Melting

Melting computes enthalpy, entropy, and melting temperature of nucleic acid duplexes to predict nucleic acid stability and hybridization behavior under varied ionic and chemical conditions.

Key Features:

• Thermodynamic calculations: Computes enthalpy, entropy, and melting temperature for nucleic acid duplexes.
• Supported hybridization types: Handles DNA/DNA, RNA/RNA, and DNA/RNA interactions.
• Nearest-Neighbor and approximative methods: Provides both an approximative approach and the Nearest-Neighbor method with selectable parameter sets, corrections, and formulae.
• Ion concentration corrections: Includes corrections for monovalent ions (sodium, potassium, Tris) and magnesium ions to adjust melting temperature predictions.
• Denaturant corrections: Applies corrections for common denaturing agents including formamide and DMSO.
• Inosine and modified bases: Integrates thermodynamic parameters for inosine and for modified bases such as locked nucleic acids, 2-hydroxyadenines, and azobenzenes.
• Complex structural parameters: Incorporates parameters and formulae for mismatches, bulge loops, CNG repeats, and dangling ends.
• Versioned enhancements: Includes the sodium-ion correction introduced in MELTING 4.2, inosine and magnesium corrections from MELTING 4.3, and the expanded thermodynamic formulae and parameter set from MELTING 5.

Scientific Applications:

• In situ hybridization: Predicts probe-target melting behavior to inform hybridization stringency and temperature selection.
• PCR primer design and optimization: Estimates primer melting temperatures and duplex stability under specified ionic and chemical conditions.
• Antigene targeting: Models duplex stability for antigene oligonucleotide interactions including modified bases.
• Microarray probe analysis: Evaluates probe-target melting characteristics for array hybridization experiments.

Methodology:

Calculations use either an approximative approach or the Nearest-Neighbor method with selectable Nearest-Neighbor parameter sets, applying thermodynamic corrections for sodium, potassium, Tris, magnesium, formamide, and DMSO and using incorporated parameters for inosine, locked nucleic acids, 2-hydroxyadenines, azobenzenes, mismatches, bulge loops, CNG repeats, and dangling ends to compute enthalpy, entropy, and melting temperature.