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New Technology Predicts Mechanochemical Changes in DNA Origami Structures
A collaborative research effort led by Professor Do-Nyun Kim at the Department of Mechanical Engineering, Seoul National University, has resulted in the development of an innovative technology designed to rapidly predict the mechanochemical transformations of DNA origami nanostructures. This promising advancement holds significant potential for various applications in bioengineering and molecular biology.
The findings from this research were published in the journal Nature Communications on July 31, 2024.
DNA origami, a technique that leverages the self-assembly properties of DNA, allows for the precision design and construction of nanostructures with specific shapes. This methodology has emerged as a focal point of study within the realm of advanced bio-convergence, as it offers diverse applications in targeted drug delivery, biosensors, and nanomedicine. Notably, the ability to manipulate the structures in response to environmental factors within biological systems is garnering increasing attention from researchers.
Traditionally, the implementation of this transformative technology has been hindered by the absence of robust modeling and computational simulation tools capable of effectively designing these adaptable mechanisms. As a result, researchers have resorted to extensive experimental approaches that often involve considerable trial and error. This gap has highlighted a critical need for efficient methodologies that can analyze the deformation behaviors of DNA nanostructures in relation to their geometric and mechanical characteristics, especially as these attributes fluctuate with varying environmental conditions.
Addressing this scientific challenge, the research team devised a method to swiftly predict alterations in the shape of DNA origami structures influenced by the concentrations of DNA-binding molecules. They began by conducting molecular dynamics simulations to quantitatively assess how the binding of Ethidium Bromide (EtBr), a well-known DNA-binding agent, impacts the geometry and mechanical stability of DNA molecules.
Through this foundational analysis, the researchers established a correlation between the concentration of binding molecules and the resulting modifications in DNA properties. This data was subsequently applied to the analysis of DNA structures, allowing for the accurate prediction of mechanochemical changes in the origami configurations as EtBr concentration varied.
One of the notable aspects of this technology is its scalability; it can be adapted to assess DNA property changes with different DNA-binding molecules. Furthermore, this predictive capability paves the way for the engineering of tunable DNA origami constructs that can modulate their shapes in accordance with the concentration and type of binding molecules. Such a breakthrough could significantly advance the field of DNA nanotechnology and open new avenues for research and application.
The study was primarily conducted by Research Professor Lee Jae-young and Researcher Kim Yang-kyun, under the leadership of Professor Kim.
More information: Jae Young Lee et al, Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies, Nature Communications (2024). DOI: 10.1038/s41467-024-50871-3
Provided by Seoul National University College of Engineering.
Citation: Technology to predict the deformation of DNA origami structures induced by DNA-binding molecules (2024, August 8) retrieved 9 August 2024 from https://phys.org/news/2024-08-technology-deformation-dna-origami-molecules.html
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