The self-assembly of DNA Holliday junctions studied with a minimal model
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base. Using this model,...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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American Institute of Physics
2009
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| _version_ | 1797061605780881408 |
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| author | Ouldridge, T Johnston, I Louis, A Doye, J |
| author_facet | Ouldridge, T Johnston, I Louis, A Doye, J |
| author_sort | Ouldridge, T |
| collection | OXFORD |
| description | In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately and allows strand displacement to occur. |
| first_indexed | 2024-03-06T20:33:36Z |
| format | Journal article |
| id | oxford-uuid:31df47cf-486b-4cf6-93be-96be489ccae8 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T20:33:36Z |
| publishDate | 2009 |
| publisher | American Institute of Physics |
| record_format | dspace |
| spelling | oxford-uuid:31df47cf-486b-4cf6-93be-96be489ccae82022-03-26T13:10:39ZThe self-assembly of DNA Holliday junctions studied with a minimal modelJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:31df47cf-486b-4cf6-93be-96be489ccae8EnglishSymplectic Elements at OxfordAmerican Institute of Physics2009Ouldridge, TJohnston, ILouis, ADoye, JIn this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately and allows strand displacement to occur. |
| spellingShingle | Ouldridge, T Johnston, I Louis, A Doye, J The self-assembly of DNA Holliday junctions studied with a minimal model |
| title | The self-assembly of DNA Holliday junctions studied with a minimal model |
| title_full | The self-assembly of DNA Holliday junctions studied with a minimal model |
| title_fullStr | The self-assembly of DNA Holliday junctions studied with a minimal model |
| title_full_unstemmed | The self-assembly of DNA Holliday junctions studied with a minimal model |
| title_short | The self-assembly of DNA Holliday junctions studied with a minimal model |
| title_sort | self assembly of dna holliday junctions studied with a minimal model |
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