Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution
| Autor: | Do-Nyun Kim, Jae Gyung Lee, Kyung Soo Kim, Tae Hwi Kim, Chanseok Lee, Jae Young Lee, Young Joo Kim, Giseok Yun |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Materials science
General Physics and Astronomy 02 engineering and technology Molecular Dynamics Simulation Microscopy Atomic Force 010402 general chemistry 01 natural sciences Molecular dynamics chemistry.chemical_compound Atomic resolution DNA nanotechnology Nanotechnology DNA origami General Materials Science Computational analysis Quantitative Biology::Biomolecules Resolution (electron density) General Engineering DNA 021001 nanoscience & nanotechnology Finite element method Nanostructures 0104 chemical sciences chemistry Nucleic Acid Conformation 0210 nano-technology Biological system |
| Zdroj: | ACS Nano. 15:1002-1015 |
| ISSN: | 1936-086X 1936-0851 7000-8000 |
| DOI: | 10.1021/acsnano.0c07717 |
| Popis: | Structural DNA nanotechnology plays an ever-increasing role in advanced biomolecular applications. Here, we present a computational method to analyze structured DNA assemblies rapidly at near-atomic resolution. Both high computational efficiency and molecular-level accuracy are achieved by developing a multiscale analysis framework. The sequence-dependent relative geometry and mechanical properties of DNA motifs are characterized by the all-atom molecular dynamics simulation and incorporated into the structural finite element model successfully without significant loss of atomic information. The proposed method can predict the three-dimensional shape, equilibrium dynamic properties, and mechanical rigidities of monomeric to hierarchically assembled DNA structures at near-atomic resolution without adjusting any model parameters. The calculation takes less than only 15 min for most origami-scale DNA nanostructures consisting of 7000-8000 base-pairs. Hence, it is expected to be highly utilized in an iterative design-analysis-revision process for structured DNA assemblies. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|