The role of loop stacking in the dynamics of DNA hairpin formation.
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We find a nonmonotonic variation of the hairpin closing time w...
| Main Authors: | , , , , |
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| Format: | Journal article |
| Language: | English |
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American Chemical Society
2014
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| _version_ | 1826285449851699200 |
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| author | Mosayebi, M Romano, F Ouldridge, T Louis, A Doye, J |
| author_facet | Mosayebi, M Romano, F Ouldridge, T Louis, A Doye, J |
| author_sort | Mosayebi, M |
| collection | OXFORD |
| description | We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We find a nonmonotonic variation of the hairpin closing time with temperature, in agreement with the experimental work of Wallace et al. (Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5584-5589). The hairpin closing process involves the formation of an initial nucleus of one or two bonds in the stem followed by a rapid zippering of the stem. At high temperatures, typically above the hairpin melting temperature, an effective negative activation enthalpy is observed because the nucleus has a lower enthalpy than the open state. By contrast, at low temperatures, the activation enthalpy becomes positive mainly due to the increasing energetic cost of bending a loop that becomes increasingly highly stacked as the temperature decreases. We show that stacking must be very strong to induce this experimentally observed behavior, and that the existence of just a few weak stacking points along the loop can substantially suppress it. Non-native base pairs are observed to have only a small effect, slightly accelerating hairpin formation. |
| first_indexed | 2024-03-07T01:29:01Z |
| format | Journal article |
| id | oxford-uuid:92f44b4b-e743-43f8-a5aa-aa99d3443b66 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T01:29:01Z |
| publishDate | 2014 |
| publisher | American Chemical Society |
| record_format | dspace |
| spelling | oxford-uuid:92f44b4b-e743-43f8-a5aa-aa99d3443b662022-03-26T23:29:03ZThe role of loop stacking in the dynamics of DNA hairpin formation.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:92f44b4b-e743-43f8-a5aa-aa99d3443b66EnglishSymplectic Elements at OxfordAmerican Chemical Society2014Mosayebi, MRomano, FOuldridge, TLouis, ADoye, JWe study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We find a nonmonotonic variation of the hairpin closing time with temperature, in agreement with the experimental work of Wallace et al. (Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5584-5589). The hairpin closing process involves the formation of an initial nucleus of one or two bonds in the stem followed by a rapid zippering of the stem. At high temperatures, typically above the hairpin melting temperature, an effective negative activation enthalpy is observed because the nucleus has a lower enthalpy than the open state. By contrast, at low temperatures, the activation enthalpy becomes positive mainly due to the increasing energetic cost of bending a loop that becomes increasingly highly stacked as the temperature decreases. We show that stacking must be very strong to induce this experimentally observed behavior, and that the existence of just a few weak stacking points along the loop can substantially suppress it. Non-native base pairs are observed to have only a small effect, slightly accelerating hairpin formation. |
| spellingShingle | Mosayebi, M Romano, F Ouldridge, T Louis, A Doye, J The role of loop stacking in the dynamics of DNA hairpin formation. |
| title | The role of loop stacking in the dynamics of DNA hairpin formation. |
| title_full | The role of loop stacking in the dynamics of DNA hairpin formation. |
| title_fullStr | The role of loop stacking in the dynamics of DNA hairpin formation. |
| title_full_unstemmed | The role of loop stacking in the dynamics of DNA hairpin formation. |
| title_short | The role of loop stacking in the dynamics of DNA hairpin formation. |
| title_sort | role of loop stacking in the dynamics of dna hairpin formation |
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