Nucleobase catalysis in the hairpin ribozyme
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 ...
متن کاملA guanine nucleobase important for catalysis by the VS ribozyme.
A guanine (G638) within the substrate loop of the VS ribozyme plays a critical role in the cleavage reaction. Replacement by any other nucleotide results in severe impairment of cleavage, yet folding of the substrate is not perturbed, and the variant substrates bind the ribozyme with similar affinity, acting as competitive inhibitors. Functional group substitution shows that the imino proton on...
متن کاملNucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme.
Existing evidence suggests that the Varkud satellite (VS) ribozyme accelerates the cleavage of a specific phosphodiester bond using general acid-base catalysis. The key functionalities are the nucleobases of adenine 756 in helix VI of the ribozyme, and guanine 638 in the substrate stem loop. This results in a bell-shaped dependence of reaction rate on pH, corresponding to groups with pK(a) = 5....
متن کاملMutagenesis of the hairpin ribozyme.
Extensive in vitro mutagenesis studies have been performed on the hairpin ribozyme and substrate in an effort to refine the overall secondary structure of the molecule and provide further insight into what elements are essential for activity. A secondary structure consisting of four helices and five loop regions remains the basic model as originally proposed. Two helices, helix 1 and 2, form be...
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ژورنال
عنوان ژورنال: RNA
سال: 2006
ISSN: 1355-8382
DOI: 10.1261/rna.11706