The Free-Energy Landscape of a Mechanically Bistable DNA Origami

Wong, Chak Kui; Doye, Jonathan P. K.

doi:10.3390/app12125875

Cited by 2 publications

(1 citation statement)

References 50 publications

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“…We next employed umbrella sampling to quantify the magnitude of curvature in rectangular origami structures with overhangs. Umbrella sampling (US) is an enhanced sampling technique that allows us to efficiently sample all values along our chosen order parameter (OP) by introducing an external harmonic potential that biases the simulation to sample all desired states of the OP that represents different conformations of the structure (see Methods) [23,[33][34][35]. To model structural curvature, we chose our OP to be the distance between the centers of mass (COM) of the origami's long edges (see Fig.…”

Section: 62nm 31nm 62nmmentioning

confidence: 99%

Hairygami: Analysis of DNA Nanostructure's Conformational Change Driven by Functionalizable Overhangs

Sample¹,

Matthies²,

Šulc³

2023

Preprint

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DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "breadboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules, with applications ranging from therapeutics and diagnostics to plasmonics and photonics. Imaging these structures using AFM or TEM is not capable to capture their full conformation ensemble as they only show their structure flattened on a surface. However, certain conformations of the nanostructure can position guest molecules into distances unaccounted for in their intended design, thus leading to spurious interactions between guest molecules that are designed to be separated. Here, we use molecular dynamics simulations to capture conformational ensemble of 2D DNA origami tiles and show that introducing single-stranded overhangs, which are typically used for functionalization of the origami with guest molecules, induces a curvature of the tile structure in the bulk. We show that the shape deformation is of entropic origin, with implications for design of robust DNA origami breadboards as well as potential approach to modulate structure shape by introducing overhangs.

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Section: 62nm 31nm 62nmmentioning

confidence: 99%

Hairygami: Analysis of DNA Nanostructure's Conformational Change Driven by Functionalizable Overhangs

Sample¹,

Matthies²,

Šulc³

2023

Preprint

View full text Add to dashboard Cite

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A mean-field theory for characterizing the closing rates of DNA origami hinges

Yeboah,

Young,

Mosioma

et al. 2024

The Journal of Chemical Physics

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The evolution of dynamic DNA nanostructures has propelled DNA nanotechnology into a robust and versatile field, offering groundbreaking applications in nanoscale communication, drug delivery, and molecular computing. Yet, the full potential of this technology awaits further enhancement through optimization of kinetic properties governing conformational changes. In this work, we introduce a mean-field theory to characterize the kinetic behavior of a dynamic DNA origami hinge where each arm bears complementary single-stranded DNA overhangs of different lengths, which can latch the hinge at a closed conformation. This device is currently being investigated for multiple applications, being of particular interest the development of DNA-based rapid diagnostic tests for coronavirus. Drawing from classical statistical mechanics theories, we derive analytical expressions for the mean binding time of these overhangs within a constant hinge. This analysis is then extended to flexible hinges, where the angle diffuses within a predetermined energy landscape. We validate our model by comparing it with experimental measurements of the closing rates of DNA nanocalipers with different energy landscapes and overhang lengths, demonstrating excellent agreement and suggesting fast angular relaxation relative to binding. These findings offer insights that can guide the optimization of devices for specific state lifetimes. Moreover, the framework introduced here lays the groundwork for further advancements in modeling the kinetics of dynamic DNA nanostructures.

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The Free-Energy Landscape of a Mechanically Bistable DNA Origami

Cited by 2 publications

References 50 publications

Hairygami: Analysis of DNA Nanostructure's Conformational Change Driven by Functionalizable Overhangs

Hairygami: Analysis of DNA Nanostructure's Conformational Change Driven by Functionalizable Overhangs

A mean-field theory for characterizing the closing rates of DNA origami hinges

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