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"md5:0c30b8f99d19b0b5695e5d7533a7dbcf", "description": "comparison of scaling exponents with notable ones from polymer theory", "key": "Fig4.csv", "size": 161 } ], "contributors": [ { "givennames": "Domen", "affiliations": [ "Department of Theoretical Physics, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia" ], "familyname": "Vaupoti\u010d", "email": "domenvaupotic@gmail.com" }, { "givennames": "Angelo", "affiliations": [ "Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy" ], "familyname": "Rosa", "email": "anrosa@sissa.it" }, { "givennames": "Luca", "affiliations": [ "Department of Physics, University of Trento, via Sommarive 14, 38123 Trento, Italy", "INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive 14, 38123 Trento, Italy" ], "familyname": "Tubiana", "email": "Luca.tubiana@unitn.it" }, { "givennames": "An\u017ee", "affiliations": [ "Department of Theoretical Physics, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia" ], "familyname": "Bo\u017ei\u010d", "email": "Anze.Bozic@ijs.si" } ], "status": "published", "keywords": [ "RNA", "polymer physics", "statistical mechanics", "scaling" ], "id": "1791", "version": 1, "license_addendum": null, "conceptrecid": "1790", "title": "Scaling properties of RNA as a randomly branching polymer", "doi": "10.24435/materialscloud:js-fx", "is_last": true, "publication_date": "Jun 08, 2023, 11:43:12", "_oai": { "id": "oai:materialscloud.org:1791" }, "license": "Creative Commons Attribution 4.0 International", "edited_by": 576, "description": "Formation of base pairs between the nucleotides of a ribonucleic acid (RNA) sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching\u2014for instance, for its spatial compactness or interaction with other biological macromolecules\u2014RNA branching topology remains largely unexplored. Here, we use the theory of randomly branching polymers to explore the scaling properties of RNAs by mapping their secondary structures onto planar tree graphs. Focusing on random RNA sequences of varying lengths, we determine the two scaling exponents related to their topology of branching. Our results indicate that ensembles of RNA secondary structures are characterized by annealed random branching and scale similarly to self-avoiding trees in three dimensions. We further show that the obtained scaling exponents are robust upon changes in nucleotide composition, tree topology, and folding energy parameters. Finally, in order to apply the theory of branching polymers to biological RNAs, whose length cannot be arbitrarily varied, we demonstrate how both scaling exponents can be obtained from distributions of the related topological quantities of individual RNA molecules with fixed length. In this way, we establish a framework to study the branching properties of RNA and compare them to other known classes of branched polymers. By understanding the scaling properties of RNA related to its branching structure, we aim to improve our understanding of the underlying principles and open up the possibility to design RNA sequences with desired topological properties.", "references": [ { "doi": "", "comment": "Paper where the data is discussed", "type": "Journal reference", "citation": "D. Vaupoti\u010d, A. Rosa, L. Tubiana, A. Bo\u017ei\u010d, The Journal of Chemical Physics, 158 (2023) (accepted)" } ] }, "revision": 2 }