Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacki...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
AIP Publishing
2015
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| _version_ | 1797058518952443904 |
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| author | Snodin, B Randisi, F Mosayebi, M Šulc, P Schreck, J Romano, F Ouldridge, T Tsukanov, R Nir, E Louis, A Doye, J |
| author_facet | Snodin, B Randisi, F Mosayebi, M Šulc, P Schreck, J Romano, F Ouldridge, T Tsukanov, R Nir, E Louis, A Doye, J |
| author_sort | Snodin, B |
| collection | OXFORD |
| description | We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na(+)] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA. |
| first_indexed | 2024-03-06T19:51:25Z |
| format | Journal article |
| id | oxford-uuid:241ae8d5-2092-4b24-b1d0-3fb7482b7bcd |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T19:51:25Z |
| publishDate | 2015 |
| publisher | AIP Publishing |
| record_format | dspace |
| spelling | oxford-uuid:241ae8d5-2092-4b24-b1d0-3fb7482b7bcd2022-03-26T11:48:02ZIntroducing improved structural properties and salt dependence into a coarse-grained model of DNA.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:241ae8d5-2092-4b24-b1d0-3fb7482b7bcdEnglishSymplectic Elements at OxfordAIP Publishing2015Snodin, BRandisi, FMosayebi, MŠulc, PSchreck, JRomano, FOuldridge, TTsukanov, RNir, ELouis, ADoye, JWe introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na(+)] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA. |
| spellingShingle | Snodin, B Randisi, F Mosayebi, M Šulc, P Schreck, J Romano, F Ouldridge, T Tsukanov, R Nir, E Louis, A Doye, J Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. |
| title | Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. |
| title_full | Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. |
| title_fullStr | Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. |
| title_full_unstemmed | Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. |
| title_short | Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. |
| title_sort | introducing improved structural properties and salt dependence into a coarse grained model of dna |
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