349: Oxidized rNTPs and Transcription Fidelity: How 8‑oxo‑rGTP Embeds RNA Damage

Hou P et al., PNAS - This study combines kinetic assays and X‑ray crystallography to show how 8‑oxo‑guanosine triphosphate (8‑oxo‑rGTP) is incorporated by RNA polymerase II and how its pairing geometry with template bases (dC vs dA) differentially alters incorporation efficiency, extension, and proofreading, thereby introducing transcription‑coupled RNA damage. Key terms: RNA damage, 8-oxo-rGTP, RNA polymerase II, transcription fidelity, oxidative stress. Study Highlights:Pol II incorporates 8‑oxo‑rGTP efficiently opposite dC with kinetics comparable to GTP, whereas incorporation opposite dA is much slower but ~150‑fold more efficient than misincorporation of undamaged rGTP. Extension proceeds rapidly from a 3′‑r8OG:dC pair but is markedly slower from a 3′‑r8OG:dA pair. TFIIS‑stimulated proofreading cleaves r8OG:dC robustly but r8OG:dA is resistant to backtracking and cleavage. Crystal structures reveal 8‑oxo‑rG adopts anti Watson–Crick geometry with dC in the A‑site but flips to syn Hoogsteen geometry with dA, where an interaction with Rpb2 E529 stabilizes a pretranslocation state. Conclusion:Oxidation of the nucleotide pool can directly undermine Pol II fidelity by enabling efficient incorporation and differential handling of 8‑oxo‑rGTP, producing transcription‑coupled RNA damage with potential consequences for RNA processing, translation, and disease. Music:Enjoy the music based on this article at the end of the episode. Article title:Structural basis of transcription -coupled RNA damage by incorporation of oxidized ribonucleotides First author:Hou P Journal:PNAS DOI:10.1073/pnas.2602266123 Reference:Hou P, Lee C, Chong J, Oh J, Wang D. Structural basis of transcription-coupled RNA damage by incorporation of oxidized ribonucleotides. PNAS. 2026;123(16):e2602266123. doi:10.1073/pnas.2602266123 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/8oxo-rgpt-transcription-rna-damage QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-24. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited sections on background, kinetic experiments, structural determinations, proofreading, translocation mechanics, and disease relevance; aligned with the canonical article.- transcript topics: Oxidative stress and oxidized ribonucleotides; 8-oxo-rGTP incorporation opposite dC and dA templates; Presteady-state kinetics and incorporation efficiency; Extension after 8-oxo-rGTP incorporation; TFIIS proofreading and backtracking with oxidized nucleotides; Structural basis: A-site anti conformation with dC; syn Hoogsteen with dA; E529 fork loop 2 interaction QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 8- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- 8-oxo-rGTP can be efficiently incorporated opposite dC, with efficiency comparable to GTP- 8-oxo-rGTP opposite dA is misincorporated ~150-fold more efficiently than rGTP misincorporation- Pol II extends more efficiently from 8-oxo-rG:d... Chapters (00:00:20) - How oxidized guanine causes cellular aging(00:05:39) - How RNA polymerase II mistakes nucleots(00:10:31) - Alzheimer's RNA polymerase: A single hydrogen bond paraly(00:16:59) - Writing errors in our brains