Molpigs
@molpigs.bsky.social
We are the MOLecular Programming Interest Group, early-career researchers in the field of molecular programming building our community through podcasts, reading groups and community activities. Links to all podcast feeds and Slack at molpi.gs
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Molpigs
@molpigs.bsky.social
· Nov 12
We've organized two reading groups on classic papers in molecular programming:
- A celebration of the late Ned Seeman, the founder of DNA nanotechnology
- Foundations of DNA computing
Let's talk about some of the great papers we've read! Each discussion will start as a quote of this post. 🧬
- A celebration of the late Ned Seeman, the founder of DNA nanotechnology
- Foundations of DNA computing
Let's talk about some of the great papers we've read! Each discussion will start as a quote of this post. 🧬
We just released the latest episode of the Molpigs podcast! This time with Megan Engel, a professor at the University of Calgary who is who uses machine learning to build better molecular models. 🧬
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
molpigs Podcast | Megan Engel: Harnessing Machine Learning to Build Better Molecular Models
Join us for a conversation with Professor Megan Engel from the University of Calgary about what it takes to build better physical models of molecules. Her work is inspired by the challenges faced by t...
podcast.molpi.gs
January 19, 2026 at 5:12 PM
We just released the latest episode of the Molpigs podcast! This time with Megan Engel, a professor at the University of Calgary who is who uses machine learning to build better molecular models. 🧬
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
Thank you for joining us! We look forward to your report on whether it's easier to teach an immunologist DNA origami or a molecular programmer immunology!
July 17, 2025 at 8:00 AM
Thank you for joining us! We look forward to your report on whether it's easier to teach an immunologist DNA origami or a molecular programmer immunology!
Podcast drop🧬! As part of the Molecular Programming Flightplan, we assembled a panel discussion on collaboration! The panel is now available as two podcasts, each with half the panel, and a bonus interview with @programmablematter.bsky.social.
Links to all major feeds here:
podcast.molpi.gs
Links to all major feeds here:
podcast.molpi.gs
July 16, 2025 at 7:19 PM
Podcast drop🧬! As part of the Molecular Programming Flightplan, we assembled a panel discussion on collaboration! The panel is now available as two podcasts, each with half the panel, and a bonus interview with @programmablematter.bsky.social.
Links to all major feeds here:
podcast.molpi.gs
Links to all major feeds here:
podcast.molpi.gs
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
Apply here: mpflightplan.com/apply-now
Apply now! — MP Decadal Flightplan
mpflightplan.com
June 23, 2025 at 8:12 PM
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
Apply here: mpflightplan.com/apply-now
Follow WONDER for networking opportunities and upcoming mentorship events aimed at increasing female representation and retention in the Molecular Programming field 🧬
Hello (bluesky) world!
We are WONDER 🧬, an organization aimed at female PhD students, early and late career researchers within DNA Nanotechnology and related fields 😊🧬
Follow us here to stay updated and sign up to our mailing list (link in bio) to never miss out on any news🧬
We are WONDER 🧬, an organization aimed at female PhD students, early and late career researchers within DNA Nanotechnology and related fields 😊🧬
Follow us here to stay updated and sign up to our mailing list (link in bio) to never miss out on any news🧬
May 2, 2025 at 7:39 PM
Follow WONDER for networking opportunities and upcoming mentorship events aimed at increasing female representation and retention in the Molecular Programming field 🧬
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.
What should our next topic be?? Leave us a comment to help us decide.
April 28, 2025 at 11:23 PM
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.
What should our next topic be?? Leave us a comment to help us decide.
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...
www.nature.com/articles/s41...
April 19, 2025 at 3:43 PM
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...
www.nature.com/articles/s41...
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....
www.science.org/doi/full/10....
April 13, 2025 at 12:44 PM
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....
www.science.org/doi/full/10....
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...
www.nature.com/articles/nna...
April 6, 2025 at 9:01 PM
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...
www.nature.com/articles/nna...
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....
www.science.org/doi/full/10....
March 30, 2025 at 10:34 AM
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....
www.science.org/doi/full/10....
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...
www.nature.com/articles/nat...
March 23, 2025 at 9:54 PM
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...
www.nature.com/articles/nat...
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). 🧬
March 20, 2025 at 11:41 AM
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). 🧬
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...
www.nature.com/articles/nat...
March 15, 2025 at 10:54 AM
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...
www.nature.com/articles/nat...
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/...
www.pnas.org/doi/10.1073/...
March 11, 2025 at 8:15 AM
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/...
www.pnas.org/doi/10.1073/...
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/...
www.pnas.org/doi/10.1073/...
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...
www.pnas.org
March 8, 2025 at 11:00 AM
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/...
www.pnas.org/doi/10.1073/...
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...
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...
March 8, 2025 at 11:00 AM
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...
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...
Link to interest form:
docs.google.com/forms/d/e/1F...
Join the Molpigs Slack:
join.slack.com/t/molpigs/sh...
List of papers:
docs.google.com/document/d/1...
docs.google.com/forms/d/e/1F...
Join the Molpigs Slack:
join.slack.com/t/molpigs/sh...
List of papers:
docs.google.com/document/d/1...
molpigs Reading Group: "Folding the path of DNA Origami"
We are organizing a third reading group on the topic of "Folding the path of DNA Origami". If you are interested, please fill in the form below!
docs.google.com
March 2, 2025 at 7:13 PM
Link to interest form:
docs.google.com/forms/d/e/1F...
Join the Molpigs Slack:
join.slack.com/t/molpigs/sh...
List of papers:
docs.google.com/document/d/1...
docs.google.com/forms/d/e/1F...
Join the Molpigs Slack:
join.slack.com/t/molpigs/sh...
List of papers:
docs.google.com/document/d/1...
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. 🧬🧬🧬
March 2, 2025 at 7:13 PM
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. 🧬🧬🧬
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
November 25, 2024 at 11:06 PM
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
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
November 25, 2024 at 11:06 PM
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
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
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
November 25, 2024 at 11:06 PM
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
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
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
November 25, 2024 at 11:06 PM
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
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
November 25, 2024 at 11:06 PM
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
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
November 25, 2024 at 11:06 PM
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
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
November 25, 2024 at 11:06 PM
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