Nucleic Acid Crystallography via Direct Selenium Derivatization: RNAs Modified with Se-Nucleobases

Abstract

Selenium-derivatized RNAs are powerful tools for structure and function studies of RNAs and their protein complexes. By taking the advantage of selenium modifications, researchers can determine novel RNA structures via convenient SAD and MAD phasing. As one of the naturally occurring tRNA modifications, 2-seleno-uridine, which presents almost exclusively at the wobble position of anticodon loop in various bacterial tRNAs (Ching et al., Proc Natl Acad Sci U S A 82:347, 1985; Dunin-Horkawicz et al., Nucleic Acids Res 34:D145-D149, 2006), becomes one of the most promising modifications for crystallographic studies. Our previous studies have demonstrated many unique properties of 2-seleno-uridine, including stability (Sun et al., RNA 19:1309-1314, 2013), minimal structural perturbation (Sun et al., Nucleic Acids Res 40:5171-5179, 2012), and enhanced base-pairing fidelity (Sun et al., Nucleic Acids Res 40:5171-5179, 2012). In this protocol, we present the efficient chemical synthesis of 2-seleno-uridine triphosphate ((Se)UTP) and the facile transcription and purification of (Se)U-containing RNAs ((Se)U-RNA).