A Preview to Adenita: Visualization and Modeling of DNA Nanostructures

Elisa De Llano, Haichao Miao, Tobias Isenberg, Meister Eduard Gröller, Ivan Viola, Ivan Barisic
A Preview to Adenita: Visualization and Modeling of DNA Nanostructures
Poster shown at 3rd Functional DNA Nanotechnology Workshop ( 6. June 2018- 8. June 2018)

Information

Abstract

We present Adenita, an open-source software that aims to provide an integrated in silico design toolkit for DNA Nanostructures. It facilitates the modular assembly of pre-existing and de novo designs, regardless of the used approach. Adenita is being developed in the context of the MARA project [1], a highly ambitious project aiming to produce a DNA nanorobot capable of targeted cell lyses. Currently, the existing design and visualization tools are insufficient to solve the specific challenges in our project. We aim to overcome these limitations with Adenita, a new semi-automated approach that we are developing as the MARA project advances. Adenita integrates visualizations [2] with user interactions and algorithms in a semi-manual approach. At the core, we use a hierarchical data model that enables us to combine both a top-down (DAEDALUS [3]) and a bottom-up (caDNAno [4]) design approach of the DNA Nanostructure. From the DNA data model, we create smooth visualizations that depict the structure in multiple scales from its atomic details to a highlevel geometric representation of the target shape. In addition, we employ different layouts for the same structure [5]: 3D structural representations, 2D caDNAno-style diagrams, and 1D display of the linear sequences. Creators enable the parametrized generation of structural motifs, while Manipulators facilitate the advanced modifications of the structural properties, such as connecting components and adding bridging strands. Analysis of the designs is still in a preliminary phase, but it already enables the straightforward estimation of distances and the melting temperatures [6] of binding regions. The first DNA nanostructures that we designed with the new tool are now under experimental evaluation.

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BibTeX

@misc{Miao2018FDN,
  title =      "A Preview to Adenita: Visualization and Modeling of DNA
               Nanostructures",
  author =     "Elisa De Llano and Haichao Miao and Tobias Isenberg and
               Meister Eduard Gr\"{o}ller and Ivan Viola and Ivan Barisic",
  year =       "2018",
  abstract =   "We present Adenita, an open-source software that aims to
               provide an integrated in silico design toolkit for DNA
               Nanostructures. It facilitates the modular assembly of
               pre-existing and de novo designs, regardless of the used
               approach. Adenita is being developed in the context of the
               MARA project [1], a highly ambitious project aiming to
               produce a DNA nanorobot capable of targeted cell lyses.
               Currently, the existing design and visualization tools are
               insufficient to solve the specific challenges in our
               project. We aim to overcome these limitations with Adenita,
               a new semi-automated approach that we are developing as the
               MARA project advances. Adenita integrates visualizations [2]
               with user interactions and algorithms in a semi-manual
               approach. At the core, we use a hierarchical data model that
               enables us to combine both a top-down (DAEDALUS [3]) and a
               bottom-up (caDNAno [4]) design approach of the DNA
               Nanostructure. From the DNA data model, we create smooth
               visualizations that depict the structure in multiple scales
               from its atomic details to a highlevel geometric
               representation of the target shape. In addition, we employ
               different layouts for the same structure [5]: 3D structural
               representations, 2D caDNAno-style diagrams, and 1D display
               of the linear sequences. Creators enable the parametrized
               generation of structural motifs, while Manipulators
               facilitate the advanced modifications of the structural
               properties, such as connecting components and adding
               bridging strands. Analysis of the designs is still in a
               preliminary phase, but it already enables the
               straightforward estimation of distances and the melting
               temperatures [6] of binding regions. The first DNA
               nanostructures that we designed with the new tool are now
               under experimental evaluation. ",
  month =      jun,
  event =      "3rd Functional DNA Nanotechnology Workshop",
  location =   "Rome",
  note =       "Poster presented at 3rd Functional DNA Nanotechnology
               Workshop (2018-06-06--2018-06-08)",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2018/Miao2018FDN/",
}