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Deni Szokoli

@szokoli.bsky.social

34 followers 53 following 27 posts

Studying ancient ribozymes. Likes group II introns a little too much. PhD @mutschlerlab.bsky.social

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Deni Szokoli @szokoli.bsky.social · Jul 2

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)

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,...

Reposted by Deni Szokoli

Jörg Vogel @jorg-vogel-lab.bsky.social · 28d

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…

Reposted by Deni Szokoli

Sofya Garushyants @garushyants.bsky.social · 23d

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!

Reposted by Deni Szokoli

Anne Simon 🧪🌱🐴🦠🍊🇨🇦🇺🇦 @annealiz1.bsky.social · Aug 28

🧪 #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/...

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

academic.oup.com

Reposted by Deni Szokoli

Filip Boskovic @filipboskovic.bsky.social · Aug 4

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

Deni Szokoli @szokoli.bsky.social · Jul 3

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

Deni Szokoli @szokoli.bsky.social · Jul 3

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

Deni Szokoli @szokoli.bsky.social · Jul 2

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

A web app for drawing and exploring nucleic acid structures.

www.rnacanvas.app

Deni Szokoli @szokoli.bsky.social · Jul 2

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.

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

Deni Szokoli @szokoli.bsky.social · Jul 2

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)

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,...

Reposted by Deni Szokoli

georghochberg.bsky.social @georghochberg.bsky.social · Jun 11

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-...

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

academic.oup.com

Reposted by Deni Szokoli

Alex Palazzo @ribonucleicacids.bsky.social · May 31

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/...

Complexity myths and the misappropriation of evolutionary theory | PNAS

Recent papers by physicists, chemists, and geologists lay claim to the discovery of new principles of evolution that have somehow eluded over a cen...

Reposted by Deni Szokoli

Phil Holliger @philholliger.bsky.social · May 29

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.

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...

Deni Szokoli @szokoli.bsky.social · May 26

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?

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...

www.science.org

Deni Szokoli @szokoli.bsky.social · May 26

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

Liana Merk @bacteriyay.bsky.social · May 24

(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!

www.biorxiv.org/content/10.1...

Prevalence of Group II Introns in Phage Genomes

Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...

www.biorxiv.org

Reposted by Deni Szokoli

CRC 392 - Molecular Evolution in Prebiotic Environments @crc392molevo.bsky.social · May 20

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
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