Deni Szokoli

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio

Antiviral reverse transcriptases reveal the evolutionary origin of telomerase Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?

Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

RNAcanvas: interactive drawing and exploration of nucleic acid structures Abstract. Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. H

🧪 #RNAsky

If you aren’t using RNAcanvas to draw your RNA structures and explore alternative structures, you are missing out! 56 citations in a year, with multiple ones in top journals like Nature, Science & Cell. Easy to use and packed with unique features! Try it!

academic.oup.com/nar/article/...

Happy to share our paper in Nano Letters!🧬 We developed programmable RNA nanostructures for detecting cotranscriptionally introduced RNA modifications using nanopores. Big congrats to first authors Iva &
Gerardo and thanks to all collaborators! 🔗https://pubs.acs.org/doi/10.1021/acs.nanolett.5c02391

Employing "a much larger ribozyme" is always the solution to any problem, in my opinion.

Thank you so much for sharing! I'm glad you like it!

Thank you! Yes, absolutely! We wouldn't know what to do without it. I strongly recommend people check it out! www.rnacanvas.app

Yes, that's correct, and honestly I was surprised with how well it worked, too. I believe the trick was paying close attention to sequence/structure motif conservation which seems to hold sufficient information to reconstruct the whole ribozyme class.

I'm grateful to my student Lukas, who did a lot of the early characterization of Arq.I2, and of course @mutschlerlab.bsky.social for his mentorship and making this project possible! And ofc @crc392molevo.bsky.social!

I will be answering any questions, so feel free to ask if you have any! (11/11)

This project was my brainchild and I'm overjoyed to finally see it published!

I want to thank my co-1st author: @noemi-n.bsky.social for all her hard work in seeing the project through until the end! I expect a lot of cool upcoming work from her, so follow her if you like group II introns! (10/11)

This work serves as a proof of concept for the viability of complex ncRNA design through inverse folding, and we hope it paves the way for the computational design of bespoke G2Is and possibly other complex ncRNAs with traits that are favorable for biotech or therapeutic applications. (9/11)

Surprisingly, we saw modest GFP expression compared to a control with an inactive intron. G2Is tend to silence host genes by cleaving the mRNA, so lowered expression is not unexpected. These results indicate that the protein-free intron is active in E. coli cells. (8/n)

According to conventional wisdom, G2Is require protein cofactors to aid in self-splicing under intracellular conditions, hindering their application as protein-free genome editors.

We designed an assay for splicing-dependent fluorescent protein expression — a GFP gene interrupted by Arq.I2 (7/n)

Unlike typical de novo designed ribozymes, Arq.I2 outperforms most wild type variants characterized thus far! It reacts with fast kinetics, having a rate of splicing comparable to those of the fastest known natural G2Is! (6/n)

All three candidates were active in vitro, some even outperforming a variant of a natural intron.
Arq.I2 is a very unusual intron — it requires extreme measures to denature it for PAGE, and remains catalytically active in the absence of monovalent cations. (5/n)

In our latest paper we combined the inverse folding algorithm aRNAque and rational design to generate unique synthetic G2Is.
aRNAque's evolutionary algorithm was able to finetune intron folding, resulting in unusually stable structures. (4/n)

Protein-free G2Is were recently found to hydrolyze dsDNA, showing potential as RNA-only genome editors (see my previous thread). However, their complexity poses a challenge to their de novo design, as only short ribozymes have ever been generated using inverse folding algorithms. (3/n)

G2Is are self-splicing retroelements found in all domains of life, and are the ancestors of the spliceosome.
Owing to dozens of tertiary interactions and a large conformational change between the steps of catalysis, they are among the largest and most complex ribozymes. (2/n)

Computational De Novo Design of Group II Introns Yields Highly Active Ribozymes Group II Introns (G2Is) are large self-splicing ribozymes with promising biotechnological applications. This study utilized RNA inverse folding to design three novel G2Is. The designed intron Arq.I2,...

Have you ever wanted to design large and complex ribozymes from scratch? I know I have!

We used RNA inverse folding to design synthetic Group II Introns (G2Is) from the bottom up, resulting in highly active #ribozymes that splice in E. coli without proteins!

#intron #RNAsky #SynBio 🧬🧵(1/n)

A general substitution matrix for structural phylogenetics. Abstract. Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

I haven't been posting much social media recently, but if there is one thing you read this week it should be THIS:
www.pnas.org/doi/10.1073/...

Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme Nature Chemistry - Models of abiotic RNA replication suffer from inherent product inhibition arising from the high stability of RNA duplexes. Now, it has been shown that RNA trinucleotide...

New paper from my group rdcu.be/eoaRr "Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme" in Nature Chemistry — great collaboration with attwaterlab.uk.

An intron endonuclease facilitates interference competition between coinfecting viruses Introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in vi...

The preprint mentions that you find thousands of hits in UniProt for these new HEGs. Do you know if these are standalone HEGs, or if they are predominantly associated with introns?

Could these HEGs block coinfection of competing phages, similar to what was found for group I introns?

Christmas came early this year! I have been wondering about this for years!

Emancipated Archaea 🦠
Nowadays, H₂-dependent archaea rely on partnerships with organisms that produce hydrogen. But on early Earth, when life began, archaea were probably on their own. So, where did they get the H₂ from? Let’s dig into the science.
#Science #OriginOfLife
(1/5)

1/10 Today in @science.org in collaboration with
the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...

Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide...

Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...

Dating Bacteria is hard due to the lack of maxima. Assuming aerobes likely postdated the GOE gave us better resolved ages, but also surprised us, but not Dr Dayhoff, showing O2 use predated its atmospheric rise by 900 Mys and helped oxygenic photosynthesis to evolve. www.science.org/doi/10.1126/...