Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes
For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson–Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark...
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| Format: | Article |
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MDPI AG
2021-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/18/9708 |
| _version_ | 1797518954723278848 |
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| author | Wayne K. Dawson Amiu Shino Gota Kawai Ella Czarina Morishita |
| author_facet | Wayne K. Dawson Amiu Shino Gota Kawai Ella Czarina Morishita |
| author_sort | Wayne K. Dawson |
| collection | DOAJ |
| description | For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson–Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark set of duplexes used to generate the parameters were GC-rich in the shorter duplexes and AU-rich in the longer duplexes, and the length of the majority of the duplexes ranged between 6 and 8 bps. We were curious if other models would generate similar results and whether adding longer duplexes of 17 bps would affect the conclusions. We developed a gradient-descent fitting program for obtaining free-energy parameters—the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), and the melting temperature (Tm)—directly from the experimental melting curves. Using gradient descent and a genetic algorithm, the duplex melting results were combined with the standard benchmark data to obtain bp parameters. Both the standard (Turner) model and a new model that includes length-dependent terms were tested. Both models could fit the standard benchmark data; however, the new model could handle longer sequences better. We developed an updated strategy for fitting the duplex melting data. |
| first_indexed | 2024-03-10T07:36:36Z |
| format | Article |
| id | doaj.art-41bf6680903a4889ae3909c61af0c172 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T07:36:36Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-41bf6680903a4889ae3909c61af0c1722023-11-22T13:26:40ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-09-012218970810.3390/ijms22189708Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA DuplexesWayne K. Dawson0Amiu Shino1Gota Kawai2Ella Czarina Morishita3Veritas In Silico, 1-11-1 Nishigotanda, Shinagawa-ku, Tokyo 141-0031, JapanVeritas In Silico, 1-11-1 Nishigotanda, Shinagawa-ku, Tokyo 141-0031, JapanDepartment of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, JapanVeritas In Silico, 1-11-1 Nishigotanda, Shinagawa-ku, Tokyo 141-0031, JapanFor the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson–Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark set of duplexes used to generate the parameters were GC-rich in the shorter duplexes and AU-rich in the longer duplexes, and the length of the majority of the duplexes ranged between 6 and 8 bps. We were curious if other models would generate similar results and whether adding longer duplexes of 17 bps would affect the conclusions. We developed a gradient-descent fitting program for obtaining free-energy parameters—the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), and the melting temperature (Tm)—directly from the experimental melting curves. Using gradient descent and a genetic algorithm, the duplex melting results were combined with the standard benchmark data to obtain bp parameters. Both the standard (Turner) model and a new model that includes length-dependent terms were tested. Both models could fit the standard benchmark data; however, the new model could handle longer sequences better. We developed an updated strategy for fitting the duplex melting data.https://www.mdpi.com/1422-0067/22/18/9708RNA secondary structurefree-energy parametersKuhn lengthcross-linking entropygradient-descent fitting programgenetic algorithm |
| spellingShingle | Wayne K. Dawson Amiu Shino Gota Kawai Ella Czarina Morishita Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes International Journal of Molecular Sciences RNA secondary structure free-energy parameters Kuhn length cross-linking entropy gradient-descent fitting program genetic algorithm |
| title | Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes |
| title_full | Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes |
| title_fullStr | Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes |
| title_full_unstemmed | Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes |
| title_short | Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes |
| title_sort | developing an updated strategy for estimating the free energy parameters in rna duplexes |
| topic | RNA secondary structure free-energy parameters Kuhn length cross-linking entropy gradient-descent fitting program genetic algorithm |
| url | https://www.mdpi.com/1422-0067/22/18/9708 |
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