Quantum Mechanical/Molecular Mechanical Simulation Study of the Mechanism of Hairpin Ribozyme Catalysis
نویسندگان
چکیده
منابع مشابه
The hairpin ribozyme: structure, assembly and catalysis.
Recent studies of the hairpin ribozyme have revealed a distinct catalytic mechanism for this small RNA motif. Inner-sphere coordinated metal ions are not required, as the inert metal ion complex cobalt hexammine promotes catalysis. Detailed kinetic analyses have defined rates of individual steps in the catalytic cycle. Functional group modification, NMR studies of subdomains and cross-linking e...
متن کاملFolding and catalysis by the hairpin ribozyme.
The hairpin ribozyme undergoes a site-specific transesterification cleavage of the phosphodiester backbone. The natural form of the ribozyme is a four-way helical junction, where two arms contain unpaired loops. This folds by pairwise coaxial stacking of helical arms, and a rotation into an antiparallel conformation in which there is close association between the loops. This probably generates ...
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Evidence that hairpin ribozymes function in the absence of bivalent cation cofactors suggests that active site nucleobases might participate directly in catalytic chemistry. We have adopted an abasic ribozyme rescue strategy to begin to dissect the roles of specific nucleobases in hairpin ribozyme activity. Loss of one active site nucleobase, G8, could be compensated by providing certain nucleo...
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Several small ribozymes carry out self-cleavage at a specific phosphodiester bond to yield 2',3'-cyclic phosphate and 5'-hydroxyl termini. Prior mechanistic and structural studies on the HDV ribozymes led to the proposal that the pK(a) of C75 is shifted toward neutrality, making it an effective general acid. Recent mechanistic studies on the hairpin ribozyme have led to models in which protonat...
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ژورنال
عنوان ژورنال: Journal of the American Chemical Society
سال: 2008
ISSN: 0002-7863,1520-5126
DOI: 10.1021/ja0759141