Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution

Lee, Jae Young; Yun, Giseok; Lee, Chanseok; Kim, Young-Joo; Kim, Kyung Soo; Kim, Tae Hwi; Kim, Do-Nyun

doi:10.1021/acsnano.0c07717

Cited by 44 publications

(61 citation statements)

References 53 publications

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“…The starting atomic structure of the 6HB design was generated using caDNAno ( 34 ) and SNUPI ( 35 ). Each atomic structure was explicitly solvated using the TIP3P water model ( 36 ) with a distance >15 Å from the structure and boundary.…”

Section: Methodsmentioning

confidence: 99%

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Lee

Kim

et al. 2021

Nucleic Acids Research

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Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.

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Section: Methodsmentioning

confidence: 99%

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Lee

Kim

et al. 2021

Nucleic Acids Research

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“…A closed ring with a higher B/C ratio would require a higher torsional stress to initiate buckling 18 , 19 . Generally, the bending rigidity is known to be proportional to N 2 , where N is the number of helices in the bundle, while the torsional rigidity increases linearly with respect to N 32 – 34 . Accordingly, the B/C ratio is approximately proportional to N, as was also confirmed computationally by normal mode analysis (NMA) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Programming ultrasensitive threshold response through chemomechanical instability

et al. 2021

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The ultrasensitive threshold response is ubiquitous in biochemical systems. In contrast, achieving ultrasensitivity in synthetic molecular structures in a controllable way is challenging. Here, we propose a chemomechanical approach inspired by Michell’s instability to realize it. A sudden reconfiguration of topologically constrained rings results when the torsional stress inside reaches a critical value. We use DNA origami to construct molecular rings and then DNA intercalators to induce torsional stress. Michell’s instability is achieved successfully when the critical concentration of intercalators is applied. Both the critical point and sensitivity of this ultrasensitive threshold reconfiguration can be controlled by rationally designing the cross-sectional shape and mechanical properties of DNA rings.

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“…Shape and rigidity control of higher-order origami structures can be obtained by efficient computer simulations enabling more realistic actualization of more complex breadboards. [179] Noble metals, [101][102][103][104][105][106][107][108][109][110]112,[115][116][117][118][119][120][121][122][123][124][125][126][127] organic dyes, [101][102][103]105,107,110,112,[115][116][117][118][119][120][121][122][123][124]126] semiconductor nanocrystals, [127] graphene, [121] light-harvesting molecules, [108] the genetic material of pathogens [104,…”

Section: Challenges and Opportunitiesmentioning

confidence: 99%

Emission Manipulation by DNA Origami‐Assisted Plasmonic Nanoantennas

Yeşilyurt

Huang

2021

Advanced Optical Materials

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Figure 1. Dimer antennas assembled by pillar DNA origamis. a) Upper panel: 80 nm AuNP dimer antenna with a single ATTO647N dye molecule at the 23 nm wide hotspot. Pillar is immobilized on neutravidin functionalized glass cover by biotin extensions on the origami. Lower panels: Intensity transients and their fluorescence decays of the dye without (left) and with (right) nanoparticles. Reproduced with permission. [101] Copyright 2012, The American Association for the Advancement of Science. b) Upper panel: Upgraded pillar origami decorated with a single silver nanoparticle (AgNP) of 80 nm and a schematic of the DNA-based fluorescence-quenching hairpin to detect the Zika-specific DNA. Lower panel: Fluorescence images of surface-immobilized pillar antennas before and after the addition of target Zika-specific DNA after 18 h incubation. Adapted with permission. [104] Copyright 2017, American Chemical Society. c) Top left: Schematic of NanoAntennas with Cleared HOtSpots (NACHOS) with two 100 nm AgNP. Top right: Three capture strands at the hotspot to detect target DNA sequence with imager strand. Bottom panel: Fluorescence images before (left), after addition of target DNA and imager strands (middle), and after addition of only the imager strands without the target (right). Reproduced with permission. [109] Copyright 2021, Springer Nature.

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Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution

Cited by 44 publications

References 53 publications

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Programming ultrasensitive threshold response through chemomechanical instability

Emission Manipulation by DNA Origami‐Assisted Plasmonic Nanoantennas

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