The expanding view of RNA and DNA function

Abstract

RNA and DNA are simple linear polymers consisting of only four major types of subunits, and yet these molecules carry out a remarkable diversity of functions in cells and in the laboratory. Each newly discovered function of natural or engineered nucleic acids enforces the view that prior assessments of nucleic acid function were far too narrow and that many more exciting findings are yet to come. This Perspective highlights just a few of the numerous discoveries over the past 20 years pertaining to nucleic acid function, focusing on those that have been of particular interest to chemical biologists. History suggests that there will continue to be many opportunities to engage chemical biologists in the discovery, creation, and manipulation of nucleic acid function in the years to come.

Figure 1

A sophisticated RNA device. (A) Arrangement of aptamer and ribozyme domains within a naturally-occurring allosteric self-splicing group I ribozyme. The aptamer senses the bacterial second messenger c-di-GMP and the ribozyme requires guanosine or one of its phosphorylated derivatives (e.g., GTP) as a substrate to initiate the first step of splicing. ORF, open reading frame; ss, splice site. (B) Key sequence and secondary structural elements within the allosteric switch. Binding of c-di-GMP to the aptamer domain stabilizes the aptamer P1 stem, which permits formation of the ribozyme P1stem, thereby enabling splicing initiated by GTP attack at the 5′ splice site (GTP-1). This configuration allows translation of the downstream ORF. In the absence of c-di-GMP, alternative pairing (blue shading) precludes formation of the ribozyme P1 stem and allows formation of an alternative ribozyme stem (green shading). This promotes GTP to attack at a position far downstream from the normal 5′ splice site (GTP-2), thus preventing translation of the downstream ORF. Figure adapted from Lee et al., 2010.

Figure 2

What do these RNAs have in common? All are in vitro evolved ribozymes that catalyze biologically relevant chemical transformations and all were published in Chemistry & Biology. (A) The “39M38tr” ribozyme, which catalyzes Diels-Alder cycloaddition between biotin maleamide and anthracene that is tethered to the 5′ end of the ribozyme via an alkyl linker (Seelig and Jäschke, 1999). (B) The “Fx3 (Flexizyme)” ribozyme, which catalyzes 3′-aminoacylation of tRNA using the cyanomethyl ester of phenylalanine or other amino acids (Murakami et al., 2003). (C) The “UV5” ribozyme, which catalyzes Michael addition between biotin cysteine and fumaramide that is tethered to the 5′ end of the ribozyme (Sengle et al., 2001). (D) The “11D2” ribozyme, which catalyzes aldol condensation between biotin-linked benzaldehyde-4-carboxamide and levulinic amide that is tethered to the 5′ end of a separate oligonucleotide (Fusz et al., 2005). (E) The “R180” ribozyme, which catalyzes peptide bond formation between an aminoacyl 5′-adenylate and an amino acid that is tethered to the 5′ end of the ribozyme via a disulfide linkage (Zhang and Cech, 1998; Sun et al., 2002). Curved arrow indicates the site of reaction. Circled B indicates a biotin moiety.