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horizon 2020

A new publication from the collaboration between LMU and baseclick

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Our ESR Eva Schönegger, together with colleagues from the company baseclick GmbH and the Carell group at LMU Münich, just published a new paper titled “Orthogonal end labelling of oligonucleotides via dual incorporation of Click reactive NTP analogues” on ChemBioChem.

The paper introduces a modular method for modifying DNA and RNA strands at both ends with click-modifiable functional groups using γ-modified ATP analogues and T4 PNK catalysis for 5′-modification, compatible with TdT-catalyzed 3′-elongation using 3′-Azido-2′,3′-ddGTP. The approach is demonstrated to be suitable for oligo-oligo ligations and ssDNA-circularization, potentially enhancing the utility of oligonucleotides in therapeutic and diagnostic applications, particularly in next-generation sequencing.

The list of publications originating from the network can be found on our Dissemination page.

Maria’s secondment experience in Oxford, UK

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After the great experience I had during my first secondment at the University of Reading, I had the chance to spend one month at the University of Oxford, in the UK, supervised by Prof. Tom Brown and Prof. Afaf El-Sagheer.

This time I was not alone, but Tania (ESR9) and Malou (ESR5) came for their secondment in the same period. The first day I went to the lab I was very excited about the new experience in such an important group and university. The group gave me a warm welcome when I arrived, and I felt happy and thrilled to be there.

During this secondment, I learnt many new techniques and developed new skills, supervised by very professional and passionate scientists, always keen to teach me.

During my stay, I used click chemistry reactions to link the Ruthenium compounds I synthesised at Chimie ParisTech – PSL to some triplex-forming oligonucleotides. I learnt how the oligonucleotides are synthesised, thanks to Prof. Afaf El-Sagheer who was always keen to teach me, and I performed the reactions helped by Diallo (ESR 6), who kindly and patiently taught and illustrated the techniques.

During this experience, I had the opportunity to learn, develop my scientific skills, and know a different scientific environment.

But it was not just science! I had great experiences like visiting the beautiful Oxford, and getting into some of the Colleges – thanks to the “local”, Sebastian (ESR1). The cherry on top was the fairy tale experience of having a formal dinner in a College!

Overall, this experience was magic! From the scientific and personal point of view. I am very happy and grateful I had the chance to live all these great adventures thanks to the NATURE-ETN project!

By Maria Dalla Pozza (ESR3)

Tania’s secondments from Warsaw to Oxford

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Our ESR Tania Sánchez Quirante from the Hocek group at the Institute of Organic Chemistry and Biochemistry in Czechia recently did two secondments at the Universities of Warsaw (Poland) and Oxford (UK).

From January to February 2023, Tania did her first secondment at the Laboratory of Chemical Biology and Biophysical Chemistry at the University of Warsaw, where she synthesized and purified modified cap RNA 70nt long and modified mRNA by in-vitro transcription. She also learned how to do in-vitro translation using the rabbit reticulocyte system.

In April 2023, she stayed at the Tom Brown group at the University of Oxford. She synthesized modified single-guide RNA 99nt long by in-vitro transcription reaction and used this sgRNA to perform CRISPR-Cas experiments. In addition, she did stability experiments of the modified sgRNA in Human serum.

Crystal clear insight: ESRs explore the world of crystallography and structural biology

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The Early-Stage Researchers (ESRs) were thrilled to participate in the 5th training week about nucleic acids and crystallography. The first two days were spent attending the Oligo 2023 conference in Oxford. They listened to experts talk about nucleic acid, base modification, aptamers, and more. They were fascinated by the new developments and ideas in this field.

After the conference, the ESRs visited the Oxford Nanopore Technologies research facilities. They gained a deep understanding of how the research industry works and how scientists turn their ideas into reality. The ESRs were impressed by the state-of-the-art facilities and the advanced equipment used for research.

The next two days were spent at the University of Reading, where the ESRs attended engaging talks about crystallography and data processing. They had the opportunity to participate in hands-on activities such as crystallisation, plate preparation, high throughput robot, and learning to recognise and collect good crystals. Finally, they collected data from the X-ray, which was an exciting experience for them.

After a free afternoon spent in London, the ESRs were welcomed at Diamond Light Source. They were given an intense tour of the different facilities and beam lines available at the synchrotron. They gained an understanding of the Cryo-EM and laser technology used in the field of structural biology for protein and nucleic acids. It was an eye-opening experience for them, and they had a lot of fun learning about this exciting field. Overall, the ESRs found the 5th training week about nucleic acids and crystallography to be an enlightening experience. They were exposed to the latest developments in the field, and the hands-on experience provided them with a deeper understanding of the processes involved. They were inspired to continue their research with renewed enthusiasm and curiosity.

By Ahmad Abdullrahman (ESR4)

Webinar on oligonucleotide synthesis

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Professor Tom Brown (University of Oxford) will be a speaker at the webinar “Traditional and Emerging Methods of Oligonucleotide Synthesis”, organised by Biotage and taking place on the 5th of April at 11am CEST.

Prof. Brown will review the history of oligonucleotide synthesis, examine how they are made currently and highlight emerging synthesis methods, including enzymatic approaches. He will also discuss the various applications of synthetic oligonucleotides, from diagnostics to therapeutics and more.

You can register here: https://go.technologynetworks.com/oligonucleotide-synthesis

NATURE-ETN ESRs publish review on DNA triplexes

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A collaborative review by ESRs Ahmad Abdullrahman from the Department of Pharmacy, Chemistry and Pharmacy Building, University of Reading (UK), and Maria Dalla Pozza from Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (France) was published in Chemical Science in August 2022.

In this review, entitled Three’s a crowd – stabilisation, structure, and applications of DNA triplexes, the ESRs put their efforts together in proficient teamwork supervised by Dr. James Hall, Prof. Christine Cardin from the University of Reading, and Prof. Gilles Gasser from Chimie ParisTech, PSL University.

They describe the main characteristics of triplex DNA structures, focusing on their application and interaction with metal compounds, highlighting the need for additional structure characterization and biological studies.

The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex-forming oligonucleotide (TFO) to a DNA duplex. Among others, the most interesting feature of TFOs is their sequence specificity in binding a duplex DNA. The authors first compare the triplex structure with the canonical B-DNA structure. Subsequently, they report the main modifications at the base, sugar and phosphate backbone levels currently available to obtain a more stable structure, considering the potential in vivo conditions.

There is significant interest in developing TFOs with potential therapeutic applications, including their use as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies is essential, stress the authors. In the review, these areas are discussed. Moreover, the possible use of photoactive Ruthenium polypyridyl complexes as a suitable photophysical payload for a TFO system is presented in this scientific paper. With the hope that future research will harness the peculiar characteristics of DNA triplexes.

Open position in Oxford, UK

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The research group of Prof. Tom Brown from the Oxford University Department of Chemistry is looking for an Early-Stage Researcher (ESR) for a period of three years. The ESR will work on a project entitled “chemically modified CRISPR systems for improved gene editing”, which aims to use cutting-edge nucleic acid chemistry to radically alter the mechanism by which the CRISPR-Cas9 system functions.

Deadline for application: 10 March 2021

Job description and application details

Picture: Bodleian Library, Oxford / Author: Zhushenje