Identification and characterization of shifted GU wobble pairs resulting from alternative protonation of RNA

Abstract

RNA can serve as an enzyme, small molecule sensor, and vaccine, and it may have been a conduit for the origin of life. Despite these profound functions, RNA is thought to have quite limited molecular diversity. A pressing question, therefore, is whether RNA can adopt novel molecular states that enhance its function. Covalent modifications of RNA have been demonstrated to augment biological function, but much less is known about non-covalent alterations such as novel protonated or tautomeric forms. Conventionally, a G*U wobble has the U shifted into the major groove. We used a cheminformatic approach to identify four structural families of shifted G*U wobbles in which the G instead resides in the major groove of RNA, which requires alternative tautomeric states of either base, or an anionic state of the U. We provide experimental support for these shifted G*U wobbles via the potent, and unconventional, in vivo reactivity of the U with dimethylsulfate (DMS) in three organisms. These shifted wobbles may play important functional roles and could serve as drug targets. Our cheminformatics approach is general and can be applied to identify alternative protonation states in other RNA motifs, as well as in DNA and proteins. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=59 SRC="FIGDIR/small/630957v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1921d65org.highwire.dtl.DTLVardef@1c8124borg.highwire.dtl.DTLVardef@28fbddorg.highwire.dtl.DTLVardef@af8d20_HPS_FORMAT_FIGEXP M_FIG C_FIG