Deni Szokoli
@szokoli.bsky.social
Studying ancient ribozymes. Likes group II introns a little too much. PhD @mutschlerlab.bsky.social
Pinned
Deni Szokoli
@szokoli.bsky.social
· Jul 2
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,...
doi.org
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)
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)
Reposted by 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
🌐 evedesign.bio
October 22, 2025 at 2:30 PM
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
🌐 evedesign.bio
Reposted by Deni Szokoli
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...
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...
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 ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
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...
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...
Reposted by Deni Szokoli
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…
September 10, 2025 at 3:40 PM
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
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!
September 15, 2025 at 5:26 PM
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
🧪 #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/...
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
August 28, 2025 at 10:33 PM
🧪 #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/...
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/...
Reposted by Deni Szokoli
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
Gerardo and thanks to all collaborators! 🔗https://pubs.acs.org/doi/10.1021/acs.nanolett.5c02391
August 4, 2025 at 5:41 PM
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
Gerardo and thanks to all collaborators! 🔗https://pubs.acs.org/doi/10.1021/acs.nanolett.5c02391
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)
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,...
doi.org
July 2, 2025 at 10:01 AM
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)
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)
Reposted by Deni Szokoli
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
June 11, 2025 at 2:01 PM
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-...
Reposted by Deni Szokoli
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/...
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...
www.pnas.org
May 31, 2025 at 1:06 PM
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/...
www.pnas.org/doi/10.1073/...
Reposted by Deni Szokoli
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...
rdcu.be
May 29, 2025 at 3:55 PM
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.
Christmas came early this year! I have been wondering about this for years!
(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...
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
May 26, 2025 at 11:43 AM
Christmas came early this year! I have been wondering about this for years!
Reposted by Deni Szokoli
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)
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)
May 20, 2025 at 9:32 AM
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)
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)
Reposted by Deni Szokoli
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...
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...
May 15, 2025 at 10:49 PM
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...
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...
Reposted by Deni Szokoli
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...
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...
www.biorxiv.org
March 26, 2025 at 10:13 PM
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...
Reposted by Deni Szokoli
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/...
April 4, 2025 at 1:20 AM
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/...
Reposted by Deni Szokoli
Here to report UltraSelex which uses single-round selection and ranking algorithm for high-affinity RNA aptamer discovery #RNA #ChemBio #chemsky #drugdiscovery
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Single-step discovery of high-affinity RNA ligands by UltraSelex - Nature Chemical Biology
A method called UltraSelex for identifying RNA aptamers has been developed. UltraSelex is noniterative and can combine biochemical partitioning, high-throughput sequencing and computational signal-to-...
www.nature.com
April 14, 2025 at 3:39 PM
Here to report UltraSelex which uses single-round selection and ranking algorithm for high-affinity RNA aptamer discovery #RNA #ChemBio #chemsky #drugdiscovery
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Rejoice! RFdiffusion2 just dropped!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Atom level enzyme active site scaffolding using RFdiffusion2
De novo enzyme design starts from ideal active site descriptions consisting of constellations of catalytic residue functional groups around reaction transition state(s), and seeks to generate protein ...
www.biorxiv.org
April 15, 2025 at 1:00 PM
Rejoice! RFdiffusion2 just dropped!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Deni Szokoli
Interested in a #postdoc in #originsoflife research? Are you a geek who loves #RNA, #RNAseq and tinkering, with a background in #biochemistry, #chemistry or #biophysics? Join #bubblelife! Apply now by email (CV + a short motivation letter)!
cordis.europa.eu/project/id/1...
cordis.europa.eu/project/id/1...
From RNA-peptide coevolution to cellular life at heated air bubbles | BubbleLife | Projekt | Fact Sheet | HORIZON | CORDIS | European Commission
"The origin of life on Earth is one of humanity's profound mysteries that lacks scientific answers. We aim to answer this fundamental question by performing pioneering experiments starting from the Da...
cordis.europa.eu
April 9, 2025 at 7:09 PM
Interested in a #postdoc in #originsoflife research? Are you a geek who loves #RNA, #RNAseq and tinkering, with a background in #biochemistry, #chemistry or #biophysics? Join #bubblelife! Apply now by email (CV + a short motivation letter)!
cordis.europa.eu/project/id/1...
cordis.europa.eu/project/id/1...
Reposted by Deni Szokoli
#ncRNA molecules are far stranger than you think. We propose that OLE RNA is bacteria's functional mimic of #mTOR, and the Das lab at Stanford proposes OLE RNA penetrates cell membranes! They also find that RNAs we called ROOL and GOLLD form 8-membered nanocages.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 31, 2024 at 2:25 PM
#ncRNA molecules are far stranger than you think. We propose that OLE RNA is bacteria's functional mimic of #mTOR, and the Das lab at Stanford proposes OLE RNA penetrates cell membranes! They also find that RNAs we called ROOL and GOLLD form 8-membered nanocages.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Out now in
@NAR_Open
! A #ribozyme can self-integrate into and hydrolyze ss- & dsDNA, offering a new avenue for the development of protein-free genome editing tools, and hinting at the possibility of a pre-translation origin of group II introns (G2Is). 🧬🧵 (1/7)
#intron #RNAworld
@NAR_Open
! A #ribozyme can self-integrate into and hydrolyze ss- & dsDNA, offering a new avenue for the development of protein-free genome editing tools, and hinting at the possibility of a pre-translation origin of group II introns (G2Is). 🧬🧵 (1/7)
#intron #RNAworld
Protein-free catalysis of DNA hydrolysis and self-integration by a ribozyme
Abstract. Group II introns are ancient self-splicing ribozymes and retrotransposons. Though long speculated to have originated before translation, their de
academic.oup.com
December 19, 2024 at 4:52 PM