UNAFold

UNAFold predicts folding, hybridization, and melting pathways of single-stranded nucleic acid sequences (RNA and DNA) to model secondary structures and melting behavior.

Key Features:

• Folding prediction: Employs free energy minimization, partition function calculations, and stochastic sampling to predict secondary structures and folding pathways of single-stranded RNA and DNA.
• Melting simulations: Computes full melting profiles including UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of molecular species as functions of temperature.
• Hybridization analysis: Simulates hybridization events and melting behavior for interacting single-stranded nucleic acids.
• Visualization: Generates images of secondary structures, hybridizations, dot plots, and melting profile plots that can include experimental results.

Scientific Applications:

• Secondary structure prediction: Predicts RNA and DNA secondary structures for sequence analysis and design.
• Melting behavior characterization: Models melting transitions and computes UV260 and Cp profiles to compare with experimental thermal denaturation data.
• Folding and hybridization pathway analysis: Maps folding and hybridization pathways of single-stranded nucleic acids using partition function and stochastic sampling outputs.
• Species composition across temperature: Determines mole fractions of molecular species as a function of temperature for thermodynamic interpretation.

Methodology:

Uses free energy minimization, partition function calculations, and stochastic sampling to predict structures and folding pathways and computes melting profiles (UV260, Cp, mole fractions), and generates structural images and dot plots.