--- _id: '10758' abstract: - lang: eng text: 5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark. acknowledgement: "We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n" article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Romeo C. A. full_name: Dubini, Romeo C. A. last_name: Dubini - first_name: Eva full_name: Korytiaková, Eva last_name: Korytiaková - first_name: Thea full_name: Schinkel, Thea last_name: Schinkel - first_name: Pia full_name: Heinrichs, Pia last_name: Heinrichs - first_name: Thomas full_name: Carell, Thomas last_name: Carell - first_name: Petra full_name: Rovo, Petra id: c316e53f-b965-11eb-b128-bb26acc59c00 last_name: Rovo orcid: 0000-0001-8729-7326 citation: ama: Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050 apa: Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., & Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050 chicago: Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au. American Chemical Society, 2022. https://doi.org/10.1021/acsphyschemau.1c00050. ieee: R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” ACS Physical Chemistry Au, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022. ista: Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246. mla: Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:10.1021/acsphyschemau.1c00050. short: R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246. date_created: 2022-02-16T11:18:21Z date_published: 2022-02-11T00:00:00Z date_updated: 2023-01-31T07:33:07Z day: '11' ddc: - '540' department: - _id: NMR doi: 10.1021/acsphyschemau.1c00050 external_id: pmid: - '35637781' file: - access_level: open_access checksum: 5ce3f907848f5c7caf77f1adfe5826c6 content_type: application/pdf creator: dernst date_created: 2022-07-29T07:53:20Z date_updated: 2022-07-29T07:53:20Z file_id: '11692' file_name: 2022_ACSPhysChemAU_Dubini.pdf file_size: 2351220 relation: main_file success: 1 file_date_updated: 2022-07-29T07:53:20Z has_accepted_license: '1' intvolume: ' 2' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '02' oa: 1 oa_version: Published Version page: 237-246 pmid: 1 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: ACS Physical Chemistry Au publication_identifier: eissn: - 2694-2445 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: link: - relation: earlier_version url: https://www.biorxiv.org/content/10.1101/2021.12.14.472563 scopus_import: '1' status: public title: 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2022' ... --- _id: '12228' abstract: - lang: eng text: The question of how RNA, as the principal carrier of genetic information evolved is fundamentally important for our understanding of the origin of life. The RNA molecule is far too complex to have formed in one evolutionary step, suggesting that ancestral proto-RNAs (first ancestor of RNA) may have existed, which evolved over time into the RNA of today. Here we show that isoxazole nucleosides, which are quickly formed from hydroxylamine, cyanoacetylene, urea and ribose, are plausible precursors for RNA. The isoxazole nucleoside can rearrange within an RNA-strand to give cytidine, which leads to an increase of pairing stability. If the proto-RNA contains a canonical seed-nucleoside with defined stereochemistry, the seed-nucleoside can control the configuration of the anomeric center that forms during the in-RNA transformation. The results demonstrate that RNA could have emerged from evolutionarily primitive precursor isoxazole ribosides after strand formation. acknowledgement: We thank Stefan Wiedemann for the synthesis of reference compounds and Pia Heinrichs for assistance in the NMR measurements of the oligonucleotides. We also thank Dr. Luis Escobar and Jonas Feldmann for valued discussions. This work was supported by the German Research Foundation (DFG) for financial support via CRC1309 (Project ID 325871075, A04), CRC1361 (Project ID 893547839, P02) and CRC1032 (Project ID 201269156, A5). This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program under grant agreement No 741912 (EpiR). We are grateful for additional funding from the Volkswagen Foundation (EvoRib). Open Access funding enabled and organized by Projekt DEAL. article_number: e202211945 article_processing_charge: No article_type: original author: - first_name: Felix full_name: Xu, Felix last_name: Xu - first_name: Antony full_name: Crisp, Antony last_name: Crisp - first_name: Thea full_name: Schinkel, Thea last_name: Schinkel - first_name: Romeo C. A. full_name: Dubini, Romeo C. A. last_name: Dubini - first_name: Sarah full_name: Hübner, Sarah last_name: Hübner - first_name: Sidney full_name: Becker, Sidney last_name: Becker - first_name: Florian full_name: Schelter, Florian last_name: Schelter - first_name: Petra full_name: Rovo, Petra id: c316e53f-b965-11eb-b128-bb26acc59c00 last_name: Rovo orcid: 0000-0001-8729-7326 - first_name: Thomas full_name: Carell, Thomas last_name: Carell citation: ama: Xu F, Crisp A, Schinkel T, et al. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 2022;61(45). doi:10.1002/anie.202211945 apa: Xu, F., Crisp, A., Schinkel, T., Dubini, R. C. A., Hübner, S., Becker, S., … Carell, T. (2022). Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202211945 chicago: Xu, Felix, Antony Crisp, Thea Schinkel, Romeo C. A. Dubini, Sarah Hübner, Sidney Becker, Florian Schelter, Petra Rovo, and Thomas Carell. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202211945. ieee: F. Xu et al., “Isoxazole nucleosides as building blocks for a plausible proto‐RNA,” Angewandte Chemie International Edition, vol. 61, no. 45. Wiley, 2022. ista: Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovo P, Carell T. 2022. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 61(45), e202211945. mla: Xu, Felix, et al. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International Edition, vol. 61, no. 45, e202211945, Wiley, 2022, doi:10.1002/anie.202211945. short: F. Xu, A. Crisp, T. Schinkel, R.C.A. Dubini, S. Hübner, S. Becker, F. Schelter, P. Rovo, T. Carell, Angewandte Chemie International Edition 61 (2022). date_created: 2023-01-16T09:49:05Z date_published: 2022-11-07T00:00:00Z date_updated: 2023-08-04T09:32:42Z day: '07' ddc: - '540' department: - _id: NMR doi: 10.1002/anie.202211945 external_id: isi: - '000866428500001' file: - access_level: open_access checksum: 4e8152454d12025d13f6e6e9ca06b5d0 content_type: application/pdf creator: dernst date_created: 2023-01-27T10:28:45Z date_updated: 2023-01-27T10:28:45Z file_id: '12422' file_name: 2022_AngewandteChemieInternat_Xu.pdf file_size: 1076715 relation: main_file success: 1 file_date_updated: 2023-01-27T10:28:45Z has_accepted_license: '1' intvolume: ' 61' isi: 1 issue: '45' keyword: - General Chemistry - Catalysis language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Isoxazole nucleosides as building blocks for a plausible proto‐RNA tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 61 year: '2022' ...