iiinova — where your digital self keeps evolving

Erik Poppleton @poppleton.phd · 23/06/2025

Reposted by Molpigs

Molecular Programmers🧬: @programmablematter.bsky.social summons us to organize a “Flightplan”, a 10-year strategic initiative for the field. The meeting will be July 21-23rd in Seattle and will be moderated by NSF program officers. Travel funding is available! Apply here: mpflightplan.com/apply-now

mpflightplan.com

Apply now! — MP Decadal Flightplan

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Molpigs @molpigs.bsky.social · 02/05/2025

Follow WONDER for networking opportunities and upcoming mentorship events aimed at increasing female representation and retention in the Molecular Programming field 🧬

Molpigs @molpigs.bsky.social · 29/04/2025

Thank you to everybody who came to our 🧬DNA origami🧬 reading group over the last 7 weeks! We all learned a ton from the discussions and revisiting these classic papers. What should our next topic be?? Leave us a comment to help us decide.

Molpigs @molpigs.bsky.social · 19/04/2025

It's time for the finale of the 🧬DNA origami🧬 reading group! This week we're thinking about how to make origami biiiiiig. When previous papers assembled multiple origami, the yield started to crash. This week's paper is an attempt to get around that problem. www.nature.com/articles/s41...

Multi-micron crisscross structures grown from DNA-origami slats - Nature Nanotechnology

Addressable DNA structures with lateral dimensions of ~2 µm can be self-assembled starting from over 1,000 distinct DNA-origami monomers via joint capture of the non-nearest neighbours.

Molpigs @molpigs.bsky.social · 13/04/2025

This week in the Molpigs 🧬DNA Origami🧬 Reading Group there are two cool concepts we're exploring: dynamic structures, and using blunt-end stacking as a structural tool instead of treating it as The Enemy. Info on how to join the discussion in the quoted thread! www.science.org/doi/full/10....

science.org

Molpigs @molpigs.bsky.social · 06/04/2025

This week in the Molpigs 🧬DNA Origami🧬 Reading Group, we're exploring how DNA origami went from tightly packed sheets/blocks, to open wireframes with complex and beautiful geometries. This paper required designing intricate strand routing, let's follow the path! www.nature.com/articles/nna...

Complex wireframe DNA origami nanostructures with multi-arm junction vertices - Nature Nanotechnology

A design approach for engineering wireframe DNA nanostructures, in which each vertex and line segment can be individually controlled, can be used to fabricate complex structures including quasicrystal...

Molpigs @molpigs.bsky.social · 30/03/2025

Welcome to the halfway point in the 🧬DNA origami🧬 reading group! This week we're reading "Folding DNA into Twisted and Curved Nanoscale Shapes", the second 2009 paper from the Shih lab demonstrating the programmability of DNA origami. www.science.org/doi/full/10....

science.org

Molpigs @molpigs.bsky.social · 23/03/2025

For week three of our 🧬DNA origami🧬 reading group we're reading the first of two 2009 papers from the Shih lab which demonstrated that you really could fold DNA into any 3D shape! This paper also demonstrated Cadnano, which remains the most used design software today. www.nature.com/articles/nat...

Self-assembly of DNA into nanoscale three-dimensional shapes - Nature

DNA has proved to be a versatile building block in the creation of complex structures through self-assembly, exploiting the intermolecular forces between the components. Here, the arrangement of DNA h...

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Molpigs @molpigs.bsky.social · 20/03/2025

The second meeting of the Origami Reading Group is tonight at 18:00 EST! Come discuss the original DNA Origami with us (spoiler, it’s shockingly sassy). 🧬

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Molpigs @molpigs.bsky.social · 15/03/2025

It's time to put the origami in our DNA Origami Reading Group! This week we're reading Rothemund's "Folding DNA to create nanoscale shapes and patterns" to understand this seminal paper in context! What did Rothemund know, and what did he intuit? Join us to discuss!🧬 www.nature.com/articles/nat...

Folding DNA to create nanoscale shapes and patterns - Nature

A robust, versatile, one-pot bottom-up nanotechnology fabrication method uses a few-hundred short DNA strands to 'staple' a very long strand into two-dimensional structures of 100 nm in diameter and r...

Molpigs @molpigs.bsky.social · 11/03/2025

First 🧬DNA Origami reading group🧬 meets today! Our first paper is a precursor to origami, where Yan and colleagues showed that you could build larger structures via scaffolded tile assembly! www.pnas.org/doi/10.1073/...

pnas.org

Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices | PNAS

The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applica...

Molpigs @molpigs.bsky.social · 08/03/2025

The first paper is something to get us in the headspace of the field pre-origami: Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices by Hao Yan et al 🧬 www.pnas.org/doi/10.1073/...

pnas.org

Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices | PNAS

The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applica...

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Molpigs @molpigs.bsky.social · 08/03/2025

Excited to start our 🧬DNA origami🧬 reading group next week! We’ll be hosting two weekly sessions: Tuesday @ 20:15 CET Thursday @ 18 EST You can still sign up by joining the reading-group channel on Slack or filling the form for email updates! Timezone converter: molpi.gs/timezones#tz...

molpi.gs

Molecular Programming Interest GroupMolecular Programming Interest Group

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Molpigs @molpigs.bsky.social · 02/03/2025

It's time for another Molpigs reading group! This time we'll be routing our brains through the history of DNA origami. We will be starting the week of March 10th and reading 1 paper/week for 7 weeks. Please fill out either the form linked in the next post or join the Molpigs Slack for updates. 🧬🧬🧬

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And that's the story. Extremely nerdy, not particularly flashy, but this little cube was one of the first demonstrations that there is, in fact, Plenty of Room at the Bottom if you have the ingenuity to get matter to self-assemble for you! 8/8

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Behold! the final gel! Building the cube up and tearing it down. Lane 4 contains the purified cube. That's cool. Lanes 5-11 are various restriction digests of the cube, which show that it breaks down in ways consistent with it having been a cube with 6 knotted faces in the first place. 7/8

The gel showing assembly and disassembly of the cube. The important lane is lane 4, which shows a single, high-weight band corresponding to the assembled and purified cube. Lanes 5-11 are then various restriction enzyme digestions, resulting in either 3, 2 or 1 interlocked DNA circles depending on which sides of the cube are cut by the enzymes.

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They could prove ligation with exonuclease digestion! Two things in this busy gel: 1. Lane 4 losing the top band meant the cube should be 10 bases-per-side, not 11. This wasn't obvious as DNA has a periodicity of 10.5 bp. 2. Lane 2 keeping the top band from lane 1 means ligation was a success! 6/8

The gel demonstrating successful ligation of the triple-catenene. Each lane shows many bands containing sub-products, but what's important is the topmost band in each lane, corresponding to the fully-formed triple catenene. Lanes 1 and 3 are the assembled catenene with 10 and 11 base-pairs per side, respectively. Lanes 2 and 4 show the same structures after digestion with an exonuclease which will remove any un-ligated strands. In lane 2, the top band is still present showing successful ligation, while in lane 4, it's gone, showing that for some reason the 11-base loops will not close.

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Here's the assembly gel where they add 5 strands to their first, circularized strand and then ligate the two halves of the cube together to get an open 'belt'. However they ran into an aggregation problem in the 6th step, which is why they did the purify-and-reconstitute step from figure 1. 5/8

Figure 2 from the paper showing stepwise assembly of the "belt" structure which can be ligated into the cube. Addition of each strand leads to a slightly higher band on the gel, until you ligate two of the 5-strand complexes together, at which point a faint target band appears and a huge aggregate stuck in the well.

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For modern molecular programmers, ligating the strands looks strange. We almost never do that today! But that was the secret sauce that let them prove they had synthesized a cube with just gels. You see, the ligated DNA strands resulted in knots, which don't fall apart on a denaturing gel. 4/8

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But keep in mind! This was a crystallography lab borrowing equipment from the neighboring biochemistry lab, doing something never done before. They didn't have any of the fancy equipment that we take for granted today. No AFM, let alone a CryoEM. So how could they prove they had a cube?? 3/8

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Here's the plan: starting with 10 linear, synthetic DNA strands, Ned's team annealed strands onto a growing belt with intermediate ligation steps, resulting in a final structure which has 6 strands, each one corresponding to one face of the cube 2/8

Figure 1 from the paper showing how you can add strands in a stepwise manner to create a cube, first creating two opposite faces separately with overhangs which can be ligated to form a "belt", then the belt can be purified into three interlocked rings, reconstituted with its strands, and then those can be ligated again to form a cube.

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In this series on the origins of DNA nanotechnology, we've so far seen a lot of DNA, not a lot of nanostructure and not a lot of technology. Today's paper introduces structure, we're looking at the first well-defined object built out of DNA, the humble cube! 🧬 1/8 www.nature.com/articles/350...

Synthesis from DNA of a molecule with the connectivity of a cube - Nature

Nature - Synthesis from DNA of a molecule with the connectivity of a cube

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Next time we'll talk about the first true nanostructure which was hinted at so many times in this paper, the DNA cube!

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Sadly, I have never been able to find a copy of either the source code or the compiled program. If anybody sees this (@programmablematter.bsky.social perhaps?) and knows where it could be found, I would love a chance to play with DNA nanotech's first design tool. 6/6

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The paper also points out that this level of sequence stringency is, in fact, not required, but the extent to which annealing and stoichiometry could overcome this limitation wasn't truly appreciated until 16 years later with the advent of DNA origami. 5/6

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In this paper Ned introduces SEQUIN, a program (written in FORTRAN!) which guided the user through which tetra- penta- and hexameric sequences they had already used in their design. This ensured that up to a specific length, the structure was basically assured to form as intended. 4/6

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But this is the beauty of nucleotides! While base pairs are specific, they're not very strong. You have to get above about 6 contiguous bases before they start sticking together (and even then, residence time is short!). So how does one go about choosing sequences to build something out of DNA? 3/6

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The big idea here is 'sequence symmetry minimization': reducing the number of different ways your sequences could come together and still form base pairs. With only 4 bases, the only sequences which can't form any alternate pairs at all are permutations of ATGC TACG which is...limiting 2/6

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De Novo Design of Sequences for Nucleic Acid Structural Engineering: Journal of Biomolecular Structure and Dynamics: Vol 8 , No 3 - Get Access

DNA nanotechnology works because of the specificity of A-T and G-C base-pairs. But isolated pairs aren't stable! Only when you have longer stretches will DNA form a helix. Before finally building the first structure, let's discuss Ned's sequence design tool. 1/6 www.tandfonline.com/doi/pdf/10.1...

tandfonline.com

We’re here to help

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This paper also tells an interesting story about how science has changed. I can't imagine trying to get something like this (or the 1982 junction paper) published today. A pure idea without even a simulation to back it up would never fly. Good change? Something lost? Interested in your opinions. 7/7

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It's a bit hard to say what the impact of this paper has been. Even today, this biochip remains impossible to actually construct, but there have been many projects which positioned (semi)conductive components using DNA scaffolds, whether that be proteins, metal particles or carbon nanotubes. 6/7

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Some ideas about using redox states of metal atoms as storage later, and we get some circuit diagrams! I have no idea how unique or viable these are, but the idea was to store information in a cubic lattice, which would allow read/write on single bits via external signals on individual "wires". 5/7

The circuit diagrams from "design of a biochip". Honestly I have no idea where to even start describing them. Each circuit has 12 input/output connections, split into two halves connected by a metal atom which serves as the 'bit' which can be read/written.

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There's a problem though. DNA on its own isn't a good conductor, you need to add something else to it. Enter trans-polyacetyline (tPA). This polymer later earned the 2000 Nobel prize as the first conductive polymer (the basis of your OLED TVs today, though tPA itself is relegated to museums). 4/7

Figure 2 from "Design of a biochip" showing various conducting polymers: linear trans-polyacetyline which could act as a molecular wire and branched ladder polymers polyphenothiazine and polyphenoxazine which could be used as junctions between polyacetyline ladders.

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The titular "biochip" was apparently an in-vogue idea at the time: a digital computing device made from biological parts. What do you need for a chip? Binary units wired together which can be read and written. What did Ned just show could do arbitrary connecting of vertices? DNA. 3/7

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In hindsight this feels like something scribbled on a bar napkin after a conference which a journal editor overheard and said "Hey! That's neat! You should write it up!" But it was also the '80s! Molecular biology and computer engineering were galloping! Of course, there were ideas left behind. 2/7

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The design of a biochip: a self-assembling molecular-scale memory device

Paper #3 in our series: the time Ned and co read too much science fiction. That's right, it's Robinson & Seeman's "The design of a biochip: a self-assembling molecular-scale memory device" published in Protein Engineering in 1987. 🧬 1/7 academic.oup.com/peds/article...

academic.oup.com

Abstract. A design for a biochip memory device based on known materials and existing principles is presented. The fabrication of this memory system relies

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The rest of the figures are further validation; showing that the strands need to be mixed in a 1:1:1:1 ratio, the electrophoretic properties of junctions are different than duplexes, and also it melts differently. Junctions are simple, yet have subtle complexities! 5/5

An outline rendering of a DNA holiday junction showing the way the two duplexes cross on top of each other.

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And here's the all-important gel! I added annotations of which strands from Fig 1 are in each well along the top. The key point they're trying to make is that the 4-strand complex makes a structure larger than 3-strand complexes, but electrophoretically smaller than a 64-base duplex would be. 4/5

Figure 2 from "An immobile nucleic acid junction constructed from oligonucleotides" showing a giant acrylamide gel with extra annotations along the top showing which strands are in wells a-r, respectively. In wells c-f we can see fast-moving bands corresponding to single strands 1-4 of the junction. Wells f-j contain each 3-strand complex, which run much slower than the single strands. Well k contains the 4-strand complex, which again is larger. Wells m-r are all of the 2-strand complexes. The 2-strand complex which bind show similar mobility to the 3-strand complexes, while the two diagonal pairs show single-strands. Wells a, b and l are duplex DNA from restriction digests to show the size of a straight duplex. The 4-strand complex is 64 nucleotides, and there is a 66 nucleotide strand in well a which is much larger.

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Behold! The junction! That sequence right at the junction, known as J1, was gospel in the DNA nanotech community for many years because, well, it worked. 3/5

Figure 1 from "An immobile nucleic acid junction constructed from oligonucleotides" showing the sequence and topology of a 4-way junction with a sequence which is asymmetric, preventing junction migration. In the caption it notes that there is no symmetry at the junction and that it contains no GC sequences longer than 2 to prevent alternate configurations.

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This is experimental validation of yesterday's paper. In it, Ned and colleagues synthesized 4 DNA strands which form a stable, 4-molecule complex. This sounds trivial and the experiments could be done in a week by an undergrad today, but the idea was novel enough for a slot in Nature in 1983! 2/5

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Wake up and smell the acrylamide! Today we're talking about the second paper in our retrospective on Ned Seeman's work, "An immobile nucleic acid junction constructed from oligonucleotides", Nature 1983. 🧬 1/5 www.nature.com/articles/305...

An immobile nucleic acid junction constructed from oligonucleotides - Nature

Nature - An immobile nucleic acid junction constructed from oligonucleotides

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Sadly, Ned passed away in 2021, but his students and colleagues remember him fondly. He was a scientific icon and his ideas and mentorship have touched thousands of scientists across many fields. www.nature.com/articles/s41...

Nadrian C. (Ned) Seeman (1945–2021) - Nature Nanotechnology

Ned Seeman, pioneer of the field of structural DNA nanotechnology, passed away on November 16, 2021.

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For me, the amazing thing about this paper is how integrates so many fields into a single idea which spawned the entire field of DNA nanotechnology. Ned needed to know biochemistry, symmetry, FORTRAN programming, condensed matter physics, and x-ray crystallography to develop this idea.

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These could then be connected via sticky ends to form 2D and 3D polyhedra and lattices. He originally hoped this could be used as easily-crystallized cages which could host hard-to-crystalize guest molecules. Alas, this was easier said than done, it took another 29 years to crystallize a 3D lattice.

Figure 6 from "Nucleic Acid Junctions and Lattices" showing schematically how one could connect the immobile junctions from the previous figures into a 2D lattice via sticky-end cohesion. The caption also points out that "This procedure is not limited in theory to rank-4 junctions nor is it limited to two dimensions."

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