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LNA™ Oligo Optimizer

LNA™ -enhanced oligonucleotides have different thermodynamic properties from traditional DNA oligonucleotides and will thus fold differently.

The LNA™ Oligo Optimizer calculates scores for self-complementarity and secondary structure of an LNA™ -enhanced oligonucleotide. These scores can be used as a rough estimate of the temperature at which an oligonucleotide will form secondary structure and self-complementarity.

Please use this base code:

  • DNA bases: A, C, G, T
  • Locked nucleic acid bases (LNA™ ) are entered as '+_', e.g, +C

Show all hybridizations with a score between:  and 


Secondary structure    Self only

Explanation of the score value:

The secondary structure of an LNA™ -enhanced oligonucleotide with a score below 20 is unlikely to be stable at room temperature. Scores above 30 are likely to produce secondary structures that are stable at room temperature. Scores below 60 can be viewed as a very rough estimate of the melting temperature (in ˚C) of the secondary structures.


If the secondary structure score of a LNA™ enhanced oligonucleotide is 40 and the predicted Tm is 60˚C, then the suggested hybridization temperature of the experiment is between 45˚C - 55˚C.

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