Ahmadi, Y. | Search bioRxiv

bioRxiv2019

Adenita: Interactive 3D modeling and visualization of DNA nanostructures

We present Adenita, a novel software tool for the design of DNA nanostructures in a user-friendly integrated environment for molecular modeling. Adenita is capable of handling large DNA origami structures, re-use them as building blocks of new designs and provide on demand feedback, thus overcoming effectively some of the limitations of existing tools. Additionally, it integrates all major established approaches to DNA nanostructure design (DNA origami, wireframe nanostructures and DNA tiles) and allows to combine them. We show-case Adenita by re-using a large nanorod designed with Cadnano [1] to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

bioinformatics↗

bioRxiv2019

Enzyme Catalytic Activity Emulated Within DNA-based Nanodevice

Artificial enzymes hold a great potential in the field of biotechnology. The currently available design strategies are limited to recruit and organise secondary and tertiary structural elements, and functional motifs of native enzymes. Here, we demonstrate an approach towards the bottom-up development of an artificial enzyme based on DNA nanotechnology. Structural analyses of the FlaI ATPase were used to identify a set of amino acids essential for the catalytic reaction. The selected amino acids were used to design four peptide-oligonucleotide conjugates (POCs). The POCs were integrated into a DNA nanostructure and reconstituted the catalytic site of FlaI. DNA origami technology was employed to maintain the relative orientations of the amino acids and their positions analogous to those in the protein catalytic site. The substrate turnover rates were found to be comparable in our artificial nanozyme (kcat = 0.3622 s-1) and the native enzyme (kcat {approx} 0.016 s-1). The nanozymes could be recycled using an ultrafiltration protocol and reused in multiple experiments allowing a reliable reproduction of the measurements. The emulation of enzymatic activity, by this novel and computable technological framework, can be of high relevance in many different areas.

synthetic biology↗