Dr. Anže Božič (IJS): The branching structure of RNA

Branching architecture characterizes synthetic and naturally-occurring macromolecues alike, its ubiquity reflecting the many favourable properties that arise because of it. In ribonucleic acid (RNA), a versatile biological heteropolymer, base pairing patterns between its four constituent nucleotides lead to a highly branched secondary structure, unique among branched macromolecules. Since RNA structure is typically inseparable from its function, branching often carries functional significance: For instance, highly-branched RNA genomes of some viruses are compact and consequently easily encapsidated during virion formation. I will show how the relationship between the structural branching of RNA and its physical properties can be studied by mapping RNA structures to mathematical trees, whose architecture can be characterized using topological indices. One can further apply the theory of randomly branching polymers to explore the scaling properties of RNA and show that ensembles of RNA structures are characterized by annealed random branching and scale similarly to self-avoiding trees in three dimensions. The obtained scaling exponents are robust and point to a yet unknown factor in RNA structure formation that makes RNA distinctly different from ideal randomly branched polymers. The aim of understanding the branching topology and the related scaling properties of RNA structure is to improve our understanding of the underlying principles, which thus far remain elusive, and open up the possibility to design RNA sequences with desired topological properties.
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