Coarse-grained modelling of a DNA origami force sensor
<p>We have simulated large-scale DNA nanostructures using the oxDNA software which uses coarse-graining at the nucleotide level. These simulations can complement experiments as they typically allow greater structural resolution and give access to a range of properties that are otherwise hard t...
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| Muut tekijät: | |
| Aineistotyyppi: | Opinnäyte |
| Kieli: | English |
| Julkaistu: |
2021
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| Aiheet: |
| _version_ | 1826307551428345856 |
|---|---|
| author | Sen, N |
| author2 | Doye, J |
| author_facet | Doye, J Sen, N |
| author_sort | Sen, N |
| collection | OXFORD |
| description | <p>We have simulated large-scale DNA nanostructures using the oxDNA software which uses coarse-graining at the nucleotide level. These simulations can complement experiments as they typically allow greater structural resolution and give access to a range of properties that are otherwise hard to measure (e.g. internal forces).</p>
<p>To address the challenges associated with parallelised force spectroscopy, we report the development of a bottom-up approach for manipulating the mechanical forces experienced by target biomolecules. We have used molecular dynamics simulations to study the mechanical unfolding of DNA hairpins using an origami-polymer force clamp which allows ensemble scale parallelisation. The target molecules are sandwiched between a rigid DNA origami and a thermo-responsive polymer particle that shrinks upon a rise in temperature. This technique does not need any dedicated single-molecule force spectroscopy instruments or surface tethering. The key features of the origami-polymer force clamp are discussed along with the characterisation of the mechanical unfolding of DNA hairpins, and how these simulations aid in the interpretation of experimental results from these devices.</p>
<p>In eukaryotic cells, the basic structural unit into which DNA is packaged is a nucleosome. We have developed models of the nucleosome in its fully wrapped and partially unwrapped states to enable the design of DNA origami force clamps that will allow the structure of the nucleosome to be determined by cryoEM while subject to force. Our work focuses on molecular dynamics simulations of the nucleosome core particle obtained from a species of African clawed frogs (Xenopus laevis). We have looked at the response of our nucleosome models to external force and determined the parameters needed to simulate it in a partially unravelled state. The next step in this study would be to optimise clamp designs that utilise the entropic spring behaviour of ssDNA to exert forces that stabilise the nucleosome in the partially unwrapped state. The ultimate goal of this project is to develop a DNA origami based force-sensor that can exert the appropriate force to cause unfolding of nucleosomes.</p>
<p>The equilibrium structure of a DNA origami can be manipulated in a controlled way using engineered defects within the design. We have explored how to use the insertion or deletion of base pairs to generate complex structures out of a 6 helix-bundle DNA origami. The particular target is a three-dimensional trefoil knot. The designs considered involve a complex interplay between twist and curvature and we report the progress we have made towards that target.</p> |
| first_indexed | 2024-03-07T07:04:49Z |
| format | Thesis |
| id | oxford-uuid:77231e16-64db-447e-a2ff-a6d509ad6243 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:04:49Z |
| publishDate | 2021 |
| record_format | dspace |
| spelling | oxford-uuid:77231e16-64db-447e-a2ff-a6d509ad62432022-04-28T11:20:58ZCoarse-grained modelling of a DNA origami force sensorThesishttp://purl.org/coar/resource_type/c_bdccuuid:77231e16-64db-447e-a2ff-a6d509ad6243Chemistry, Physical and theoreticalEnglishHyrax Deposit2021Sen, NDoye, J<p>We have simulated large-scale DNA nanostructures using the oxDNA software which uses coarse-graining at the nucleotide level. These simulations can complement experiments as they typically allow greater structural resolution and give access to a range of properties that are otherwise hard to measure (e.g. internal forces).</p> <p>To address the challenges associated with parallelised force spectroscopy, we report the development of a bottom-up approach for manipulating the mechanical forces experienced by target biomolecules. We have used molecular dynamics simulations to study the mechanical unfolding of DNA hairpins using an origami-polymer force clamp which allows ensemble scale parallelisation. The target molecules are sandwiched between a rigid DNA origami and a thermo-responsive polymer particle that shrinks upon a rise in temperature. This technique does not need any dedicated single-molecule force spectroscopy instruments or surface tethering. The key features of the origami-polymer force clamp are discussed along with the characterisation of the mechanical unfolding of DNA hairpins, and how these simulations aid in the interpretation of experimental results from these devices.</p> <p>In eukaryotic cells, the basic structural unit into which DNA is packaged is a nucleosome. We have developed models of the nucleosome in its fully wrapped and partially unwrapped states to enable the design of DNA origami force clamps that will allow the structure of the nucleosome to be determined by cryoEM while subject to force. Our work focuses on molecular dynamics simulations of the nucleosome core particle obtained from a species of African clawed frogs (Xenopus laevis). We have looked at the response of our nucleosome models to external force and determined the parameters needed to simulate it in a partially unravelled state. The next step in this study would be to optimise clamp designs that utilise the entropic spring behaviour of ssDNA to exert forces that stabilise the nucleosome in the partially unwrapped state. The ultimate goal of this project is to develop a DNA origami based force-sensor that can exert the appropriate force to cause unfolding of nucleosomes.</p> <p>The equilibrium structure of a DNA origami can be manipulated in a controlled way using engineered defects within the design. We have explored how to use the insertion or deletion of base pairs to generate complex structures out of a 6 helix-bundle DNA origami. The particular target is a three-dimensional trefoil knot. The designs considered involve a complex interplay between twist and curvature and we report the progress we have made towards that target.</p> |
| spellingShingle | Chemistry, Physical and theoretical Sen, N Coarse-grained modelling of a DNA origami force sensor |
| title | Coarse-grained modelling of a DNA origami force sensor |
| title_full | Coarse-grained modelling of a DNA origami force sensor |
| title_fullStr | Coarse-grained modelling of a DNA origami force sensor |
| title_full_unstemmed | Coarse-grained modelling of a DNA origami force sensor |
| title_short | Coarse-grained modelling of a DNA origami force sensor |
| title_sort | coarse grained modelling of a dna origami force sensor |
| topic | Chemistry, Physical and theoretical |
| work_keys_str_mv | AT senn coarsegrainedmodellingofadnaorigamiforcesensor |