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The effect of the conserved bases in the stem II on Y-shape conformation of Hammerhead ribozyme was studied by NMR. On wild type, Hammerhead ribozyme forms Y-shape conformation, similar to the crystal structure, while on the mutation of G10.1C11.1 in the stem II by C10.1G11.1, that form the different conformation. This come from stability of the shared GA-AG base pairs, which affect the stacking between stem III and A14U7 base pair. On the mutation, this stacking is weak, so U4 turn does not occur, consequently stems II and I are linear.

Effect of the conserved bases G10.1C11.1 in the stem II on Y-shape conformation of Hammerhead ribozyme