Site-specific RNA Functionalization via DNA-induced Structure

Site-specific RNA functionalization is in high demand, but remains a challenge, particularly for RNAs produced by transcription rather than by total synthesis. Recent studies have described acylimidazole reagents that react in high yields at 2-OH groups in RNAs. To date, the reactions occur stochastically at non-base-paired regions of RNA, covering much of the RNA in scattered acyl esters. Localized reactions, if possible, could prove useful in many applications, providing functional handles at specific sites and sequences of the biopolymer. Here we describe a DNA-directed strategy for in vitro functionalization of RNA at site-localized 2-OH groups. The method, RNA Acylation at Induced Loops (RAIL), utilizes complementary helper DNA oligonucleotides that expose gaps or loops at selected positions while protecting the remainder in DNA-RNA duplexes. Reaction with acylimidazole reagents is then carried out, providing high yields of 2-OH conjugation at predetermined sites. Subsequent removal of the DNA provides the RNA functionalized as desired. Experiments reveal optimal helper oligodeoxynucleotide designs and conditions for the reaction, and tests of the approach were carried out to control ribozyme activities and to label RNAs with dual-color fluorescent dyes. The RAIL approach offers a simple new strategy for site-specific labeling and controlling RNAs of any length and origin.