Integrated computer-aided engineering and design for DNA assemblies

Abstract

Functional properties of modern engineering products result from merging the geometry and material properties of underlying components into sophisticated overall assemblies. The foundation of this design process is an integration of computer aided design (CAD) tools that allow rapid geometric modifications with robust simulation tools to guide design iterations (i.e. computer-aided engineering, CAE). Recently, DNA has been used to make nanodevices for a myriad of applications across fields including medicine, nanomanufacturing, synthetic biology, biosensing, and biophysics. However, currently these self-assembled DNA nanodevices rely primarily on geometric design, and hence, they have not demonstrated the same sophistication as real-life products. We present an iterative design pipeline for DNA assemblies that integrates CAE based on coarse-grained molecular dynamics with a versatile CAD approach that combines topdown automation with bottom-up control over geometry. This intuitive framework redefines the scope of structural complexity and enhances mechanical and dynamic design of DNA assemblies.

CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells

“…To run the simulations more efficiently, GPU acceleration was implemented using the OSC (Ohio Supercomputer Center) resources. Analysis of the structural properties was performed using the software MagicDNA ( 27 ) and Python-based analysis tool package ( https://github.com/sulcgroup/oxdna_analysis_tools ) ( Supplementary Table S3 ; Supplementary Figures S2, S3, S6, S7, S10, S11, S14, S15, S18, S19, S22, S23, S26, S27 and S29–S34 ; Supplementary Movies S1–S4 ). Lastly, UCSF Chimera software was used for image and video rendering (Figure 1C ; Supplementary Figures S1, S5, S9, S13, S17, S21, S25 and S28 ) ( 28 ).…”

Optimization of Nanoparticles for Smart Drug Delivery: A Review

“…Drug delivery systems based on deformable peptides have been widely studied in tumor targeted therapy, for example, proton-driven tumor vaccine composed of deformable peptides for tumor immunotherapy [2], and an intracellular delivery system of chimeric peptides based on transmembrane peptides for acute liver injury in mice [3]. With the help of software, researchers can take tiny strands of DNA and fold them into complex structures, complete with components such as rotors and hinges that can move and perform tasks, such as drug delivery and cargo handling [108]. A nano-robot based on DNA origami technology can precisely locate tumor tissue and effectively inhibit tumor growth and metastasis.…”

Unified Nanotechnology Format: One Way to Store Them All

“…For example, the file format of vHelix [ 6 ], an application focused on designing wireframe DNA origami, is based on Autodesk Maya ASCII files. Similarly, the file format of MagicDNA [ 31 ], a tool for multi-component DNA origami assembly, is based on Matlab files.…”

“… Structure of Robot arm with tweezer [ 31 ] converted from oxDNA to UNF and back using the oxView application. …”