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1. Coarse-Grained Simulations of DNA and RNA Systems with Oxdna and Oxrna Models: Tutorial

   Sample, Matthew L; Matthies, Michael; Sulc, Petr (February 2024, ACM Digital Library)

   We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and nanotechnology settings. The tutorial is aimed at new users asking "Where should I start if I want to use oxDNA". We assume no prior background in using the model. This tutorial shows basic examples that can get a novice user started with the model, and points the prospective user towards additional reading and online resources depending on which aspect of the model they are interested in pursuing. 

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2. Coarse-grained nucleic acid–protein model for hybrid nanotechnology

   https://doi.org/10.1039/D0SM01639J  

   Procyk, Jonah; Poppleton, Erik; Šulc, Petr (April 2021, Soft Matter)

   null (Ed.)

   The emerging field of hybrid DNA–protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with the versatility of protein interactions. However, the design and computational study of these hybrid structures is difficult due to the system sizes involved. To aid in the design and in silico analysis process, we introduce here a coarse-grained DNA/RNA–protein model that extends the oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on an anisotropic network model representation. Fully equipped with analysis scripts and visualization, our model aims to facilitate hybrid nanomaterial design towards eventual experimental realization, as well as enabling study of biological complexes. We further demonstrate its usage by simulating DNA–protein nanocage, DNA wrapped around histones, and a nascent RNA in polymerase. 

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3. Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation

   https://doi.org/10.1093/nar/gkaa417  

   Poppleton, Erik; Bohlin, Joakim; Matthies, Michael; Sharma, Shuchi; Zhang, Fei; Šulc, Petr (May 2020, Nucleic Acids Research)

   Abstract This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures. 

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4. Coarse-grained modeling of DNA–RNA hybrids

   https://doi.org/10.1063/5.0199558  

   Ratajczyk, Eryk_J; Šulc, Petr; Turberfield, Andrew_J; Doye, Jonathan_P_K; Louis, Ard_A (March 2024, The Journal of Chemical Physics)

   We introduce oxNA, a new model for the simulation of DNA–RNA hybrids that is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA–RNA hydrogen bonding interaction, we fit the model’s thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model’s applicability, we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami. 

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5. Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

   https://doi.org/10.1093/nar/gkab762  

   Jun, Hyungmin; Wang, Xiao; Parsons, Molly F; Bricker, William P; John, Torsten; Li, Shanshan; Jackson, Steve; Chiu, Wah; Bathe, Mark (September 2021, Nucleic Acids Research)

   Abstract Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches. 

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