<p>Genetically-encoded libraries represent a breakthrough in the large-scale screening of chemical matter. Within such technologies, encoded libraries of synthetic macrocycles generated by ring-closing metathesis hold significant potential to address conventionally undruggable targets. To date, however, the mutual incompatibility of olefin metathesis catalysts and nucleic acids, exacerbated by short catalyst lifetimes in water, has limited advance. Described herein is the synthesis of nucleic acid-tagged macrocycles via ring-closing metathesis (RCM) in neat water, using an anionic, water-soluble ruthenium catalyst designed for this purpose. The ruthenium complex exhibits high compatibility with different oligonucleotide tags, including DNA and RNA oligomers and a chemically-stabilized DNA congener, furnishing the target macrocycles with useful conversions and recovery of the nucleic acid. This advance paves the way for uptake of ring-closing metathesis in water for encoded-library technologies, and for broader applications of nucleic acids, potentially including RNA-oligonucleotide drugs.</p>