| Autor: |
Thanh VH; Department of Computer Science, Aalto University, Espoo, Finland.; Certara UK Limited (Simcyp Division), Sheffield, United Kingdom., Korpela D; Department of Computer Science, Aalto University, Espoo, Finland., Orponen P; Department of Computer Science, Aalto University, Espoo, Finland. |
| Jazyk: |
angličtina |
| Zdroj: |
Journal of computational biology : a journal of computational molecular cell biology [J Comput Biol] 2021 Sep; Vol. 28 (9), pp. 892-908. Date of Electronic Publication: 2021 Apr 26. |
| DOI: |
10.1089/cmb.2020.0606 |
| Abstrakt: |
Computational prediction of ribonucleic acid (RNA) structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA secondary structure formation, including pseudoknots, that takes into account the cotranscriptional effects. We propose a single - nucleotide resolution kinetic model of the folding process of RNA molecules, where the polymerase-driven elongation of an RNA strand by a new nucleotide is included as a primitive operation, together with a stochastic simulation method that implements this folding concurrently with the transcriptional synthesis. Numerical case studies show that our cotranscriptional RNA folding model can predict the formation of conformations that are favored in actual biological systems. Our new computational tool can thus provide quantitative predictions and offer useful insights into the kinetics of RNA folding. |
| Databáze: |
MEDLINE |
| Externí odkaz: |
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