Ionic interactions and the global conformations of the hammerhead ribozyme

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Abstract
Here we investigate the global conformation of the hammerhead ribozyme. Electrophoretic studies demonstrate that the structure is folded in response to the concentration and type of ions present. Folding based on colinear alignment of arms II and III is suggested, with a variable angle subtended by the remaining helix I. In the probable active conformation, a small angle is subtended between helices I and II. Using uranyl photocleavage, an ion binding site has been detected in the long single-stranded region. The folded conformation could generate a pre-activation of the scissile bond to permit in-line attack of the 2′- hydroxyl group, with a bound metal ion playing an integral role in the chemistry.