A method was developed that permits covalent cross-links of different linker lengths to be introduced into RNA at defined positions. The previous observation that a cross-link between stems I and II of the hammerhead ribozyme was confirmed and further explored. By examining the catalytic consequences of varying the position and length of this cross-link, we conclude that the previously proposed conformational dampening model cannot sufficiently explain the increase in ligation rate induced by the cross-link. Rather, the cross-link constrains the cleaved hammerhead into a structure that more closely resembles the transition state, thereby increasing the reverse ligation rate relative to a non-cross-linked control.
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