Sequence-dependent thermodynamics of a coarse-grained DNA model.
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-d...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Language: | English |
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2012
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| _version_ | 1826304735760613376 |
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| author | Šulc, P Romano, F Ouldridge, T Rovigatti, L Doye, J Louis, A |
| author_facet | Šulc, P Romano, F Ouldridge, T Rovigatti, L Doye, J Louis, A |
| author_sort | Šulc, P |
| collection | OXFORD |
| description | We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software. |
| first_indexed | 2024-03-07T06:22:18Z |
| format | Journal article |
| id | oxford-uuid:f31bea34-ac8b-4525-bf5c-7081eae4ba07 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T06:22:18Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | oxford-uuid:f31bea34-ac8b-4525-bf5c-7081eae4ba072022-03-27T12:09:21ZSequence-dependent thermodynamics of a coarse-grained DNA model.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:f31bea34-ac8b-4525-bf5c-7081eae4ba07EnglishSymplectic Elements at Oxford2012Šulc, PRomano, FOuldridge, TRovigatti, LDoye, JLouis, AWe introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software. |
| spellingShingle | Šulc, P Romano, F Ouldridge, T Rovigatti, L Doye, J Louis, A Sequence-dependent thermodynamics of a coarse-grained DNA model. |
| title | Sequence-dependent thermodynamics of a coarse-grained DNA model. |
| title_full | Sequence-dependent thermodynamics of a coarse-grained DNA model. |
| title_fullStr | Sequence-dependent thermodynamics of a coarse-grained DNA model. |
| title_full_unstemmed | Sequence-dependent thermodynamics of a coarse-grained DNA model. |
| title_short | Sequence-dependent thermodynamics of a coarse-grained DNA model. |
| title_sort | sequence dependent thermodynamics of a coarse grained dna model |
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