Modelling the folding pathway of DNA nanostructures
<p>DNA origami is a robust technique for bottom-up nano-fabrication. It encodes a target shape into uniquely addressable interactions between a set of short 'staple' strands and a long 'scaffold' strand. The mechanisms of self-assembly, particularly regarding kinetics, need...
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| Format: | Thesis |
| Language: | English |
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2022
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| _version_ | 1817932254524997632 |
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| author | Najafi, B |
| author2 | Turberfield, A |
| author_facet | Turberfield, A Najafi, B |
| author_sort | Najafi, B |
| collection | OXFORD |
| description | <p>DNA origami is a robust technique for bottom-up nano-fabrication. It encodes a target shape into uniquely addressable interactions between a set of short 'staple' strands and a long 'scaffold' strand. The mechanisms of self-assembly, particularly regarding kinetics, need to be better understood. Origami design usually relies on optimising the thermodynamic stability of the target structure, and thermal annealing remains the most fool-proof assembly protocol. This work focuses on studying the folding pathway of three types of origami through simulations: a reconfigurable T-junction origami, several traditional origami, and origami with coated scaffolds.</p>
<p>The T-junction origami is intended as an economically feasible method of changing the uniqueness of interactions. My contribution to this work is to characterise the basic structural motif through oxDNA, a nucleotide-resolution model of DNA. The thesis then focuses on extending a domain-level model of DNA origami to study several experimental origami designs. We reveal design-dependent free energy barriers using biased simulations and relate this to the observed hysteresis in experiments. We also highlight the role of specific design elements in determining the folding pathway. A novel method of lowering the temperature of error-free assembly using coated scaffolds is then presented, with simulations indicating the existence of an activation barrier. By exposing particular regions of the scaffold, we can lower assembly time and temperature.</p> |
| first_indexed | 2024-03-07T07:46:29Z |
| format | Thesis |
| id | oxford-uuid:23ca884b-f547-4458-9e43-494fd6c2f6a3 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-12-09T03:35:00Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | oxford-uuid:23ca884b-f547-4458-9e43-494fd6c2f6a32024-12-01T18:34:03ZModelling the folding pathway of DNA nanostructuresThesishttp://purl.org/coar/resource_type/c_db06uuid:23ca884b-f547-4458-9e43-494fd6c2f6a3DNAChemistry, Physical and theoreticalMonte Carlo methodSampling (Statistics)PhysicsEnglishHyrax Deposit2022Najafi, BTurberfield, ALouis, AKhalid, SRovigatti, L<p>DNA origami is a robust technique for bottom-up nano-fabrication. It encodes a target shape into uniquely addressable interactions between a set of short 'staple' strands and a long 'scaffold' strand. The mechanisms of self-assembly, particularly regarding kinetics, need to be better understood. Origami design usually relies on optimising the thermodynamic stability of the target structure, and thermal annealing remains the most fool-proof assembly protocol. This work focuses on studying the folding pathway of three types of origami through simulations: a reconfigurable T-junction origami, several traditional origami, and origami with coated scaffolds.</p> <p>The T-junction origami is intended as an economically feasible method of changing the uniqueness of interactions. My contribution to this work is to characterise the basic structural motif through oxDNA, a nucleotide-resolution model of DNA. The thesis then focuses on extending a domain-level model of DNA origami to study several experimental origami designs. We reveal design-dependent free energy barriers using biased simulations and relate this to the observed hysteresis in experiments. We also highlight the role of specific design elements in determining the folding pathway. A novel method of lowering the temperature of error-free assembly using coated scaffolds is then presented, with simulations indicating the existence of an activation barrier. By exposing particular regions of the scaffold, we can lower assembly time and temperature.</p> |
| spellingShingle | DNA Chemistry, Physical and theoretical Monte Carlo method Sampling (Statistics) Physics Najafi, B Modelling the folding pathway of DNA nanostructures |
| title | Modelling the folding pathway of DNA nanostructures |
| title_full | Modelling the folding pathway of DNA nanostructures |
| title_fullStr | Modelling the folding pathway of DNA nanostructures |
| title_full_unstemmed | Modelling the folding pathway of DNA nanostructures |
| title_short | Modelling the folding pathway of DNA nanostructures |
| title_sort | modelling the folding pathway of dna nanostructures |
| topic | DNA Chemistry, Physical and theoretical Monte Carlo method Sampling (Statistics) Physics |
| work_keys_str_mv | AT najafib modellingthefoldingpathwayofdnananostructures |