Talks and Poster Presentations (with Proceedings-Entry):
H. Miao, T. Isenberg, E. Gröller, I. Viola et al.:
"A Preview to Adenita: Visualization and Modeling of DNA Nanostructures";
Poster: 3rd Functional DNA Nanotechnology Workshop,
- 2018-06-08; in: "book of abstracts",
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 , 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  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 ) and a bottom-up (caDNAno ) 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 high-level geometric representation of the target shape. In addition, we employ different layouts for the same structure : 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  of binding regions. The first DNA nanostructures that we designed with the new tool are now under experimental evaluation.
Electronic version of the publication:
Created from the Publication Database of the Vienna University of Technology.