Adenita

Adenita enables in silico design and visualization of static and dynamic DNA nanostructures for modeling, modification, and analysis in DNA nanotechnology.

Key Features:

• Multiscale data model: Represents and facilitates visualization and manipulation of DNA-based structures at multiple levels of abstraction.
• Support for DNA origami types: Handles multilayer DNA origami, wireframe DNA origami, and DNA tiles.
• Load and de novo creation: Allows loading existing DNA origami structures or creating new structures from scratch.
• On-the-fly modification and analysis: Provides editors that enable real-time modification and analysis of nanostructures during design.
• Modular combination and reuse: Enables combination and reuse of existing DNA nanostructures as modular building blocks to assemble superstructures.
• Integration of alternative molecules: Supports inclusion of proteins and aptamers within DNA nanostructure designs.
• Export for oxDNA: Exports structures for downstream oxDNA simulations.

Scientific Applications:

• DNA origami design and prototyping: Design and modification of multilayer, wireframe, and tile-based DNA origami structures.
• Multiscale structural modeling and analysis: Analyze DNA nanostructures across different abstraction levels to inform design decisions.
• Modular assembly and superstructure design: Combine and repurpose existing nanostructures, such as transforming large nanorods into novel architectures.
• Hybrid DNA–protein/aptamer constructs: Design DNA-based assemblies that incorporate proteins and aptamers for applications in medicine, biotechnology, physics, and biocomputing.
• Preparation for coarse-grained simulation: Export designs for oxDNA to enable downstream molecular dynamics and simulation-based analysis.

Methodology:

Uses a multiscale data model to represent DNA nanostructures at multiple abstraction levels, supports loading or de novo creation and editing via internal editors, allows integration of proteins and aptamers, and provides export functionality for oxDNA simulations.