Thermo Fisher Scientific Tm Calculator

Modified Allawi & SantaLucia Method:

\[ Tm = \frac{\Delta H}{\Delta S + R \ln \left( \frac{C_T}{4} \right)} - 273.15 + 16.6 \log_{10} \left( \frac{[salt]}{1.0 + 0.7[salt]} \right) \]

Melting Temperature (Tm):

Unit Converter ▲

Unit Converter ▼

From:	To:

1. What is the Tm Calculator?

The Thermo Fisher Scientific Tm Calculator uses the modified Allawi & SantaLucia method to calculate melting temperature (Tm) of DNA oligonucleotides. This method provides accurate Tm values for PCR primer design and other molecular biology applications.

2. How Does the Calculator Work?

The calculator uses the modified Allawi & SantaLucia equation:

\[ Tm = \frac{\Delta H}{\Delta S + R \ln \left( \frac{C_T}{4} \right)} - 273.15 + 16.6 \log_{10} \left( \frac{[salt]}{1.0 + 0.7[salt]} \right) \]

Where:

\( \Delta H \) — Enthalpy change (kcal/mol)
\( \Delta S \) — Entropy change (cal/mol·K)
\( R \) — Gas constant (1.987 cal/mol·K)
\( C_T \) — Total oligo concentration (M)
\( [salt] \) — Salt concentration (M)

Explanation: The equation accounts for nearest-neighbor thermodynamics and salt correction to provide accurate melting temperature predictions.

3. Importance of Tm Calculation

Details: Accurate Tm calculation is crucial for PCR primer design, hybridization experiments, and other molecular biology applications where DNA melting temperature is critical.

4. Using the Calculator

Tips: Enter DNA sequence (5' to 3'), salt concentration (typically 0.05M for standard PCR), and oligo concentration (typically 0.25μM for standard PCR).

5. Frequently Asked Questions (FAQ)

Q1: What's the difference between this and basic Wallace rule Tm?
A: This method uses nearest-neighbor thermodynamics which is much more accurate than the simple Wallace rule (4°C × (G+C) + 2°C × (A+T)).

Q2: What salt concentration should I use?
A: Standard PCR conditions typically use 50mM KCl (0.05M). For other applications, use the actual salt concentration of your reaction.

Q3: Why does oligo concentration matter?
A: Tm is concentration-dependent because it affects the equilibrium between single-stranded and double-stranded DNA.

Q4: What sequence length is optimal?
A: Typically 18-30 nucleotides for PCR primers. The method works for sequences from about 10 to 60 nucleotides.

Q5: How does this compare to other Tm calculation methods?
A: This method is considered one of the most accurate for short DNA sequences, especially under standard PCR conditions.