti-cancer genes from whales.
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.
Such a simple concept took this long to discover? Now we just need a way of packing the DNA strings into blank cells reliably.
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 really blows my mind about this is that they are using off-the-shelf T4 Ligase to ligate the junctions. I figured this was going to be some tour-de-force of enzyme engineering, but nope, all the reagents are pretty much commercially available.
It is super clever and exciting. Note that people have been able to assemble short (<100 bases) DNA oligomer fragments of synthetic DNA into longer fragments using "splint" oligos since forever. But in this case, each splint has to be custom engineered to only bind to the junction of interest (in practice it is pretty tricky and expensive to do this.) These guys figured out a way to use engineered sequences to make the match, and used a clever (but also more or less standard) way to chew up the engineered stuff, leaving behind only the desired long assembly with no scars at the end of the process.