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bioRxiv · 10.1101/454124

Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach

Sakuraba, S.·Iwakiri, J.·Hamada, M.·Kameda, T.·Tsuji, G.·Kimura, Y.·Abe, H.·Asai, K.
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Abstract

In RNA secondary structure prediction, nearest-neighbor parameters are used to determine the stability of a given structure. We derived the nearest-neighbor parameters for RNAs containing inosine-cytosine pairs. For parameter derivation, we developed a method that combines UV adsorption measurement experiments with free-energy calculations using molecular dynamics simulations. The method provides fast drop-in parameters for modified bases. Derived parameters were compared and found to be consistent with existing parameters for canonical RNAs. A duplex with an internal inosine-cytosine pair is 0.9 kcal/mol more unstable than the same duplex with an internal guanine-cytosine pair, and is as stable as the one with an internal adenine-uracil pair (only 0.1 kcal/mol more stable) on average.

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Sakuraba, S., Iwakiri, J., Hamada, M., Kameda, T., Tsuji, G., Kimura, Y., Abe, H., Asai, K.. 2018-10-26. Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach. https://doi.org/10.1101/454124

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