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.

Viral RNA as a Branched Polymer / Vaupotič, Domen; Rosa, Angelo; Podgornik, Rudolf; Tubiana, Luca; Božič, Anže. - 24:(2023), pp. -26. [10.1007/978-3-031-36815-8_1]

Viral RNA as a Branched Polymer

Rosa, Angelo
Membro del Collaboration group
;
Podgornik, Rudolf
Membro del Collaboration group
;
Tubiana, Luca
Membro del Collaboration group
;
2023-01-01

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.
2023
24
Physical Virology
26
Vaupotič, Domen; Rosa, Angelo; Podgornik, Rudolf; Tubiana, Luca; Božič, Anže
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11767/135082
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