NanoTiler

NanoTiler assembles RNA nanostructures by detecting and extracting internal multi-branch junctions and kissing loops from Protein Data Bank (PDB) entries and combining those building blocks with idealized A-form helix fragments to produce and optimize 3D RNA architectures for self-assembly.

Key Features:

• Detection and Annotation: Identifies and annotates RNA structural elements such as internal multi-branch junctions and kissing loops with emanating stem stubs extracted from PDB to form an RNA junction database.
• Building Block Assembly: Utilizes annotated RNA building blocks combined with idealized fragments of A-form helices to assemble larger 3D nanostructures.
• Combinatorial and Optimization Capabilities: Performs a combinatorial search of available building blocks and optimizes block positions, including topology classification and sequence optimization to promote correct self-assembly.
• Flexibility Analysis: Incorporates analysis of building-block flexibility and conformational adaptation to larger structural contexts, including considerations required to induce ring closure during automated exploration.
• Focus on Kissing Loops (KL): Emphasizes evaluation of kissing loop flexibility and potential distortions to improve design of RNA self-assembly interfaces.

Scientific Applications:

• RNA nanotechnology design: Supports design of experimentally viable RNA-based nanostructures for nanotechnology research.
• Targeted drug delivery systems: Enables construction of RNA architectures applicable to targeted drug delivery.
• Biosensors: Enables design of RNA-based biosensor components.
• Molecular machines: Facilitates design of RNA constructs for nanoscale molecular machines.

Methodology:

Initially treats RNA building blocks as rigid objects to test design objectives, performs combinatorial search and position optimization of blocks with topology classification and sequence optimization, and incorporates experimental data on building-block flexibility to account for conformational adaptation.