New publication on Angew. Chem from Reading-Dublin collaboration

Tayler David Prieto (ESR2, University of Reading) published, together with colleagues from the Cardin group in Reading and the Kellett group at DCU, a paper on Angewandte Chemie (International Edition) titled “Probing a major DNA weakness: resolving the groove and sequence selectivity of the diimine complex [Λ-Ru(phen)2phi]2+”. This work notably benefitted from the use of the infrastructure at Diamond Light Source Ltd.

The paper demonstrates, for the first time, a crystal structure showing groove selectivity by an intercalating ruthenium complex.

It is available in Open Access on the publisher’s website.

New publication on super cytotoxic Re(I) complexes

Collaborative work between researchers from the University of the Free World in South Africa and the Gasser group at PSL University has just been published in Inorganic Chemistry. This work notably includes a contribution from our ESR Maria Dalla Pozza.

This paper presents Re(I) carbonyl complexes with exceptionally low nanomolar cytotoxic activity toward prostate cancer cells, demonstrating further the future viability of utilising rhenium in the fight against cancer.

It is available Open Access here.

Tayler presents his work around the world

Our ESR Tayler David Prieto from the University of Reading presented his work on synthetic and structural studies of ruthenium complexes as DNA major groove binders at different conferences.

He first presented a poster at the 16th  International Symposia of Applied Bioinorganic Chemistry (ISABC), which took place in Ioannina, Greece from the 11th to the 14th of June 2023. On the 7th of July, he did an oral presentation about it at the 19th Royal Society of Chemistry’s Nucleic Acid Forum in London, UK. His journey continued in Adelaide, Australia, for the 20th International Conference on Biological Inorganic Chemistry (ICBIC20), where he gave another oral presentation.

The poster can be found here.

The aim of his project, in collaboration with Diamond Light Source and the Kellett group at Dublin City University, is to provide the first crystallographic evidence of a ruthenium polypyridyl complex binding from the DNA major groove; potentially, as one component of a DNA-binding triplex-forming oligonucleotide (TFO) assembly.

Maria’s secondment experience in Oxford, UK

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

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

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

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

DCU and LMU publish review on Third Generation Sequencing of Epigenetic DNA

The Kellett (DCU) and Carell (LMU) groups recently published a collaborative review titled ‘Third Generation Sequencing of Epigenetic DNA’ in Angewandte Chemie. The review is open access and covers the latest developments in sequencing techniques adapted and developed for ‘third generation’ sequencing platforms, which promise to provide the fastest and most convenient means of DNA sequencing to date.

Cytosine modifications have been shown to influence gene regulation, in turn effecting disease and development, thus facile methods for sequencing these base modifications by exploiting the chemistries of these new devices is an active area of research. Despite extensive reviews covering sequencing technologies and base modifications independently, to our knowledge, this is the first publication to highlight the emerging potential of third generation sequencing technologies to expedite epigenetic research.

During the first in-person NATURE-ETN training week organised in the Institute for Chemical Epigenetic – Munich (ICE-M), Dr Markus Müller and Dr. Pascal Giehr delivered seminars focused on epigenome sequencing which provided valuable background in techniques developed to facilitate the decoding of this secondary information layer in DNA. Work Package 3 in NATURE-ETN aims to generate new techniques for sequencing and imaging epigenetic bases. DCU and LMU have access to third generation sequencing devices, so this review will provide a helpful reference point for researchers in the network.  

Eva publishes about click chemistry-based library preparation for long-read third-generation sequencing

The communication paper of ESR Eva Schönegger and Dr. Antony Crisp from baseclick GmbH in collaboration with the LMU Munich, Institute for Chemical Epigenetics Munich was published in September 2022 in Bioconjugate Chemistry.

In this communication paper, entitled Click Chemistry Enables Rapid Amplification of Full-Length Reverse Transcripts for Long-Read Third Generation Sequencing, Eva, Dr. Antony Crisp, Dr. Markus Müller and coworkers describe the development of a novel click chemistry-based method for the generation and amplification of full-length cDNA libraries from total RNA.

In this work, supervised by Prof. Thomas Carell (LMU) and Dr. Thomas Frischmuth (baseclick), the use of click chemistry circumvents the need for the problematic template-switching reaction.

The use of PCR primers containing two overhanging 3′-nucleotides is one essential modification of the described workflow resulting in a significantly improved read-through compatibility of the 1,4-disubstituted 1,2,3-triazole-containing cDNA, where these modifications normally hinder amplification. This enables to use an insert size which is twice as large compared to the state-of-the art click chemistry-based technique, PAC-seq.

Taking the known advantages of PAC-seq, such as suppression of PCR artefacts, into consideration, the described library preparation method could enable various applications, including improved analyses of mRNA splicing variants and fusion transcripts.