Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach
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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Preprint| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
bioRxiv.org - (2022) vom: 25. Mai Zur Gesamtaufnahme - year:2022 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Sakuraba, Shun [VerfasserIn] |
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| Links: |
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| doi: |
10.1101/454124 |
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| funding: |
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| PPN (Katalog-ID): |
XBI000379948 |
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| 100 | 1 | |a Sakuraba, Shun |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach |
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| 520 | |a 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. | ||
| 700 | 1 | |a Iwakiri, Junichi |e verfasserin |4 aut | |
| 700 | 1 | |a Hamada, Michiaki |e verfasserin |4 aut | |
| 700 | 1 | |a Kameda, Tomoshi |e verfasserin |4 aut | |
| 700 | 1 | |a Tsuji, Genichiro |e verfasserin |4 aut | |
| 700 | 1 | |a Kimura, Yasuaki |e verfasserin |4 aut | |
| 700 | 1 | |a Abe, Hiroshi |e verfasserin |4 aut | |
| 700 | 1 | |a Asai, Kiyoshi |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t bioRxiv.org |g (2022) vom: 25. Mai |
| 773 | 1 | 8 | |g year:2022 |g day:25 |g month:05 |
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| 856 | 4 | 0 | |u http://dx.doi.org/10.1101/454124 |z kostenfrei |3 Volltext |
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