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• W3204726579 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, and validate it 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." @default.
• W3204726579 created "2021-10-11" @default.
• W3204726579 creator A5003090060 @default.
• W3204726579 creator A5022750933 @default.
• W3204726579 creator A5059837446 @default.
• W3204726579 creator A5082711456 @default.
• W3204726579 date "2021-09-27" @default.
• W3204726579 modified "2023-10-16" @default.
• W3204726579 title "The interplay of supercoiling and thymine dimers in DNA" @default.
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• W3204726579 doi "https://doi.org/10.1101/2021.09.27.461905" @default.
• W3204726579 hasPublicationYear "2021" @default.
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