DNA nanotweezers studied with a coarse-grained model of DNA
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length and torsion...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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American Physical Society
2010
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| _version_ | 1826298079390728192 |
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| author | Ouldridge, T Louis, A Doye, J |
| author_facet | Ouldridge, T Louis, A Doye, J |
| author_sort | Ouldridge, T |
| collection | OXFORD |
| description | We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple machine driven by hybridization and strand displacement. |
| first_indexed | 2024-03-07T04:41:21Z |
| format | Journal article |
| id | oxford-uuid:d1c23ce8-0c44-41e7-8aa4-66047e599cad |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:41:21Z |
| publishDate | 2010 |
| publisher | American Physical Society |
| record_format | dspace |
| spelling | oxford-uuid:d1c23ce8-0c44-41e7-8aa4-66047e599cad2022-03-27T07:59:08ZDNA nanotweezers studied with a coarse-grained model of DNAJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:d1c23ce8-0c44-41e7-8aa4-66047e599cadEnglishSymplectic Elements at OxfordAmerican Physical Society2010Ouldridge, TLouis, ADoye, JWe introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple machine driven by hybridization and strand displacement. |
| spellingShingle | Ouldridge, T Louis, A Doye, J DNA nanotweezers studied with a coarse-grained model of DNA |
| title | DNA nanotweezers studied with a coarse-grained model of DNA |
| title_full | DNA nanotweezers studied with a coarse-grained model of DNA |
| title_fullStr | DNA nanotweezers studied with a coarse-grained model of DNA |
| title_full_unstemmed | DNA nanotweezers studied with a coarse-grained model of DNA |
| title_short | DNA nanotweezers studied with a coarse-grained model of DNA |
| title_sort | dna nanotweezers studied with a coarse grained model of dna |
| work_keys_str_mv | AT ouldridget dnananotweezersstudiedwithacoarsegrainedmodelofdna AT louisa dnananotweezersstudiedwithacoarsegrainedmodelofdna AT doyej dnananotweezersstudiedwithacoarsegrainedmodelofdna |