Steric interference modification of the hammerhead ribozyme

Although the structure of the hammerhead ribozyme is well characterized, many questions remain about its catalytic mechanism. Extensive evidence suggests the necessity of a conformational change en route to the transition state. We report a steric interference modification approach for investigating this change. By placing large 2′ modifications at residues insensitive to structurally conservative 2′-deoxy modifications, we hoped to discover structural effects distal to the site of modification. Of twenty residues tested, six were identified where the addition of 2′ bulk inhibits cleavage, even though these bulky modifications could be accommodated in the crystal structure without steric clash. It is proposed that these 2′-modifications inhibit cleavage by preventing formation of the alternate, active conformation. Since these 2′ effects are present in both domain I and domain II of the hammerhead, the entire catalytic core must undergo conformational changes during catalysis.