LAUSR

5‐Cyanomethyluridine (cnm5U) and 5‐cyanouridine (cn5U), the two uridine analogues, were synthesized and incorporated into RNA oligonucleotides. Base‐pairing stability and specificity studies in RNA duplexes indicated that cnm5U slightly decreased the stability of the duplex but retained the base‐pairing preference. In contrast, cn5U dramatically decreased both base‐pairing stability and specificity between U:A and other noncanonical U:G, U:U, and U:C pairs. In addition, the cn5U:G pair was found to be stronger than the cn5U:A pair and the other mismatched pairs in the context of a RNA duplex; this implied that cn5U might slightly prefer to recognize G over A. Our mechanistic studies by molecular simulations showed that the cn5U modification did not directly affect the base pairing of the parent nucleotide; instead, it weakened the neighboring base pair in the 5′ side of the modification in the RNA duplexes. Consistent with the simulation data, replacing the Watson–Crick A:U pair to a mismatched C:U pair in the 5′‐neighboring site did not affect the overall stability of the duplex. Our work reveals the significance of the electron‐withdrawing cyano group in natural tRNA systems and provides two novel building blocks for constructing RNA‐based therapeutics.