UV photodamage pathways and the evolutionary selection of thymine over uracil in early genetic systems

UV photodamage pathways and the evolutionary selection of thymine over uracil in early genetic systems Contributed by Peter M. Rentzepis; received May 13, 2026; accepted July 11, 2026; reviewed by Ali O. Er, Sadik Esener, and Dmitri Voronine Significance Why DNA uses thymine instead of uracil remains photochemically unresolved, since thymine is more susceptible to ultraviolet (UV) damage. Resolving this paradox is central to understanding how life emerged and persisted under intense early Earth UV radiation. Using absorption, fluorescence, and Raman spectroscopy under UVC irradiation conditions relevant to primordial Earth, we show that although thymine is more photoreactive, it preferentially channels UV damage into reversible lesions amenable to nonenzymatic self-repair. These findings support the concept that nucleobases evolved as “molecular sunscreens” that protect genetic integrity by localizing and controlling damage rather than avoiding it. Our spectroscopic measurements establish a reference framework that enables sensitive detection and quantification of UV-induced damage, with applications in pathogen diagnostics and UV disinfection monitoring. Abstract The evolutionary selection of thymine over uracil in DNA presents a paradox from a photostability perspective, since thymine is found to be more susceptible to photodamage from the intense UV radiation present on the early Earth. This study addresses this paradox by providing a comparative spectroscopic analysis of thymine and uracil under controlled 265 nm UV irradiation. To that effect, we used steady-state absorption, fluorescence, and Raman spectroscopy to quantify and compare the photochemical behavior and damage kinetics of the two nucleobases. Our results show that thymine is inherently more photoreactive than uracil, exhibiting a faster overall rate of photodamage, a broader absorption band that increases spectral overlap with the primordial UVC spectrum, and a redshifted absorption maximum located in a spectral region where solar intensity was substantially higher. However, kinetic analysis of lesion pathways reveals that thymine forms irreversible (6-4) photoproducts at a significantly lower rate than uracil, instead directing UV-induced damage primarily toward the reversible cyclobutane pyrimidine dimer pathway. These findings support the hypothesis that canonical nucleobases were evolutionarily optimized not to minimize photodamage but to localize damage within the bases and direct lesion formation toward reversible pathways amenable to nonenzymatic self-repair. Data, Materials, and Software Availability All study data are included in the main text. Acknowledgments This study was supported by Air Force Office of Scientific Research Grant number FA9550-20-1-0139 and Texas A&M Engineering Experiment Station funds. Author contributions K.K.A., N.K., and P.M.R. designed research; K.K.A. and N.K. performed research; P.M.R. contributed new reagents/analytic tools; K.K.A., N.K., and P.M.R. analyzed data; and K.K.A. and P.M.R. wrote the paper. Competing interests The authors declare no competing interest. References 1 T. Misteli, The self-organizing genome: Principles of genome architecture and function. Cell 183, 28–45 (2020). 2 M. Thanbichler, S. C. Wang, L. Shapiro, The bacterial nucleoid: A highly organized and dynamic structure. J. Cell. Biochem. 96, 506–521 (2005). 3 J. D. Watson, F. H. C. Crick, Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953). 4 A. D. Hershey, M. Chase, Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36, 39–56 (1952). 5 O. T. Avery, C. M. Macleod, M. McCarty, Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J. Exp. Med. 79, 137–158 (1944). 6 R. C. Spitale, D. Incarnato, Probing the dynamic RNA structurome and its functions. Nat. Rev. Genet. 24, 178–196 (2023). 7 S. Minchin, J. Lodge, Understanding biochemistry: Structure and function of nucleic acids. Essays Biochem. 63, 433–456 (2019). 8 J. O’Brien, H. Hayder, Y. Zayed, C. Peng, Overview of microRNA biogenesis, mechanisms of actions, and circulation. Front. Endocrinol. (Lausanne) 9, 402 (2018). 9 H. Peng, B. Latifi, S. Müller, A. Lupták, I. A. Chen, Self-cleaving ribozymes: Substrate specificity and synthetic biology applications. RSC Chem. Biol. 2, 1370–1383 (2021). 10 R. 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Nature 190, 690–694 (1961). Information & Authors Information Published in Classifications Copyright Copyright © 2026 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY). Data, Materials, and Software Availability All study data are included in the main text. Submission history Received: May 13, 2026 Accepted: July 11, 2026 Published online: August 3, 2026 Published in issue: August 18, 2026 Keywords Acknowledgments This study was supported by Air Force Office of Scientific Research Grant number FA9550-20-1-0139 and Texas A&M Engineering Experiment Station funds. Author contributions K.K.A., N.K., and P.M.R. designed research; K.K.A. and N.K. performed research; P.M.R. contributed new reagents/analytic tools; K.K.A., N.K., and P.M.R. analyzed data; and K.K.A. and P.M.R. wrote the paper. Competing interests The authors declare no competing interest. Notes Reviewers: A.O.E., Western Kentucky Universty; S.E., Oregon Health and Science University; and D.V., University of South Florida. Authors Metrics & Citations Metrics Altmetrics Citations Cite this article UV photodamage pathways and the evolutionary selection of thymine over uracil in early genetic systems, Proc. Natl. Acad. Sci. U.S.A. 123 (33) e2615278123, https://doi.org/10.1073/pnas.2615278123 (2026). Copied! Copying failed. Export the article citation data by selecting a format from the list below and clicking Export. View Options View options Download this article as a PDF file. PDFPDF and Supporting Information Download the article PDF and supporting information. Download PDF and supporting informationeReader View this article with eReader. eReaderFigures Tables Media References References References 1 T. Misteli, The self-organizing genome: Principles of genome architecture and function. Cell 183, 28–45 (2020). 2 M. Thanbichler, S. C. Wang, L. Shapiro, The bacterial nucleoid: A highly organized and dynamic structure. J. Cell. Biochem. 96, 506–521 (2005). 3 J. D. Watson, F. H. C. Crick, Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953). 4 A. D. Hershey, M. Chase, Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36, 39–56 (1952). 5 O. T. Avery, C. M. Macleod, M. McCarty, Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J. Exp. Med. 79, 137–158 (1944). 6 R. C. Spitale, D. Incarnato, Probing the dynamic RNA structurome and its functions. Nat. Rev. Genet. 24, 178–196 (2023). 7 S. Minchin, J. Lodge, Understanding biochemistry: Structure and function of nucleic acids. Essays Biochem. 63, 433–456 (2019). 8 J. O’Brien, H. Hayder, Y. Zayed, C. Peng, Overview of microRNA biogenesis, mechanisms of actions, and circulation. Front. Endocrinol. (Lausanne) 9, 402 (2018). 9 H. Peng, B. Latifi, S. Müller, A. Lupták, I. A. Chen, Self-cleaving ribozymes: Substrate specificity and synthetic biology applications. RSC Chem. Biol. 2, 1370–1383 (2021). 10 R. Nouri et al., Unveiling putative modulators of mutable collagenous tissue in the brittle star Ophiomastix wendtii: An RNA-Seq analysis. BMC Genomics 25, 1013 (2024). 11 F. Crick, Central dogma of molecular biology. Nature 227, 561–563 (1970). 12 N. Liu, J. Du, J. Ge, S. B. Liu, DNA damage-inducing endogenous and exogenous factors and research progress. Nucleosides Nucleotides Nucleic Acids 44, 969–1001 (2025). 13 Y. Wang et al., Research progress on the role and mechanism of DNA damage repair in germ cell development. Front. Endocrinol. (Lausanne) 14, 1234280 (2023). 14 Z. Razzaghi, A. Ahmadzadeh, Examination of the biological effects of sunlight on the skin: A review. J. Lasers Med. Sci. 16, e52 (2025). 15 R. Huang, P. K. Zhou, DNA damage repair: Historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct. Target. Ther. 6, 254 (2021). 16 C. E. Crespo-Hernández, B. Cohen, P. M. Hare, B. Kohler, Ultrafast excited-state dynamics in nucleic acids. Chem. Rev. 104, 1977–2020 (2004). 17 J. Cadet, S. Mouret, J.-L. Ravanat, T. Douki, Photoinduced damage to cellular DNA: Direct and photosensitized reactions. Photochem. Photobiol. 88, 1048–1065 (2012). 18 S. Häcker, M. Schrödter, A. Kuhlmann, H.-A. Wagenknecht, Probing of DNA photochemistry with C-nucleosides of xanthones and triphenylene as photosensitizers to study the formation of cyclobutane pyrimidine dimers. JACS Au 3, 1843–1850 (2023). 19 V. Labet et al., UV-induced formation of the thymine–thymine pyrimidine (6-4) pyrimidone photoproduct—A DFT study of the oxetane intermediate ring opening. Photochem. Photobiol. Sci. 12, 1509–1516 (2013). 20 A. Giussani, L. Serrano-Andrés, M. Merchán, D. Roca-Sanjuán, M. Garavelli, Photoinduced formation mechanism of the thymine-thymine (6–4) adduct. J. Phys. Chem. B 117, 1999–2004 (2013). 21 L. A. Ortiz-Rodríguez, C. Reichardt, S. J. Hoehn, S. Jockusch, C. E. Crespo-Hernández, Detection of the thietane precursor in the UVA formation of the DNA 6-4 photoadduct. Nat. Commun. 11, 3599 (2020). 22 K. F. Hung, J. M. Sidorova, P. Nghiem, M. Kawasumi, The 6-4 photoproduct is the trigger of UV-induced replication blockage and ATR activation. Proc. Natl. Acad. Sci. U.S.A. 117, 12806–12816 (2020). 23 R. Chaturvedi, E. C. Long, On the chemistry of sunlight-induced DNA lesions: A perspective on the alkaline chemical-induced reactivities of photo-damaged pyrimidine intra-strand dimers. Photochem. Photobiol. 100, 1698–1712 (2024). 24 R. P. Sinha, D. P. Hader, UV-induced DNA damage and repair: A review. Photochem. Photobiol. Sci. 1, 225–236 (2002). 25 H. Yokoyama, R. Mizutani, Structural biology of DNA (6-4) photoproducts formed by ultraviolet radiation and interactions with their binding proteins. Int. J. Mol. Sci. 15, 20321–20338 (2014). 26 G. P. Pfeifer, Formation and processing of UV photoproducts: Effects of DNA sequence and chromatin environment. Photochem. Photobiol. 65, 270–283 (1997). 27 L. M. Kundu, U. Linne, M. Marahiel, T. Carell, RNA is more UV resistant than DNA: The formation of UV-induced DNA lesions is strongly sequence and conformation dependent. Chemistry 10, 5697–5705 (2004). 28 E. J. Wurtmann, S. L. Wolin, RNA under attack: Cellular handling of RNA damage. Crit. Rev. Biochem. Mol. Biol. 44, 34–49 (2009). 29 Y. K. Law, J. Azadi, C. E. Crespo-Hernández, E. Olmon, B. Kohler, Predicting thymine dimerization yields from molecular dynamics simulations. Biophys. J. 94, 3590–3600 (2008). 30 F. Dehez et al., Conformational polymorphism or structural invariance in DNA photoinduced lesions: Implications for repair rates. Nucleic Acids Res. 45, 3654–3662 (2017). 31 Y. Umezawa, M. Nishio, Thymine-methyl/pi interaction implicated in the sequence-dependent deformability of DNA. Nucleic Acids Res. 30, 2183–2192 (2002). 32 R. S. Hunter, T. van Mourik, DNA base stacking: The stacked uracil/uracil and thymine/thymine minima. J. Comput. Chem. 33, 2161–2172 (2012). 33 T. Douki, A. von Koschembahr, J. Cadet, Insight in DNA repair of UV-induced pyrimidine dimers by chromatographic methods. Photochem. Photobiol. 93, 207–215 (2017). 34 S. J. Crucilla et al., UV-driven self-repair of cyclobutane pyrimidine dimers in RNA. Chem. Commun. (Camb). 59, 13603–13606 (2023). 35 C. L. Kufner et al., Selection of early life codons by ultraviolet light. ACS Cent. Sci. 11, 147–156 (2025). 36 P. G. Higgs, N. Lehman, The RNA World: Molecular cooperation at the origins of life. Nat. Rev. Genet. 16, 7–17 (2015). 37 G. F. Joyce, Ribozymes: Building the RNA world. Curr. Biol. 6, 965–967 (1996). 38 J. C. Chaput, M. Egli, P. Herdewijn, The XNA alphabet. Nucleic Acids Res. 53, gkaf635 (2025). 39 N. J. Green, J. Xu, J. D. Sutherland, Illuminating life’s origins: UV photochemistry in abiotic synthesis of biomolecules. J. Am. Chem. Soc. 143, 7219–7236 (2021). 40 S. Ranjan, Z. R. Todd, P. B. Rimmer, D. D. Sasselov, A. R. Babbin, Nitrogen oxide concentrations in natural waters on early Earth. Geochem. Geophys. Geosyst. 20, 2021–2039 (2019). 41 K. Leu, B. Obermayer, S. Rajamani, U. Gerland, I. A. Chen, The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nucleic Acids Res. 39, 8135–8147 (2011). 42 P. Forterre, The two ages of the RNA world, and the transition to the DNA world: A story of viruses and cells. Biochimie 87, 793–803 (2005). 43 A. M. Lesk, Why does DNA contain thymine and RNA uracil? J. Theor. Biol. 22, 537–540 (1969). 44 C. Menor-Salván, M. Ruiz-Bermejo, Experimental models on the prebiotic formation of biopolymer building blocks. 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