Tm Prediction

Unlock the precision of LNA-enhanced oligonucleotide research with our dedicated Tm Prediction Calculator. Designed for the unique melting properties of LNA-modified sequences, our tool provides quick and reliable melting temperature (Tm) predictions crucial for your experimental success.

Advanced Thermodynamic Models

Powered by a sophisticated modified nearest-neighbor thermodynamic model, and informed by LNA-specific melting temperature data, our calculator incorporates two distinct prediction models:

• DNA Tm prediction: This model predicts the Tm of a complex formed between the LNA oligo and a complementary DNA strand.
• RNA Tm prediction: This model that predicts the Tm of a complex formed between an LNA oligo and a complementary RNA strand.

Both models are based on experimental data from thousands of oligonucleotide hybridizations. For oligonucleotides of 15–27 nucleotides in length, the resulting predictions have a precision of 1.70 and 2.07°C for RNA and DNA targets, respectively.

Optimized Hybridization Recommendations

We generally recommend starting with a hybridization temperature 30°C below the RNA Tm when detecting RNA targets. This temperature translates to approximately 20°C below the DNA Tm. For example, the oligo C+TG+AC+CGT+ATG+GTC+TA+TA will have RNA Tm and DNA Tm of 86 and 70°C, respectively.

Remember, individual experiments may require specific optimization of hybridization temperatures for the best results.

Model Assumptions and Limitations

The Tm calculation models are based on a modified nearest-neighbor thermodynamic model combination and data from measurements of oligonucleotides ranging from 15–27 nucleotides in length.

Our predictions are based on the following:

• Applicable for oligos ranging from 6 to 80 bases.
• Assumes a salt (Na+) concentration of 115 mM.
• Solutions are neutral, with pH between 7 and 8.
• Oligo concentrations set at 1 µM for RNA and 2 µM for DNA Tm calculations.
• These models do not account for the impact of divalent cations, triphosphates, or various chemical modifications beyond LNA.

The presence of 2’ O-Me modifications is estimated to elevate the Tm by approximately 1.3°C for each modification, though this effect is not currently integrated into our calculations.