Assignment of cytosine N3 resonances in nucleic acids via intrabase three-bond coupling to amino protons

Coherences were observed between (15)N3 of cytosine and its trans amino pro ton (H42) using a modified gradient-based heteronuclear single quantum cohe rence (HSQC) pulse sequence optimized for three-bond proton-nitrogen coupli ngs. The method is demonstrated with a 22-nucleotide RNA fragment of the P5 abc region of a group I intron uniformly labeled with N-15. Use of intrares idue (15)N3-amino proton couplings to assign cytosine (15)N3 signals comple ments the recently proposed J(NN) HNN COSY [Dingley, A.J. and Grzesiek, S. (1998) J. Am. Chem. Soc., 120, 8293-8297] method of identifying hydrogen-bo nded base pairs in RNA.