Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and len...
| Main Authors: | , , , , , |
|---|---|
| Format: | Journal article |
| Published: |
AIP Publishing
2018
|
| _version_ | 1826278113081819136 |
|---|---|
| author | Fonseca, P Romano, F Schreck, J Ouldridge, T Doye, J Louis, A |
| author_facet | Fonseca, P Romano, F Schreck, J Ouldridge, T Doye, J Louis, A |
| author_sort | Fonseca, P |
| collection | OXFORD |
| description | Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs. |
| first_indexed | 2024-03-06T23:39:05Z |
| format | Journal article |
| id | oxford-uuid:6eacc38d-58e4-437f-84bb-beb285c35488 |
| institution | University of Oxford |
| last_indexed | 2024-03-06T23:39:05Z |
| publishDate | 2018 |
| publisher | AIP Publishing |
| record_format | dspace |
| spelling | oxford-uuid:6eacc38d-58e4-437f-84bb-beb285c354882022-03-26T19:25:57ZMulti-scale coarse-graining for the study of assembly pathways in DNA-brick self-assemblyJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:6eacc38d-58e4-437f-84bb-beb285c35488Symplectic Elements at OxfordAIP Publishing2018Fonseca, PRomano, FSchreck, JOuldridge, TDoye, JLouis, AInspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs. |
| spellingShingle | Fonseca, P Romano, F Schreck, J Ouldridge, T Doye, J Louis, A Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly |
| title | Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly |
| title_full | Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly |
| title_fullStr | Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly |
| title_full_unstemmed | Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly |
| title_short | Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly |
| title_sort | multi scale coarse graining for the study of assembly pathways in dna brick self assembly |
| work_keys_str_mv | AT fonsecap multiscalecoarsegrainingforthestudyofassemblypathwaysindnabrickselfassembly AT romanof multiscalecoarsegrainingforthestudyofassemblypathwaysindnabrickselfassembly AT schreckj multiscalecoarsegrainingforthestudyofassemblypathwaysindnabrickselfassembly AT ouldridget multiscalecoarsegrainingforthestudyofassemblypathwaysindnabrickselfassembly AT doyej multiscalecoarsegrainingforthestudyofassemblypathwaysindnabrickselfassembly AT louisa multiscalecoarsegrainingforthestudyofassemblypathwaysindnabrickselfassembly |