Visual OligoMelting Temperature Calculation
The melting temperature (Tm) is the temperature at which half of the oligonucleotide duplex is dissociated. Visual Oligo uses standard methods for Tm prediction of DNA and RNA.
Basic Tm (nearest-neighbor)
Tm is commonly estimated from sequence length and GC content, or using nearest-neighbor thermodynamic parameters. The basic formula incorporates salt concentration (monovalent cations), oligonucleotide concentration, and duplex vs hairpin assumptions.
Salt adjustment
Tm depends on salt concentration: higher salt stabilizes duplexes and increases Tm. Use the Salt Adjusted Tm tool to compute Tm at your assay conditions. Standard buffers (e.g. 50 mM Na⁺, 1 M Na⁺) are often used as reference.
Salt Adjusted Tm →GC content
GC base pairs have three hydrogen bonds (vs two for AT), so higher GC% generally increases Tm. The GC Content Calculator gives base composition and GC% for your sequence, which is used in simple Tm formulas and design rules.
GC Content Calculator →Using Visual Oligo
Enter DNA or RNA sequence in Oligo Properties for MW, Tm, GC%, and ε260. Use Salt Adjusted Tm for molarity and dilution; use the 3D viewer for DNA/RNA structures. Data sources include GenBank, IUPAC, RNAcentral, and PDB.