NATURE-ETN’s beyond state-of-the-art scientific and technological progress focused on:
1. Developing new methods for artificial gene editing. Firstly, we made significant contributions to this field by developing new DNA-binding and -damaging metallodrugs. The project then attempted to produce advanced nucleic acid-metallodrug hybrids with sequence-specific gene targeting properties. Here, artificial gene-editing systems were developed using triplex-forming oligonucleotides conjugated to metallodrugs using click chemistry methods. A number of new metallodrugs that can be light and chemically activated were produced (cf. Gasser et al., RSC Chem. Biol., 2022, 3; Kellett et al., RSC Med. Chem., 2024, 15, Kellett et al., Angew. Chemie, 2023, e202305759). Another aim was to crystallise and structurally characterise new metal complexes that can bind in the major groove of DNA. Here, expertise from the Cardin group: i.) Cardin et al., Angew. Chemie, 2024, e202318863; ii.) Cardin et al., Chem. Sci., 2024, 15) was used to identify the structures of new DNA damaging agents. Several of the metallodrugs were then modified and attached to gene targeting groups, such as triplex-forming oligonucleotides, and examined for their sequence-specific interactions with cancer causing genes.
2. Synthesis and delivery of nucleic acid therapeutics that promote cell-based cancer immunotherapy. NATURE-ESRs engaged in the development of geranylated nucleosides to anchor RNA to nanoparticles for transfection. Moreover, one ESR focused on establishing prebiotically plausible scenarios of an RNA–peptide world and this work was published in Nature (Carell et al., Nature, 2022, 605). Another of NATURE’s ESR investigated the stabilisation effects of a specific nucleobase called m6A in RNA constructs, including guide-RNA in combination with dCas13-fused methyltransferases. Further research was dedicated to the design of antisense oligonucleotides containing artificial cleaving agents which have Cas13-like behaviour, but without the protein component. The outcome from this research strategy could have a major future impact on cancer therapy since the work aims to both simultaneously reduce immunogenicity and enhance mRNA expression.
3. Generation of new reagents for high-sensitivity epigenetic base detection. Reading the epigenetic status of DNA bases encoded in the human genome gives us vital information related to gene expression (Carell et al., Nature Communications, 2021, 12; Carell, Kellett et al. Angew. Chemie, 2023, e202215704). NATURE-ETN ESRs focused on sequencing the epigenome and addressed current limitations in sequencing technologies. ESRs attempted to develop breakthrough materials for epigenetic base oxidation for use in next-generation sequencing (NGS). Progress was made on establishing analytical methods for quantification of cAzadC and metabolites prepared using isotopically labelled compounds for metabolic assays. The successful development of this analytical protocol may now enable rapid and parallel monitoring of dC and metabolites thereby revolutionising epigenetic monitoring and diagnostics. In parallel, new Fe(IV)-oxo complexes were investigated as potential new agents capable of oxidising 5mC and 5hmC to 5fC. In this area of research, baseclick GmbH, a NATURE-ETN industrial beneficiary, aimed to exploit other important avenues for probe development. One strategy identified a click chemistry-based method for the generation and amplification of full-length cDNA libraries from total RNA for next-generation sequencing.
