Novel 2D and 3D multiple-quantum bi-directional HCNCH experiments for the correlation of ribose and base protons/carbons in C-13/N-15 labeled RNA

Multiple-quantum 2D and 3D bi-directional HCNCH experiments are presented f or the correlation of base and ribose protons/carbons in C-13/N-15 labeled HIV-1 TAR RNA. In both 2D and 3D experiments, the magnetization of H1' is t ransferred to H6/H8 and H1' through H1'-C1'-N1/9-C6/8-H6/8 and H1'-C1'-N1/9 -C1'-H1' pathways, and the magnetization of H6/8 is transferred to H1' and H6/8 through H6/8-C6/8-N1/9-C1'-H1' and H6/8-C6/8-N1/9-C6/8-H6/8 pathways. Chemical shifts of four different nuclei (H1', C1', C6/8 and H6/8) are samp led in the 2D experiment. The correlation of base and ribose protons/carbon s is established by the rectangular arrangement of crossover and out-and-ba ck peaks in the proton/carbon correlated spectrum. The rectangular connecti ons can be further resolved using the nitrogen dimension in a H-1/C-13/N-15 3D experiment. Furthermore, by taking advantage of the well separated chem ical shifts of N1 (pyrimidine) and N9 (purine), the 2D spectrum can be simp lified into two sub-spectra based on their base type. Both experiments were tested on a C-13/N-15 labeled 27-mer HIV-1 TAR RNA containing a UUCG hairp in loop.