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Constantinos Patinios

@copabio.bsky.social
83 followers 97 following 48 posts

Group leader at VU LSC-EMBL PI for Genome Editing Technologies, Vilnius, Lithuania Genome engineer CRISPR-Cas DNA replication stall and repair

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Constantinos Patinios @copabio.bsky.social · 02/07/2026
Hello @micronaut.bsky.social. Some of our gRNAs are indeed targeting either of the strand but we did not observe black and white differences. However, the set of gRNAs is too small to draw a definite conclusion. I suggest trying nicking either of the strands if this is a concern for your phage :)
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
That would be amazing indeed 😀
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
We did not test this but I would cautiously say, not necessarily. If phage SSBs (or other repair proteins) are recruited to fix the nick, then it could work in other phages as well. What would be interesting is to know how phages fix ssDNA breaks and how universal it is.
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
Whilst we suspect repair is Gp2.5 or SSB related, it is difficult to prove as these proteins are essential for phage viability. Also, these proteins interact with the polymerase so I would doubt if they can be used universally.
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
Many thanks to Frank Englert, Sarshad K. Valappil, Jonas Kubilius, @drjonesky.bsky.social , @vivekmutalik.bsky.social , and Chase Beisel. #Bacteriophage #PhageEngineering #GenomeEditing #CRISPR #PhageTherapy
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
4/4 We then used this library to isolate T7 variants capable of infecting otherwise resistant, LPS-deficient E. coli hosts, showing how scalable phage genome editing can be used to expand host range.
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
3/4 Maintaining high phage titers also makes the method well suited for large-scale mutagenesis. Using nCas9, we generated a library of more than 440,000 T7 tail-fiber variants in a single editing step.
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
2/4 We unexpectedly found that Cas9 nickase, which introduces only a single-strand DNA break, can edit selected phage genomes with remarkably high efficiency while preserving phage titers. Unlike many existing approaches, this avoids multi-step workflows, counterselection, and extensive screening.
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Constantinos Patinios @copabio.bsky.social · 29/06/2026
1/4 Excited to share our new preprint on phage genome editing: Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes Preprint: lnkd.in/dv4g5kW6
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Constantinos Patinios @copabio.bsky.social · 20/01/2026
🔗 Discover more: bit.ly/3LUzM2U #EMBO #GenomeEditing #CRISPR #SyntheticBiology #Microbiology #Biotechnology #Vilnius #LifeSciences
bit.ly
Dr C. Patinios Awarded EMBO Installation Grant to Advance Genome Editing Research in Lithuania
Vilnius University is a prestigious institution of science and studies in Lithuania, which develops world-class science and develops science-based international studies.
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Constantinos Patinios @copabio.bsky.social · 20/01/2026
This work will drive new genome editing technologies and uncover fundamental DNA repair mechanisms, with impact across microbiome research, synthetic biology, industrial biotechnology, and healthcare.
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Constantinos Patinios @copabio.bsky.social · 20/01/2026
🧬 My project, “Pause-Repair-Edit,” aims to move beyond current CRISPR tools by developing safer genome editing approaches that pause DNA replication to activate natural repair pathways—opening genome editing to many microorganisms that are currently hard to engineer.
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Constantinos Patinios @copabio.bsky.social · 20/01/2026
🚀 Excited to share that I’ve been awarded an EMBO Installation Grant to establish my research group at the EMBL Partnership Institute, Vilnius University Life Sciences Center! The grant provides €50,000/year for 5 years to build an internationally competitive lab and advance genome editing research.
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Oleg Dmytrenko @olehdmy.bsky.social · 07/01/2026
Our paper is out! Hiding in plain sight among Cas12a nucleases, Cas12a3 cleaves not its RNA target but the 3′ ends of tRNA. Huge thanks to all who made this possible, especially the Beisel lab, Biao & Dirk for the structure, & @sebastianglatt.bsky.social for all things tRNA. doi.org/10.1038/s415...
nature.com
RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity - Nature
Cas12a3 nucleases constitute a distinct clade of type V CRISPR–Cas bacterial immune systems that preferentially cleave the 3′ tails of tRNAs after recognition of target RNA to induce growth arres...
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eLife @elife.bsky.social · 24/09/2025
Openness means more than access. We’re pleased to announce that we now publish Replication Studies, helping make science more reliable, transparent, and trustworthy. buff.ly/Gebypvq
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Constantinos Patinios @copabio.bsky.social · 07/09/2025
Thank you Jens
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Constantinos Patinios @copabio.bsky.social · 05/09/2025
Thank you Nicholas 😊
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Constantinos Patinios @copabio.bsky.social · 05/09/2025
Amazing Martin!! All the best with the new lab and the amazing research you do!!!
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Reposted by Constantinos Patinios
Nature Biotechnology @natbiotech.nature.com · 04/09/2025
Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - @helmholtz-hiri.bsky.social go.nature.com/4n7zDpG
go.nature.com
Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature Biotechnology
Append editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.
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Constantinos Patinios @copabio.bsky.social · 04/09/2025
Big shout-out to first authors Darshana Gupta, (myself :) ) & Harris V. Bassett, senior author Chase L. Beisel, and project initiator Scott P. Collins 🙌
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Constantinos Patinios @copabio.bsky.social · 04/09/2025
This opens up brand-new possibilities for precision editing and studying DNA repair!
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Constantinos Patinios @copabio.bsky.social · 04/09/2025
We developed append editing, a genome-editing strategy that installs ADP-ribose groups onto DNA to unlock new repair outcomes: 🔹 In bacteria → precise, scar-free edits via homologous recombination 🔹 In eukaryotes → unique T→A or T→C base substitutions not possible with current editors
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Constantinos Patinios @copabio.bsky.social · 04/09/2025
🚀 New publication alert! 🚀 We just published in @natbiotech.nature.com: 👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes doi.org/10.1038/s415...
doi.org
Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature Biotechnology
Append editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.
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Constantinos Patinios @copabio.bsky.social · 07/05/2025
Learn more ➡️ www.gmc.vu.lt/en/lsc-embl/...
gmc.vu.lt
The Laboratory of Dr. Constantinos Patinios
VU Gyvybės mokslų centras jungia tris VU padalinius – Biomokslų, Biotechnologijos ir Biochemijos institutus. Centras įkurtas vystant integruotą mokslo, studijų ir verslo centrą (slėnį) „Saulėtekis“.
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Constantinos Patinios @copabio.bsky.social · 07/05/2025
Deadline: Open until a suitable candidate is found. 📧 Send your CV + Motivation Letter to: constantinos.patinios@gmc.vu.lt
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Constantinos Patinios @copabio.bsky.social · 07/05/2025
🧬 Our work focuses on next-generation genome editing tools for bacteria, yeasts, and phages — with a special focus on DNA replication stalling and repair!
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Constantinos Patinios @copabio.bsky.social · 07/05/2025
🌍 Based in beautiful Vilnius, Lithuania 🔬 Access to state-of-the-art equipment and facilities 💼 Competitive salary, personalized mentorship, and cutting-edge research!
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Constantinos Patinios @copabio.bsky.social · 07/05/2025
If you’re passionate about genome editing or synthetic biology… If you want tailored mentorship to drive independent research and launch your career… This is the place for you! ✨
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Constantinos Patinios @copabio.bsky.social · 07/05/2025
🚀 Join the Patinios Lab at the VU LSC - EMBL Partnership Institute for Genome Editing Technologies! We are looking for a Postdoctoral Researcher to join our growing team! 🔎
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European Research Council (ERC) @erc.europa.eu · 11/03/2025
Good news on this 35th anniversary of the #Restoration of #Independence in #Lithuania! A new ERC project from a Lithuanian researcher can now go ahead, as they were able to secure alternative EU funding for her ERC Consolidator Grant. How did this happen? Find out in the thread 🧵👇
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Constantinos Patinios @copabio.bsky.social · 14/03/2025
Excited to see our SIBR work out in Trends in Biotechnology :) doi.org/10.1016/j.ti... This is the first study I have coordinated from start to finish, and it brings me immense satisfaction to see it published. For a brilliant description of the tech check this: www.linkedin.com/feed/update/...
doi.org
Redirecting
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
Huge thanks to Simona Della Valle, Enrico Orsi and Sjoerd Creutzburg for driving this work. Happy editing :)
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
If you want to use SIBR2.0 for your gene/protein of interest, you can visit the SIBR Site Finder site: colab.research.google.com/drive/162gIZ...
colab.research.google.com
Google Colab
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
SIBR2.0 can virtually control the expression of any gene/protein of interest, in a wide range of (if not all) mesophilic prokaryotes
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
By using SIBR2.0-Cas12a we achieved ~70% editing efficiency, in just 48h after electroporation
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
We show that SIBR2.0 is great for inhibiting the translation of the T7 RNAP in E. coli and then we used it to tightly and inducibly express the Cas12a protein in C. necator
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
his means that even with the alternative translation site present in the SIBR sequence, a non-functional and split protein will be produced
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
This is where magic happened!! We developed SIBR2.0 :) SIBR2.0 includes the introduction of SIBR within the coding sequence of the gene of interest, splitting it into 2 distinct exons
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
The alternative site for translation appeared to be gene- and organism- specific
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
Then, we attempted to do the same for Cas12a but were unsuccessful. Surprisingly, we discovered an alternative translation initiation site within the SIBR sequence, which allowed for the translation of fully functional Cas12a proteins
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
Initially, we used the previously developed SIBR system (check here: doi.org/10.1093/nar/...) to tightly control and delay Cas9-based counterselection. This setup resulted in >80% editing efficiency in C. necator, in just 48 hours after electroporation, outcompeting any other method out there
doi.org
Validate User
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
I am happy to announce our preprint for building a streamlined and efficient genome editing pipeline in the industrially relevant Cupriavidus necator H16 using -MY FAVOURITE- SIBR-Cas system
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Constantinos Patinios @copabio.bsky.social · 25/11/2024
SIBR2.0 is now out in a preprint!! doi.org/10.1101/2024...
doi.org
Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system
Cupriavidus necator H16 is a promising microbial platform strain for CO2 valorisation. While C. necator is amenable to genome editing, existing tools are often inefficient or rely on lengthy protocols...
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Constantinos Patinios @copabio.bsky.social · 20/11/2024
Huge thanks to all authors and collaborators, especially to Darshana Gupta, Harris Bassett and Chase Beisel for leading this study, and to Scott Collins for initiating this study
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Constantinos Patinios @copabio.bsky.social · 20/11/2024
Altogether, our approach, leverages the addition of a chemical moiety to DNA to expand current modalities for precision gene editing
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Constantinos Patinios @copabio.bsky.social · 20/11/2024
In contrast, ADP-ribosylation of eukaryotic genomes, drives substitution of the ADPr-thymine to adenine or a mixture of adenine and cytosine with limited insertions or deletions
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Constantinos Patinios @copabio.bsky.social · 20/11/2024
ADP-ribosylation of bacterial genomes drives efficient homologous recombination, offering flexible and scar-free genome editing without base replacement nor counter-selection
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Constantinos Patinios @copabio.bsky.social · 20/11/2024
Using a DarT2-nCas9 fusion protein, we program site-specific ADP-ribosylation of thymines within a target DNA sequence
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Constantinos Patinios @copabio.bsky.social · 20/11/2024
In our work, we harness the bacterial anti-phage toxin DarT2 to append ADP-ribosyl moieties to DNA, unlocking distinct editing outcomes in bacteria versus eukaryotes
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Constantinos Patinios @copabio.bsky.social · 20/11/2024
Unlike other genome editors (e.g. Base Editors) which remove chemical groups from DNA bases, AE is designed to add/append chemical modifications to DNA bases
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