RNAsoft

RNAsoft predicts RNA and DNA secondary structures and designs RNA sequences that fold into specified secondary structures for applications including nanostructure construction, molecular tagging in polymer libraries, and therapeutic interventions.

Key Features:

• Secondary Structure Prediction: Predicts secondary structures of paired RNA and DNA molecules using standard thermodynamic models.
• Combinatorial Tag Testing: Evaluates sets of combinatorial DNA and RNA tags to detect and avoid unwanted secondary-structure formation in molecular libraries.
• RNA Structure Design (RNA-SSD): Designs RNA sequences to adopt a specified secondary structure using the RNA Secondary Structure Designer (RNA-SSD), which employs stochastic local search techniques.

Scientific Applications:

• Investigating Biological RNA Functions: Enables design of RNAs with defined structural properties to probe functional roles of biological RNAs.
• Creation of New Ribozymes and Artificial Nanostructures: Supports engineering of novel ribozymes and construction of RNA-based nanostructures by producing sequences that fold into predetermined structures.
• Molecular Tagging in Polymer Libraries: Assesses combinatorial DNA/RNA tags to preserve integrity and functionality of polymer libraries.
• Therapeutic Interventions: Facilitates design of RNA sequences with desired folding properties for applications in therapeutic development.

Methodology:

Structure prediction is based on standard thermodynamic models; the RNA-SSD algorithm applies stochastic local search for inverse folding; performance has been compared to RNAinverse from the Vienna RNA Package and empirically validated on computationally predicted biological sequences and artificially generated structures.