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Petr Šulc

@petrsulc.bsky.social

580 followers 910 following 34 posts

Associate Professor at Arizona State University, and ERC grant PI at TU Munich. We play with DNA and RNA to make nanoscale structures and devices. Find out more at our lab page: sulclab.org

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Reposted by Petr Šulc

Benjamin D. Greenbaum @bengrbm.bsky.social · 4d

Thank you @mskcancercenter.bsky.social for highlighting our work on #viralmimicry in our genome, its evolution, the selective forces on it, and its potential role in cancer.

A great years long collaborative effort with @petrsulc.bsky.social, @daniel-decarvalho.bsky.social, & many great colleagues!

Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · 4d

Dr. @bengrbm.bsky.social has tried to shed light on the innate immune system and how it affects cancer cells as they evolve.

Now Dr. Greenbaum’s lab has been taking a deep dive into modeling viral mimicry, trying to understand how this could shape cancer cells’ development process. bit.ly/3VWadA8

Petr Šulc @petrsulc.bsky.social · 8d

While this work presents a first step towards 'decoding the repeatome' in human genome, it also presents a fast an accessible framework to assess stimulatory potential of transcripts coming from various experimental datasets.

Petr Šulc @petrsulc.bsky.social · 8d

Complementary to this hypothesis, it is also possible that maintaining these patterns is also beneficial for the repeat families, as we argue in the case of the highly studied family of LINE-1 repeats, where high CpG content might help prevent their deleterious effect on organism's fitness.

Petr Šulc @petrsulc.bsky.social · 8d

We argue that these repeats might have been co-opted to trigger innate immune system response upon translational dysregulation, such as in cancer cells. We checked experimentally that repeat transcripts that we marked as anomalous do bind to pattern recognition receptors of innate immune system.

Petr Šulc @petrsulc.bsky.social · 8d

It allows us to quantify how anomalous given sequence is with respect to what one would expect from a typical transcript from human genomes. The two chosen motifs, CpG content and double-stranded regions,are hallmarks of RNA viruses and our immune system recognizes them as immunostimulatory targets.

Petr Šulc @petrsulc.bsky.social · 8d

In our work, we instead focus on developing statistical mechanics-based framework to identify anomalous sequence (CpGf) and structure (long double-stranded segment) motifs in transcripts of these regions, which are known to be recognized by innate immune system receptors.

Petr Šulc @petrsulc.bsky.social · 8d

A majority of our genome does not code for proteins nor has any established regulatory function. These regions are sometimes called 'junk DNA'. Their function, or lack of, is a very active topic of research.

Petr Šulc @petrsulc.bsky.social · 8d

🧪 In our new work (just published in Cell Genomics) with Benjamin Greenbaum , John LaCava, Daniel De Carvalho, PhD , Simona Cocco and Remi Monasson labs, we venture into the dark matter of human genome:
www.cell.com/cell-genomic...

🧵A shot thread summary below in comments:⬇️

Repeats mimic pathogen-associated patterns across a vast evolutionary landscape

An emerging hallmark of disease is transcription of pathogen-associated molecular patterns from within the genome–known as viral mimicry. We propose a statistical physics framework to measure “selecti...

Reposted by Petr Šulc

Erik Poppleton @floppleton.bsky.social · Aug 25

On this first day of #DNA31, reminder for the mol pro community that I put together this feed which picks up the last 3 days of posts from our community! Enjoy the meeting! 🧬

Erik Poppleton @floppleton.bsky.social · Nov 11

Are there any other scientists from molecular programming here? That's self-assembly, chemical computation, rational design et al. I made a mol pro feed which works like the Science (🧪) feed. Let me know, I add you to the list, you post with a 🧬 emoji. Let's assemble!

bsky.app/profile/flop...

Petr Šulc @petrsulc.bsky.social · Jul 17

A great effort to chart possible future paths for the molecular programming field

Molpigs @molpigs.bsky.social · Jul 16

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

Petr Šulc @petrsulc.bsky.social · Jun 7

The predictions were verified experimentally. Our results have implications for DNA/RNA molecular computing, design of DNA computing systems that interface with RNA triggers, and as we show in our presented model, it can also have implications for predicting the kinetics in CRISPR-based systems.

Petr Šulc @petrsulc.bsky.social · Jun 7

It shows that just by permuting the distribution of bases in the duplex (while keeping AT / CG base pair number constant), the kinetics of the reaction can be altered by orders of magnitude, stemming from the details of differences in stability between hybrid and canonical bases in DNA/RNA systems.

Petr Šulc @petrsulc.bsky.social · Jun 7

It is also of importance for biological systems like CRISPR-Cas9. In this collaboration, Eryk Ratajczyk supervised by Louis, Doye and Turberfield groups from Oxford, uses our new oxDNA-oxRNA hybrid coarse-grained model to study the strand displacement RNA invades DNA duplex.

Petr Šulc @petrsulc.bsky.social · Jun 7

🧪🧬
Our new paper is just out in PNAS:
www.pnas.org/doi/10.1073/...

It is about nucleic acid strand displacement, which is a key reaction in molecular computation, and part of the success of the oxDNA model comes from the fact it can efficiently simulate this process.

1/4🧵

Controlling DNA–RNA strand displacement kinetics with base distribution | PNAS

DNA–RNA hybrid strand displacement underpins the function of many natural and engineered systems. Understanding and controlling factors affecting D...

Petr Šulc @petrsulc.bsky.social · Apr 26

Great work by our student Navraj and Subhajit, building on top of the ground work of previous database by @floppleton.bsky.social and Michael Matthies

Petr Šulc @petrsulc.bsky.social · Apr 26

Just in time for #FNANO conference in Snowbird, UT, our updated and improved version of nanobase.org server is online. Just like the PDB database helped to share protein structures, we want to create a community resource for the DNA/RNA/protein nanotechnology design researchers to share their work

A repository for DNA/RNA nanotechnology

Petr Šulc @petrsulc.bsky.social · Apr 8

4/4: Our crystal example thus provides a falsifiability test for classical nucleation theory, showing need for also taking into account structural fluctuations.

Excellent work by Camilla Beneduce and Diogo Pinto from John Russo's group in Rome!

Petr Šulc @petrsulc.bsky.social · Apr 8

3/4 However, we find that one of the three possible crystal phases is strongly preferred, due to the crystal lattice ordering being similar to the local ordering in the liquid phase.

Petr Šulc @petrsulc.bsky.social · Apr 8

2/4: The assumptions of CNT rely on the free energy difference between bulk phase and the melt, and the interfacial free energy. In this work, we look at a two component system that forms a polymorph: it can nucleate into three different lattices with same interfacial and bulk free-energy.

Petr Šulc @petrsulc.bsky.social · Apr 8

🧪In our new paper (journals.aps.org/prl/abstract...) in collaboration with Russo, Romano, Rovigatti and Sciortino groups in Rome / Venice, we look at Classical Nucleation Theory: a popular model of nucleation process, n is a key phenomena in self-assembly, self-organization and phase transitions.

Falsifiability Test for Classical Nucleation Theory

Classical nucleation theory (CNT) is built upon the capillarity approximation, i.e., the assumption that the nucleation properties can be inferred from the bulk properties of the melt and the crystal....

journals.aps.org

Petr Šulc @petrsulc.bsky.social · Mar 24

Thank you Ulrich, it was a pleasure visiting Heidelberg and meeting you. Many thanks to the amazing group of @kgoepfrich.bsky.social for hosting me!

Petr Šulc @petrsulc.bsky.social · Mar 17

Great collaboration with @laklab-tubs.bsky.social , simulations carried out by my student Josh Evans

Aidin Lak @laklab-tubs.bsky.social · Mar 17

Very excited to introduce mismatch-assisted toehold exchange (MATE) concept for the first time, our new magnetic diagnostics cascades:
biorxiv.org/content/10.1...
Excellent work by Rebecca, "Metrology4life" 2nd PhD student and Great collaboration with @petrsulc.bsky.social

Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-Based Nucleic Acid Diagnostics

Sensitive, simple, and rapid detection of nucleic acid sequences at point-of-care (POC) settings is still an unmet quest. Magnetic readout assays combined with toehold-mediated strand displacement (TM...

Petr Šulc @petrsulc.bsky.social · Feb 5

If you change something in the candano file, it has to be loaded again from scratch into oxview. The scadnano tool has recently been expanded to also allow for visualization in embedded oxview window. Having an interactive cadnano-like interface inside oxView is currently on our TBD wishlist

Petr Šulc @petrsulc.bsky.social · Feb 5

🧬 A new tutorial article from our student Sarah, walking step by step through DNA origami simulation using oxDNA model, with the help of oxview.org and oxdna.org free tools. No prior experience assumed, and also accompanied by a video: youtu.be/5-rgMekX8gE
onlinelibrary.wiley.com/doi/10.1002/...

How We Simulate DNA Origami

This tutorial provides a detailed step-by-step description on how to import DNA origami designs into the oxDNA model and characterize the origami's properties (such as equilibrium shape and flexibili...

onlinelibrary.wiley.com

Petr Šulc @petrsulc.bsky.social · Jan 20

Thank you!