Higher-order structure of RNA by MS-based approaches
Dan Fabris
The RNA Institute, University at Albany
The observation that less than 1.5% of the human genome codes for actual proteins has lead to the realization that sequence information alone is insufficient to elucidate the function of the vast majority of nucleic acids in living organisms. The recent discovery of riboswitches has keenly reasserted the critical role played by higher-order structure in determining the function of non-coding elements. Beyond sequencing, approaches based on mass spectrometry (MS) can provide direct information about base-pairing and long-range interactions, which respectively define the secondary and tertiary structure of nucleic acids. The ability to observe intact assemblies with other nucleic acid elements and cognate proteins enables the investigation of their quaternary structure. For these reasons, we have been employing electrospray ionization (ESI) with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to investigate the structure-function relationships of the 5' untranslated region (5'-UTR) of the genome of HIV-1 and its assemblies with the chaperone nucleocapsid (NC) protein. The presentation will illustrate the development of solution and gas-phase approaches for elucidating the 3D structure and spatial organization of RNA and its functional assemblies with proteins and small molecule ligands.