Modelling toehold-mediated RNA strand displacement
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential...
| Main Authors: | , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Cell Press
2015
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| _version_ | 1797112129372815360 |
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| author | Šulc, P Ouldridge, TE Romano, F Doye, JPK Louis, AA |
| author_facet | Šulc, P Ouldridge, TE Romano, F Doye, JPK Louis, AA |
| author_sort | Šulc, P |
| collection | OXFORD |
| description | We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5′ end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds. |
| first_indexed | 2024-03-07T08:19:52Z |
| format | Journal article |
| id | oxford-uuid:3d606bca-c491-4ada-af54-8b41f1236204 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:19:52Z |
| publishDate | 2015 |
| publisher | Cell Press |
| record_format | dspace |
| spelling | oxford-uuid:3d606bca-c491-4ada-af54-8b41f12362042024-01-24T09:57:14ZModelling toehold-mediated RNA strand displacementJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:3d606bca-c491-4ada-af54-8b41f1236204EnglishSymplectic Elements at OxfordCell Press2015Šulc, POuldridge, TERomano, FDoye, JPKLouis, AAWe study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5′ end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds. |
| spellingShingle | Šulc, P Ouldridge, TE Romano, F Doye, JPK Louis, AA Modelling toehold-mediated RNA strand displacement |
| title | Modelling toehold-mediated RNA strand displacement |
| title_full | Modelling toehold-mediated RNA strand displacement |
| title_fullStr | Modelling toehold-mediated RNA strand displacement |
| title_full_unstemmed | Modelling toehold-mediated RNA strand displacement |
| title_short | Modelling toehold-mediated RNA strand displacement |
| title_sort | modelling toehold mediated rna strand displacement |
| work_keys_str_mv | AT sulcp modellingtoeholdmediatedrnastranddisplacement AT ouldridgete modellingtoeholdmediatedrnastranddisplacement AT romanof modellingtoeholdmediatedrnastranddisplacement AT doyejpk modellingtoeholdmediatedrnastranddisplacement AT louisaa modellingtoeholdmediatedrnastranddisplacement |