The Size of RNA as an Ideal Branched Polymer

TitleThe Size of RNA as an Ideal Branched Polymer
Publication TypeJournal Article
Year of Publication2011
AuthorsL. T. Fang, W. M. Gelbart and A. Ben-Shaul
Refereed DesignationRefereed
Journal TitleJournal of Chemical Physics
Volume135
Issue15
Pages155105
Start Page155105-1
Date Published10/2011
Short TitleSize of RNA
Type of ArticleTheoretical
ISSN Number0021-9606
Keywordsmass-size scaling, RNA as tree graphs, RNA branching, RNA size, theory
Abstract

Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e.g., denatured states) of the same sequence of monomers. To elucidate the dependence of compactness on the nature and extent of branching, we represent ssRNA secondary structures as tree graphs which we treat as ideal branched polymers, and use a theorem of Kramers for evaluating their root-mean-square radius of gyration, Rg. We consider two sets of sequences - random and viral - with nucleotide sequence lengths (N) ranging from 100 to 10,000. The RNAs of icosahedral viruses are shown to be more compact (i.e., to have smaller Rg) than the random RNAs. For the random sequences we find that Rg varies as N^1/3. These results are contrasted with the scaling of Rg for ideal randomly-branched polymers (N^1/4), and with that from recent modeling of (relatively short, N < 161) RNA tertiary structures (N^2/5).

URLhttp://dx.doi.org/10.1063/1.3652763
DOI10.1063/1.3652763