Modelling DNA Origami Self-Assembly at the Domain Level
| Autor: | Thomas E. Ouldridge, Andrew J. Turberfield, Katherine E. Dunn, Frits Dannenberg, Jonathan Bath, Marta Kwiatkowska |
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| Rok vydání: | 2015 |
| Předmět: |
Single-stranded-DNA
Folding DNA Stacking General Physics and Astronomy FOS: Physical sciences 02 engineering and technology Computer Science::Human-Computer Interaction Condensed Matter - Soft Condensed Matter Physics Atomic Molecular & Chemical 010402 general chemistry Models Biological 01 natural sciences Fluorescence Planar q-bio.BM Engineering DNA origami Computer Simulation Statistical physics Physical and Theoretical Chemistry Nanoscale shapes Physics cond-mat.soft Sequence Science & Technology Chemical Physics Stacking hybridization Biomolecules (q-bio.BM) DNA 021001 nanoscience & nanotechnology 0104 chemical sciences Nanostructures Folding (chemistry) Hysteresis Range (mathematics) Quantitative Biology - Biomolecules Persistence lengths Rational design FOS: Biological sciences Physical Sciences Chemical Sciences Nucleic Acid Conformation Thermodynamics Soft Condensed Matter (cond-mat.soft) Coaxial 0210 nano-technology Coaxial stacking Algorithms |
| DOI: | 10.48550/arxiv.1509.03066 |
| Popis: | We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami. |
| Databáze: | OpenAIRE |
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