Measuring the 3D Size of Large RNA Molecules
|Title||Measuring the 3D Size of Large RNA Molecules|
|Publication Type||Conference Paper|
|Year of Publication||2008|
|Authors||Gopal, A, Egecioglu, D, Fang, LTai, Knobler, CM, Gelbart, WM, Niebuhr, M, Rao, ALN|
|Conference Name||APS Meeting Abstracts|
Large single-stranded (ss) RNAs are ubiquitous in cells and constitute the genomic content of many viral species. Besides being the primary means of intra-cellular information transfer, some of their functions require them to form stable structural motifs. ssRNA molecules possess intrinsic self-complementarity leading to a partially double-stranded, branched, secondary structure. We measure, in solution, the physical dimensions of several sequences of ssRNA ranging from a few hundred to a few thousand nucleotides in length. Sizes are reported as radii of gyration (Rg) and hydrodynamic radii (Rh), respectively determined by small-angle x-ray scattering (SAXS) and fluorescence correlation spectroscopy (FCS). For RNAs of fixed nucleotide length (˜2000) and composition, we find that Rgs and Rhs can vary by over 30%. By changing solvent conditions, we demonstrate that these size discrepancies are a generic property of the secondary structure arising from sequence-dependent base-pairing. Some viral RNAs that self-assemble into spherical protein capsids have highly evolved sequences that code for unusually compact size and shape.