Question Regarding the Utility of the NNN Model for DNA Secondary Structure Energetics

[YAFANZ]

Dear Authors,

Thank you for sharing this fantastic work on DNA folding thermodynamics.

I have a question regarding the practical utility of the NNN model. Specifically, can this model be directly used to estimate the secondary structure folding energy of a given single-stranded or double-stranded DNA sequence, in a manner similar to the ViennaRNA package used in RNA biology?

If so, I would greatly appreciate your guidance on how to apply the model for this purpose, or whether there are recommended scripts or workflows available.

Thank you very much for your time and for this insightful contribution.

Best regards,
Yafan