Structural Characterization of an Intramolecular RNA Triple Helix by NMR Spectroscopy

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Abstract
A chemically synthesized 29‐base RNA oligomer, designed to fold to form an intramolecular triple helix at acid pH, has been studied by NMR spectroscopy. The molecule consisted of seven U·A·U or C+·G·C base triples joined by two pyrimidine tetra‐loops. The fold was such that the third strand was Hoogsteen base‐paired in the major groove of a Watson‐Crick paired double helix. The nature and size of the molecule required the use of an assignment strategy using two‐ and three‐dimensional homonuclear methods, complemented by a natural abundance 13C correlation experiment. The assignment of the majority of the exchangeable and non‐exchangeable resonances is presented. The data suggest a C3′‐endo sugar puckering for all the nucleotides involved in base triples. A preliminary structural model consistent with the NMR data is presented.