The hairpin ribozyme achieves catalytic cleavage through interaction of essential nucleotides located in two distinct helical domains that include internal loops. Initial docking of the two domains is ion dependent and appears to be followed by a structural rearrangement that allows the ribozyme to achieve a catalytically active state that can undergo cleavage. The proposed structural rearrangement may also be ion dependent and is now of increased importance due to recent evidence that docking is not rate limiting and that metal ions are unlikely to be involved in the chemical cleavage step. An initial structural model of the docked hairpin ribozyme included a proposal for a ribose zipper motif that involves two pairs of hydroxyl groups at A10 and G11 in domain A pairing with C25 and A24 in domain B, respectively. We have used a chemical functional group substitution technique to study whether this proposed ribose zipper is likely to be present in the active, conformationally rearranged ribozyme that is fit for cleavage. We have chemically synthesized a series of individually modified hairpin ribozymes containing 2‘-analogues of nucleosides, that include 2‘-deoxy and 2‘-deoxy-2‘-fluoro at each of the four nucleoside positions, 2‘-amino-2‘-deoxy, 2‘-deoxy-2‘-thio, and 2‘-arabino at position C25, and 2‘-oxyamino at position A10, as well as some double substitutions, and we studied their cleavage rates under both single- and multiple-turnover conditions. We conclude that at least some of the hydrogen-bonding interactions in the ribose zipper motif, either as originally proposed or in a recently suggested structural variation, are unlikely to be present in the active rearranged form of the ribozyme that undergoes cleavage. Instead, we provide strong evidence for a very precise conformational positioning for the residue C25 in the active hairpin. A precise conformational requirement would be expected for C25 if it rearranges to form a base-triple with A9 and the essential residue neighboring the cleavage site G+1, as recently proposed by another laboratory. Our results provide further support for conformational rearrangement as an important step in hairpin ribozyme cleavage.

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Istex/Checkpoint

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{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Istex
   |étape=   Checkpoint
   |type=    RBID
   |clé=     ISTEX:43917CF41A93B27C99D8FAEF24D7CC4EFDE97A69
   |texte=   Investigation of the Proposed Interdomain Ribose Zipper in Hairpin Ribozyme Cleavage Using 2‘-Modified Nucleosides
}}