Notes

Potential RNA experimental sources to refitting experiment

• Frechet, D., Ehrlich, R., Remy, P., & Gabarro-Arpa, J. (1979). Thermal perturbation differential spectra of ribonucleic acids. U. Nearest neighbour interactions. Nucleic Acids Research, 7(7), 1981–2001. doi:10.1093/nar/7.7.1981

Thermodynamic properties of dinucleotide monophosphates (delta H, delta S, and fraction of stacking and unstacking) two-state model to U.V. melting curves

• Ezra, F. S., Lee, C.-H., Kondo, N. S., Danyluk, S. S., & Sarma, R. H. (1977). Conformational properties of purine-pyrimidine and pyrimidine-purine dinucleoside monophosphates. Biochemistry, 16(9), 1977–1987. doi:10.1021/bi00628a035

Chemical shift, coupling constants, and popultaion distribution of conformers (stacked ratio, C3'-endo, etc.)

• Lee, C.-H., Ezra, F. S., Kondo, N. S., Sarma, R. H., & Danyluk, S. S. (1976). Conformational properties of dinucleoside monophosphates in solution: dipurines and dipyrimidines. Biochemistry, 15(16), 3627–3639. doi:10.1021/bi00661a034

Chemical shift, coupling constants, and popultaion distribution of conformers (stacked ratio, C3'-endo, etc.)

Dynamical behaviors of RNA systems reported by previous literatures

• Zhao, J., Kennedy, S. D., Berger, K. D., & Turner, D. H. (2020). Nuclear Magnetic Resonance of Single Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. doi:10.1021/acs.jctc.9b00912

Intercalated tetramer systems inconsistent with NMR spectra for r(CAAU), r(AAAA), and r(GACC)

Useful RNA experimental summary

• Bernetti. M, Bussi. G, Integrating experimental data with molecular simulations to investigate RNA structural dynamics, Curr Opin Struct Biol, 2023, 102503