I am currently evaluating the free energy change of the interaction between single strand DNA and single-strand RNA. e.g., 5'-AAATTT-'3 + 5'-AAAUUU-3'
I note that the online available sources to calculate duplex free energy are NUPACK
http://www.nupack.org/utilities/show/241939?token=WxkbDkM8p3
and IDT.
However, these softwares only allow DNA-DNA or RNA-RNA duplex calculation.
several papers might have attempted to calculate RNA-DNA free energy but restricted to the designed sequences. e.g., Article Kinetics and Thermodynamics of DNA, RNA, and Hybrid Duplex Formation
Is there any reference to obtaining free energy of single bp DNA-RNA so that we can estimate the entire hybrid free energy?
You can read: Free energy estimation of short DNA duplex hybridizations
Article Free energy estimation of short DNA duplex hybridizations
also: Tm website calculator for DNA and RNA
https://www.researchgate.net/project/Tm-website-calculator-for-DNA-and-RNA
Mohamed Khedawy Thanks for the suggestion but what i am looking for is about the free energy DNA hybridizing with RNA. The reference only tells us either one pair
For relative free energies (relative stability of two DNA:RNA duplexes differing in one nucleobase): classical molecular dynamics simulations coupled with free energy calculations (e.g., linear interaction energy/linear response approximation); choose one nucleobase of DNA or RNA as the free energy probe. It is computationally feasible to evaluate all combinations of base pairs at the positions 2 to 5. (The terminal base pairs are more accessible to water and therefore less stable.)
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