Nanobase.org: a repository for DNA and RNA nanostructures

Abstract

We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.

Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein–DNA Nanostructures

“…The interactive design that supports design of DNA and protein nanostructures, as well as setting up ANM-oxDNA simulations, has been implemented in oxView tool, available at and . The structures designed in this work are available in , an online repository of nanostructures …”

“…The structures designed in this work are available at no charge via nanobase.org, an online repository of nanostructures. 26…”

“…Our modeling approaches are based on two tools that we recently developed: a coarse-grained model of DNA and proteins, called ANM-oxDNA, 24 and the OxView design tool, 25 originally developed for DNA nanostructures but since extended to support visualization and editing of protein−DNA nanostructures. 19 Additionally, we extended the online simulation server, oxDNA.org 26 to support ANM-oxDNA simulations and performed many of the simulations in this paper as part of that service, which we make freely available to the community for in-silico testing and verification of protein−DNA hybrid designs. We first designed a DNA origami tetrahedral cage with four available triangular void spaces for incorporating the KDPG aldolase-DNA conjugate (Figure 1A,B).…”

DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation

“…The square-lattice DNA origami structure was designed using CaDNAno, and it is accessible at nanobase.org . The 7249 base scaffold (M13mp18, Bayou Biolabs LLC) and 186 synthetic staple strands were folded in 1× TAE (Alfa Aesar, #J63931) and 12 mM MgCl 2 (Alfa Aesar, #J61014) using a 1:10 scaffold/staples ratio and 1:100 for modified staples.…”

“…The square-lattice DNA origami structure was designed using CaDNAno, 49 and it is accessible at nanobase.org. 60 The 7249 base scaffold (M13mp18, Bayou Biolabs LLC) and 186 synthetic staple strands were folded in 1× TAE (Alfa Aesar, #J63931) and 12 mM MgCl 2 (Alfa Aesar, #J61014) using a 1:10 scaffold/staples ratio and 1:100 for modified staples. Unmodified staples as well as staples internally modified with Cy5 (iCy5, product #1476) and Cy3 (iCy3, product #1474) were purchased from Integrated DNA Technologies, INC, and biotin-functionalized staples as well as staples terminally modified at the 3′-end with Cy5 were purchased from Biomers GmbH.…”