Kinetics and Thermodynamics of Watson–Crick Base Pairing Driven DNA Origami Dimerization
| Autor: | Chanon Tuntivate, John Zenk, Rebecca Schulman |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
Base pair
Kinetics Thermodynamics 02 engineering and technology Microscopy Atomic Force 010402 general chemistry 01 natural sciences Biochemistry Catalysis Reversible reaction Colloid and Surface Chemistry Reaction rate constant Sticky and blunt ends DNA origami Base Pairing Chemistry DNA General Chemistry 021001 nanoscience & nanotechnology Nanostructures 0104 chemical sciences Yield (chemistry) Nucleic Acid Conformation 0210 nano-technology Dimerization Linker |
| Zdroj: | Journal of the American Chemical Society. 138:3346-3354 |
| ISSN: | 1520-5126 0002-7863 |
| DOI: | 10.1021/jacs.5b10502 |
| Popis: | We investigate the kinetics and thermodynamics of DNA origami dimerization using flat rectangle origami components and different architectures of Watson-Crick complementary single-stranded DNA ("sticky end") linking strategies. We systematically vary the number of linkers, the length of the sticky ends on the linker, and linker architecture and measure the corresponding yields as well as forward and reverse reaction rate constants through fluorescence quenching assays. Yields were further verified using atomic force microscopy. We calculate values of H° and ΔS° for various interface designs and find nonlinear van't Hoff behavior, best described by two linear equations, suggesting distinct regimes of dimerization between those with and those without well-formed interfaces. We find that self-assembly reactions can be tuned by manipulating the interface architecture without suffering a loss in yield, even when yield is high, ∼75-80%. We show that the second-order forward reaction rate constant (k(on)) depends on both linker architecture and number of linkers used, with typical values on the order of 10(5)-10(6) (M·s)(-1), values that are similar to those of bimolecular association of small, complementary DNA strands. The k(on) values are generally non-Arrhenius, tending to increase with decreasing temperature. Finally, we use kinetic and thermodynamic information about the optimal linking architecture to extend the system to an infinite, two-component repeating lattice system and show that we can form micron-sized lattices, with well-formed structures up to 8 μm(2). |
| Databáze: | OpenAIRE |
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