Folding and Characterization of a Bio-responsive Robot from DNA Origami

Amir, Yaniv; Abu-Horowitz, Almogit; Bachelet, Ido

doi:10.3791/51272

Cited by 5 publications

(3 citation statements)

References 27 publications

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“…Based on that, several works [53, 28, 29] proposed that each NP can be described using a finite number of states with some physical and chemical properties. For example, a DNA origami NP that contains a payload may have three states: close with payload, close without payload, and open [3].…”

Section: Related Workmentioning

confidence: 99%

Graph-Based Pharmacokinetic-Pharmadynamic Modeling for Large Scale Systems: Nanoparticles Case

Lazebnik

Weitman

Kaminka

2022

Preprint

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Pharmaceutical nanoparticles (NPs) carrying molecular payloads are used for medical purposes such as diagnosis and medical treatment. They are designed to modify the pharmacokinetics-pharmacodynamics (PKPD) of their associated payloads, to obtain better clinical results. Currently, the research process of discovering the PKPD properties of new candidates for efficient clinical treatment is complicated and time-consuming. In silico experiments are known to be powerful tools for studying biological and clinical processes and therefore can significantly improve the process of developing new and optimizing current NPs-based drugs. However, the current PKPD models are limited by the number of parameters they can take into consideration and the ability to solve large-scale in vivo settings, thus providing relatively large errors in predicting treatment outcomes. In this study, we present a novel mathematical graph-based model for PKPD of NPs-based drugs. The proposed model is based on a population of NPs performing a directed walk on a graph describing the blood vessels and organs, taking into consideration the interactions between the NPs and their environment. In addition, we define a mechanism to perform different prediction queries on the proposed model to analyze two in vivo experiments with eight different NPs, done on mice, obtaining a fitting of 0.84 +- 0.01 and 0.66 +- 0.01 (mean +- standard deviation), respectively, comparing the in vivo values and the in silico results.

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Section: Related Workmentioning

confidence: 99%

Graph-Based Pharmacokinetic-Pharmadynamic Modeling for Large Scale Systems: Nanoparticles Case

Lazebnik

Weitman

Kaminka

2022

Preprint

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“…. A comprehensive protocol for the design and self-assembly of DNA nanostructures has been published already 19,20,21,22 . The shape-specific staple strands were ordered, selfassembled and further purified based on a protocol described by Stahl et al 23 (step 2).…”

Section: Representative Resultsmentioning

confidence: 99%

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

Ahmadi

Barišić

2019

JoVE

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DNA origami nanostructures hold an immense potential to be used for biological and medical applications. However, low-salt conditions and nucleases in physiological fluids induce denaturation and degradation of self-assembled DNA nanostructures. In non-viral gene delivery, enzymatic degradation of DNA is overcome by the encapsulation of the negatively charged DNA in a cationic shell. Herein, inspired by gene delivery advancements, a simple, one-step and robust methodology is presented for the stabilization of DNA origami nanostructures by coating them with chitosan and linear polyethyleneimine. The polycation coating efficiently protects DNA origami nanostructures in Mg-depleted and nuclease-rich media. This method also preserves the full addressability of enzyme-and aptamer-based functionalization of DNA nanostructures.

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“…In order to confirm the authenticity of the pathogen, DNA was extracted from vegetative mycelium (Amir et al. 2015), and the internal transcribed spacer (ITS) region was amplified using the ITS primers ITS1 and ITS4. The sequences of these and all other primers used in this study are provided in Table S1.…”

Section: Methodsmentioning

confidence: 99%

Fus3 is a pathogenicity factor of Botryosphaeria dothidea on kiwifruit

Shin,

Deising,

Jeun

2024

Journal of Phytopathology

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The ascomycete fungus Botryosphaeria dothidea is the causal agent of postharvest rot in kiwifruit. Production and spreading of conidia, differentiation of infection hyphae and invasion of intact fruit surfaces are required to cause fruit rot disease. In several pathogenic fungi, the homologue of the Saccharomyces cerevisiae mitogen activated protein kinase (MAPK) gene Fus3 has been identified as a pathogenicity factor. To investigate the role of the Fus3 homologue in B. dothidea, the gene was deleted and the resulting ∆fus3 mutants were characterized. On artificial media, strong growth defects of ∆fus3 strains were observed, mycelia were non‐pigmented, and mutants were unable to conidiate. Scanning electron microscopy showed that the wild‐type strain differentiated thick hyphae on the surface of kiwifruits, and nose‐down growth of hyphae indicated tight attachment to the fruit. In contrast, hyphae of ∆fus3 strains mutants were thinner and did not firmly attach to the fruit surface. Importantly, pathogenicity test revealed that ∆fus3 strains were unable to cause disease symptoms on intact kiwifruits. These results shown here identify Fus3 of B. dothidea as a novel pathogenicity factor of the ripe rot pathogen on kiwifruit.

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Folding and Characterization of a Bio-responsive Robot from DNA Origami

Cited by 5 publications

References 27 publications

Graph-Based Pharmacokinetic-Pharmadynamic Modeling for Large Scale Systems: Nanoparticles Case

Graph-Based Pharmacokinetic-Pharmadynamic Modeling for Large Scale Systems: Nanoparticles Case

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

Fus3 is a pathogenicity factor of Botryosphaeria dothidea on kiwifruit

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