RNA three-dimensional structure determination using experimental constraints

RNAs function not only as bridges between the genetic information stored in DNA and the final protein products, as stated in the Central Dogma; recently, RNA has also been found to play diverse roles in almost every aspect of cell life (Cruz and Westhof, 2009; Nilsen, 2007; Sharp, 2009; Wan et al., 2011), from regulating transcription and translation (e.g., siRNA, miRNA, or riboswitch regulator motifs; Edwards et al., 2007) to catalyzing mRNA splicing (spliceosome RNA or self-splicing introns; Vicens and Cech, 2006) and protein synthesis (rRNA). These newly discovered RNA functions either are encoded in their primary sequences, through complementarity to target sequences, or originate from their ability to form complex secondary and high-order tertiary structures. The 3D RNA structures, formed by packing of base-paired helices, allow specific interactions with themselves or other biomolecules, including proteins, nucleic acids, and small-molecule ligands. The well-defined 3D structures of RNAs also determine the accessibility of specific sequences important for function. These novel functions of structural RNAs have been uncovered and characterized by studying a small fraction of the known RNA world. Whereas only 2% of a typical eukaryotic genome is translated into proteins, ?90% is transcribed into some kind of noncoding RNA, including antigene, long noncoding, small regulatory, and scaffolding RNAs (Janowski and Corey, 2010; Sharp, 2009; Wan et al., 2011; Wang et al., 2011a; Wang et al., 2011b). A large portion of these unknown RNAs form functional 3D structures, which remain to be characterized. The fact that RNAs adopt specific 3D structures in order to perform their functions also makes them potential drug targets (Hermann and Westhof, 1998; Sucheck and Wong, 2000). Indeed, many well-known antibiotics bind to the RNA component of the bacterial ribosome. More recently, it was discovered that riboswitches could be targets for antibiotics (Kim et al., 2009; Lee et al., 2009; Mulhbacher et al., 2010; Ott et al., 2009). Therefore, the knowledge of the underlying RNA and RNA complex structures can not only enhance our understanding of RNA functions but also aid in design of novel drugs using structure-based rational drug design.