AbstractOligonucleotide N3′ → P5′ phosphoramidates (3′‐phosphoramidates) are DNA analogs that are presently under investigation as potential therapeutic agents. These compounds may also hold promise as a diagnostic tool. Here, we describe a rapid method for the analysis of single‐stranded RNA fragments utilizing 3′‐phosphoramidate oligonucleotides as probes in conjunction with capillary gel electrophoresis (CGE). 3′‐Phosphoramidate 9‐mers were mixed with complimentary RNA, and CGE was used to monitor duplex formation. Complimentary strands of RNA and 3′‐phosphoramidate formed duplexes that gave unique relative mobilities based on an internal standard. The ability of CGE to discriminate between perfect duplexes and duplexes that contain a base mismatch was also investigated. However, the primary focus of this work was to determine CGE's ability to detect the presence of the 3′‐phosphoramidates/RNA duplex under routine electrophoretic running conditions. Polyacrylamide gel electrophoresis analysis was utiliz