Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids
| Autor: | Davide Michieletto, Giada Forte, Davide Marenduzzo, Enzo Orlandini |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
topology
Biomedical Engineering Biophysics Bioengineering Computational biology Biochemistry Genome Biomaterials chemistry.chemical_compound DNA modelling DNA braids DNA integration supercoiling Nucleic Acid Conformation DNA DNA Superhelical Braid A-DNA DNA Integration Dna viral Topology (chemistry) Research Articles Physics Quantitative Biology::Biomolecules Life Sciences–Physics interface chemistry DNA supercoil Superhelical Biotechnology |
| Zdroj: | Journal of the Royal Society Interface |
| Popis: | We theoretically study the integration of short viral DNA in a DNA braid made up by two entwined double-stranded DNA molecules. We show that the statistics of single integration events substantially differ in the straight and buckled, or plectonemic, phase of the braid and are more likely in the latter. We further discover that integration is most likely close to plectoneme tips, where the larger bending energy helps overcome the associated energy barrier and that successive integration events are spatio-temporally correlated, suggesting a potential mechanistic explanation of clustered integration sites in host genomes. The braid geometry we consider provides a novel experimental set-up to quantify integration in a supercoiled substrate in vitro , and to better understand the role of double-stranded DNA topology during this process. |
| Databáze: | OpenAIRE |
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