Tm Prediction
LNA-enhanced oligonucleotides have different melting properties from DNA oligonucleotides. To use this melting temperature prediction (Tm) tool, just enter your sequence below and press "calculate". DNA nucleotides are entered as A, C, T or G, and LNA nucleotides are written +A, +C, +T or +G.
Insights
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.