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Viral RNA as a Branched Polymer

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Physical Virology

Part of the book series: Springer Series in Biophysics ((BIOPHYSICS,volume 24))

Abstract

Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this chapter, we focus on its structure and discuss how long RNA molecules can be treated as branched polymers through planar graphs. We describe the major results that can be obtained by this approach, in particular the observation that viral RNA genomes have a characteristic compactness that sets them aside from similar random RNAs. We also discuss how different parameters used in the current RNA folding software influence the resulting structures and how they can be related to experimentally observable quantities. Finally, we show how the connection to branched polymers can be extended to take advantage of known results from polymer physics and can be further moulded to include additional interactions, such as excluded volume or electrostatics.

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Acknowledgements

A.B. acknowledges support by Slovenian Research Agency (ARRS) under Contract No. P1-0055. L.T. acknowledges support by MIUR through the Rita Levi Montalcini grant and financial support from ICSC—Centro Nazionale di Ricerca in High Performance Computing, Big Data and Quantum Computing, funded by European Union—NextGenerationEU. R.P. acknowledges support from the Key Project No. 12034019 of the Natural Science Foundation of China. R.P. also thanks J.D. Farrell for his comments on an earlier version of the manuscript. The authors acknowledge networking support by the the COST Action No. CA17139 (EUTOPIA).

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Vaupotič, D., Rosa, A., Podgornik, R., Tubiana, L., Božič, A. (2023). Viral RNA as a Branched Polymer. In: Comas-Garcia, M., Rosales-Mendoza, S. (eds) Physical Virology. Springer Series in Biophysics, vol 24. Springer, Cham. https://doi.org/10.1007/978-3-031-36815-8_1

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