title: Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures.
abstract: Long RNA molecules are at the core of gene regulation across all kingdoms of life, while also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with nonrepeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. To test whether a branched polymer model can estimate the overall sizes of large RNAs, we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long noncoding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation-one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of maximum ladder distance. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low ionic-strength sizes. These results suggest that sizes of long RNA molecules are determined by the branching pattern of their secondary structures. We also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single-stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs.
authors.affiliation: Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
authors.forename: Alexander
authors.initials: A
authors.lastname: Borodavka
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel.
authors.forename: Surendra W
authors.initials: SW
authors.lastname: Singaram
authors.affiliation: Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Stockley
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California.
authors.forename: William M
authors.initials: WM
authors.lastname: Gelbart
authors.affiliation: The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel.
authors.forename: Avinoam
authors.initials: A
authors.lastname: Ben-Shaul
authors.affiliation: Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom. Electronic address: r.tuma@leeds.ac.uk.
authors.forename: Roman
authors.initials: R
authors.lastname: Tuma
mesh_terms: D001483:Base Sequence; D057446:Hydrodynamics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics
chemical_list: D012313:RNA