Predict melting temperature using three nearest-neighbor parameter tables (SantaLucia 1998, Sugimoto 1996, Breslauer 1986). Reports consensus Tm ± spread for single sequences or batches up to 5,000.
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When to use
Do not use for
Individual parameter tables can be off by 2–5°C for certain sequence compositions. Averaging across three independent tables cancels out table-specific biases, producing a more reliable prediction — analogous to ensemble methods in machine learning.
When the three tables disagree by >5°C, it usually means the sequence has extreme GC content, unusual stacking patterns, or is in a length range where the tables were not well-calibrated. Treat these predictions with caution and consider experimental Tm measurement.
The simplified salt correction (16.6 log10[Na+]) is accurate for monovalent cations but does not account for Mg²⁺. If your buffer has significant Mg²⁺, actual Tm may be 2–5°C higher than predicted.
Doubling the oligo concentration only shifts Tm by ~0.4°C. The default of 250 nM is suitable for most PCR applications. Adjust only if your protocol uses significantly different concentrations.
Palindromic sequences (where the sequence equals its reverse complement) have a symmetry correction of −1.4 cal/mol·K applied to ΔS. This slightly raises Tm compared to non-palindromic sequences of the same composition.
Three nearest-neighbor parameter tables (SantaLucia 1998, Sugimoto 1996, Breslauer 1986) with SantaLucia initiation parameters and symmetry correction. Salt correction via simplified Owczarzy (16.6 log10[Na+]). Consensus Tm is the arithmetic mean of three table predictions. Spread is max-min. Outlier threshold: 5°C.
Last validated 2026-04-08. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.
ConductScience Consensus Tm Predictor (v1.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/consensus-tm-predictor
SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA. 1998;95(4):1460-1465. doi:10.1073/pnas.95.4.1460
Sugimoto N, et al. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 1996;24(22):4501-4505. doi:10.1093/nar/24.22.4501
Breslauer KJ, et al. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA. 1986;83(11):3746-3750. doi:10.1073/pnas.83.11.3746
The nearest-neighbor model treats DNA duplex stability as the sum of stacking interactions between adjacent base pairs. Each of the 10 unique dinucleotide combinations (AA/TT, AT, TA, CA/TG, GT/AC, CT/AG, GA/TC, CG, GC, GG/CC) has experimentally determined enthalpy (ΔH) and entropy (ΔS) values.
Three major parameter sets exist: SantaLucia (1998) unified parameters from seven labs, Sugimoto (1996) from direct calorimetric measurements, and Breslauer (1986) from early UV melting studies. Each set was derived from different experimental conditions and analysis methods, leading to systematic differences in predictions.
The SantaLucia table also includes initiation parameters that depend on the terminal base pairs (AT vs GC termini), while the Sugimoto and Breslauer tables use zero initiation. Self-complementary (palindromic) sequences receive an additional symmetry correction of −1.4 cal/mol·K to the entropy.
Cations neutralize the negatively charged phosphate backbone, stabilizing the DNA duplex. Higher salt concentration raises Tm significantly — moving from 10 mM to 1 M Na+ can shift Tm by 20–30°C.
This tool uses the simplified Owczarzy correction: ΔTm = 16.6 log10([Na+]). This approximation works well for monovalent cations in the 10–1000 mM range. For buffers containing Mg²⁺ (common in PCR), Tm may be 2–5°C higher than predicted.
