The interplay of supercoiling and thymine dimers in DNA

• Published in: Nucleic acids research Vol. 50; no. 5; pp. 2480 - 2492
• Main Authors: Lim, Wilber, Randisi, Ferdinando, Doye, Jonathan P K, Louis, Ard A
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 21.03.2022
• Subjects: Computational Biology; DNA Damage; DNA Repair; DNA, Superhelical - chemistry; Nucleic Acid Conformation; Pyrimidine Dimers - chemistry; Thymine; Ultraviolet Rays
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkac082

Abstract Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here, we introduce a model of thymine dimers in the oxDNA forcefield, parametrized by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.