Title: MENDEL: an automated design tool for DNA nanotechnology
Designing complex DNA nanostructures is a complicated process that requires efficient software to calculate and populate structural details. Most of the published software require manual manipulation and careful inspection of the models that increase the time cost and user error and decrease the flexibility of designing process. We created a python library that we coined MENDEL as a flexible and robust solution for automatic design of complex DNA nanostructures. MENDEL receives a set of sequential commands and creates the structures by following logical steps. Each step instructs the growth of the DNA nanostructure either by adding new nucleotides or repeating sections of arbitrary size and shape. User is able to monitor the design progress by executing the commands in Blender software’s scripting mode. Figure 1 shows an example of using MENDEL library to design a triple-layered origami that represents the word “MENDEL.” MENDEL generates the geometry preview, which helps to understand the design details. Moreover, for convenience, the exported file is compatible with caDNAno. Figure 2 shows the exported model when opened in caDNAno, and Figure 3 shows the modeling results obtained from CanDo for different number of layers. Future work include improving nucleotide twist and rise calculations, supporting honeycomb designs, detecting overlaps, inserting and skipping nucleotides, and generating molecular file formats such as Protein Data Bank (PDB). more »« less
Guerrero, Jorge Eduardo; Zadegan, Reza
(, FNANO (Foundations of Nanoscience))
null
(Ed.)
Structural DNA nanotechnology is a powerful technique for bottom-up self-assembly of nanoscale structures. Potential applications are vast and only limited by the researchers' imagination. For large and complex structures, the manual or semi-automatic designing process is time-consuming and requires a detailed inspection of the model, leading to user error. We introduce MENDEL, a software library that allows the automatic, extensive, and parametric DNA nanostructures design in this work. MENDEL contains a set of commands that automate the designing process, allow the abstraction of turning sites, compute staples, and parametrize scaling and repetitive features; thus, reducing user error, design complications, and time-to-complete. Running MENDEL through Blender renders a 3D representation of the model. Also, for community convenience, MENDEL generates caDNAno/CanDo compatible files. MENDEL is available as open-source software at https://github.com/SBMI-LAB/MENDEL.
Doty, David; Lee, Benjamin L; Stérin, Tristan
(, DNA 2020: Proceedings of the 26th International Conference on DNA Computing and Molecular Programming)
null
(Ed.)
We introduce scadnano (short for "scriptable cadnano"), a computational tool for designing synthetic DNA structures. Its design is based heavily on cadnano [Douglas et al., 2009], the most widely-used software for designing DNA origami [Paul W. K. Rothemund, 2006], with three main differences: 1) scadnano runs entirely in the browser, with no software installation required. 2) scadnano designs, while they can be edited manually, can also be created and edited by a well-documented Python scripting library, to help automate tedious tasks. 3) The scadnano file format is easily human-readable. This goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. The format is also somewhat more expressive than that of cadnano, able to describe a broader range of DNA structures than just DNA origami.
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.
Abeywickrama, Avishi; Adamson, Douglas H; Schniepp, Hannes C; Schniepp, Hannes C
(, Harvard Dataverse)
Atomic force microscopy (AFM) image raw data, force spectroscopy raw data, data analysis/data plotting, and force modeling. File Formats The raw files of the AFM imaging scans of the colloidal probe surface are provided in NT-MDTs proprietary .mdt file format, which can be opened using the Gwyddion software package. Gwyddion has been released under the GNU public software license GPLv3 and can be downloaded free of charge at http://gwyddion.net/. The processed image files are included in Gwyddions .gwy file format. Force spectroscopy raw files are also provided in .mdt file format, which can be opened using NT-MDTs NOVA Px software (we used 3.2.5 rev. 10881). All the force data were converted to ASCII files (*.txt) using the NOVA Px software to also provide them in human readable form with this data set. The MATLAB codes used for force curve processing and data analysis are given as *.m files and can be opened by MATLAB (https://www.mathworks.com/products/matlab) or by a text editor. The raw and processed force curve data and other values used for data processing are stored in binary form in *.mat MATLAB data files, which can be opened by MATLAB. Organized by figure, all the raw and processed force curve data are given in Excel worksheets (*.xlsx), one per probe/substrate combination. Data (Folder Structure) The data in the dataverse is best viewed in Tree mode. Codes for Force Curve Processing The three MATLAB codes used for force curve processing are contained in this folder. The text file Read me.txt provides all the instructions to process raw force data using these three MATLAB codes. Figure 3B, 3C – AFM images The raw (.mdt) and processed (.gwy) AFM images of the colloidal probe before and after coating with graphene oxide (GO) are contained in this folder. Figure 4 – Force Curve GO The raw data of the force curve shown in Figure 4 and the substrate force curve data (used to find inverse optical lever sensitivity) are given as .mdt files and were exported as ASCII files given in the same folder. The raw and processed force curve data are also given in the variables_GO_Tip 18.mat and GO_Tip 18.xlsx files. The force curve processing codes and instructions can be found in the Codes for Force Curve Processing folder, as mentioned above. Figure 5A – Force–Displacement Curves GO, rGO1, rGO10 All the raw data of the force curves (GO, rGO1, rGO10) shown in Figure 5A and the corresponding substrate force curve data (used to find inverse optical lever sensitivity) are given as .mdt files and were exported as ASCII files given in the same folder. The raw and processed force curve data are also given in *.mat and *.xlsx files. Figure 5B, 5C – Averages of Force and Displacement for Snap-On and Pull-Off Events All the raw data of the force curves (GO, rGO1, rGO10) for all the probes and corresponding substrate force curve data are given as .mdt files and were exported as ASCII files given in this folder. The raw and processed force curve data are also provided in *.mat and *.xlsx files. The snap-on force, snap-on displacement, and pull-off displacement values were obtained from each force curve and averaged as in Code_Figure5B_5C.m. The same code was used for plotting the average values. Figure 6A – Force–Distance Curves GO, rGO1, rGO10 The raw data provided in Figure 5A – Force Displacement Curves GO, rGO1, rGO10 folder were processed into force-vs-distance curves. The raw and processed force curve data are also given in *.mat and *.xlsx files. Figure 6B – Average Snap-On and Pull-Off Distances The same raw data provided in Figure 5B, 5C – Average Snap on Force, Displacement, Pull off Displacement folder were processed into force-vs-distance curves. The raw and processed force curve data of GO, rGO1, rGO10 of all the probes are also given in *.mat and *.xlsx files. The snap-on distance and pull-off distance values were obtained from each force curve and averaged as in Code_Figure6B.m. The code used for plotting is also given in the same text file. Figure 6C – Contact Angles Advancing and receding contact angles were calculated using each processed force-vs-distance curve and averaged according to the reduction time. The obtained values and the code used to plot is given in Code_Figure6C.m. Figure 9A – Force Curve Repetition The raw data of all five force curves and the substrate force curve data are given as .mdt files and were exported as ASCII files given in the same folder. The raw and processed force curve data are also given in *.mat and *.xlsx files. Figure 9B – Repulsive Force Comparison The data of the zoomed-in region of Figure 9A was plotted as Experimental curve. Initial baseline correction was done using the MATLAB code bc.m, and the procedure is given in the Read Me.txt text file. All the raw and processed data are given in rGO10_Tip19_Trial1.xlsx and variables_rGO10_Tip 19.mat files. The MATLAB code used to model other forces and plot all the curves in Figure 9B is given in Exp_vdW_EDL.m.
Vetturini, Anthony J.; Cagan, Jonathan; Taylor, Rebecca E.
(, Nucleic Acids Research)
Abstract Recent advances in computer-aided design tools have helped rapidly advance the development of wireframe DNA origami nanostructures. Specifically, automated tools now exist that can convert an input polyhedral mesh into a DNA origami nanostructure, greatly reducing the design difficulty for wireframe DNA origami nanostructures. However, one limitation of these automated tools is that they require a designer to fully conceptualize their intended nanostructure, which may be limited by their own preconceptions. Here, a generative design framework is introduced capable of generating many wireframe DNA origami nanostructures without the need for a predefined mesh. User-defined objectives that guide the generative process are input as either single- or multi-objective optimization problems. A graph grammar is used to both contextualize physical properties of the DNA nanostructure and control the types of generated design features. This framework allows a designer to explore upon and ideate among many generated nanostructures that comply with their own unique constraints. A web-based graphical user interface is provided, allowing users to compare various generated solutions side by side in an interactive environment. Overall, this work illustrates how a constrained generative design framework can be implemented as an assistive tool in exploring design-feature trade-offs of wireframe DNA nanostructures, resulting in novel wireframe nanostructures.
Guerrero, Jorge, and Zadegan, Reza. MENDEL: an automated design tool for DNA nanotechnology. Retrieved from https://par.nsf.gov/biblio/10273991. DNA26: 26th International Conference on DNA Computing and Molecular Programming .
Guerrero, Jorge, & Zadegan, Reza. MENDEL: an automated design tool for DNA nanotechnology. DNA26: 26th International Conference on DNA Computing and Molecular Programming, (). Retrieved from https://par.nsf.gov/biblio/10273991.
Guerrero, Jorge, and Zadegan, Reza.
"MENDEL: an automated design tool for DNA nanotechnology". DNA26: 26th International Conference on DNA Computing and Molecular Programming (). Country unknown/Code not available. https://par.nsf.gov/biblio/10273991.
@article{osti_10273991,
place = {Country unknown/Code not available},
title = {MENDEL: an automated design tool for DNA nanotechnology},
url = {https://par.nsf.gov/biblio/10273991},
abstractNote = {Designing complex DNA nanostructures is a complicated process that requires efficient software to calculate and populate structural details. Most of the published software require manual manipulation and careful inspection of the models that increase the time cost and user error and decrease the flexibility of designing process. We created a python library that we coined MENDEL as a flexible and robust solution for automatic design of complex DNA nanostructures. MENDEL receives a set of sequential commands and creates the structures by following logical steps. Each step instructs the growth of the DNA nanostructure either by adding new nucleotides or repeating sections of arbitrary size and shape. User is able to monitor the design progress by executing the commands in Blender software’s scripting mode. Figure 1 shows an example of using MENDEL library to design a triple-layered origami that represents the word “MENDEL.” MENDEL generates the geometry preview, which helps to understand the design details. Moreover, for convenience, the exported file is compatible with caDNAno. Figure 2 shows the exported model when opened in caDNAno, and Figure 3 shows the modeling results obtained from CanDo for different number of layers. Future work include improving nucleotide twist and rise calculations, supporting honeycomb designs, detecting overlaps, inserting and skipping nucleotides, and generating molecular file formats such as Protein Data Bank (PDB).},
journal = {DNA26: 26th International Conference on DNA Computing and Molecular Programming},
author = {Guerrero, Jorge and Zadegan, Reza},
editor = {null}
}
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