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Updated: Jul 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

UNAFold: software for nucleic acid folding and hybridization.

Nicholas R Markham¹, Michael Zuker

¹Xerox Litigation Services, Albany, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)

|August 21, 2008

Summary

UNAFold is a software package for simulating nucleic acid folding, hybridization, and melting pathways. It provides comprehensive analysis of secondary structures and melting profiles for DNA and RNA sequences.

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Last Updated: Jul 2, 2026

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RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

Bioinformatics
Computational Biology
Molecular Biophysics

Background:

Accurate prediction of nucleic acid secondary structures and melting behaviors is crucial for understanding molecular mechanisms.
Existing tools may lack comprehensive simulation capabilities for both folding and melting processes.

Purpose of the Study:

To introduce UNAFold, an integrated software package for simulating nucleic acid folding, hybridization, and melting.
To provide a versatile tool for analyzing secondary structures and predicting melting profiles of nucleic acid sequences.

Main Methods:

UNAFold integrates free energy minimization, partition function calculations, and stochastic sampling for secondary structure prediction.
The package computes full melting profiles, including UV absorbance, heat capacity, and species mole fractions as a function of temperature.
It supports visualization of secondary structures, hybridizations, and dot plots, and generates various melting profile plots.

Main Results:

UNAFold successfully simulates folding, hybridization, and melting pathways for single-stranded nucleic acids.
The software generates detailed melting profiles and visual representations of molecular structures.
It is compatible with Unix, Linux, and Mac OS X platforms and is command-line driven.

Conclusions:

UNAFold offers a unified approach to simulating nucleic acid dynamics, enhancing the study of molecular interactions.
The package provides researchers with a powerful and flexible tool for in-silico analysis of nucleic acid behavior.
UNAFold is available for download, encouraging further development and application in molecular biology research.