Exploring RNA oligomerization and ligand binding by fluorescence correlation spectroscopy and small angle X-ray scattering

Eileen Magbanua; Petr V Konarev; Dmitri I Svergun; Ulrich Hahn

doi:10.1007/978-1-62703-667-2_19

Exploring RNA oligomerization and ligand binding by fluorescence correlation spectroscopy and small angle X-ray scattering

Methods Mol Biol. 2014:1086:321-34. doi: 10.1007/978-1-62703-667-2_19.

Authors

Eileen Magbanua¹, Petr V Konarev, Dmitri I Svergun, Ulrich Hahn

Affiliation

¹ MIN Faculty, Chemistry Department, Institute for Biochemistry and Molecular Biology, Hamburg University, Hamburg, Germany.

PMID: 24136613
DOI: 10.1007/978-1-62703-667-2_19

Abstract

RNA forms defined structures and binds specifically to target molecules. The combination of data which results from fluorescence correlation spectroscopy (FCS) and small angle X-ray scattering (SAXS) measurements can be used to determine intermolecular interactions between RNA and its binding partners. To define oligomerization states of free RNA and its complexes with bound target molecules, hydrodynamic radii, radii of gyration as well as the maximum sizes of the components have to be determined and compared. Furthermore, the program OLIGOMER allows calculating the portions of monomeric and dimeric RNA, for instance, within a mixture.

MeSH terms

Binding Sites
Ligands
Nucleic Acid Conformation
RNA / chemistry*
RNA / metabolism
Scattering, Small Angle*
Spectrometry, Fluorescence / methods*
X-Ray Diffraction / methods*

Substances

Ligands
RNA