The "hammerhead" RNA self-cleaving domain can be assembled from two molecules: a large (approximately 34 nucleotide) ribozyme containing most of the catalytically essential nucleotides and small 13 substrate cleavage site. Four such hammerheads that contained identical catalytic core sequences but differed in base composition helices are involved binding had been reported to vary rates by more than 70-fold under similar reaction conditions. Steady-state kinetic analyses reveal kcat values...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics of intermolecular cleavage by hammerhead ribozymesMartha J. Fedor and Olke C. UhlenbeckCite this: Biochemistry 1992, 31, 48, 12042–12054Publication Date (Print):December 8, 1992Publication History Published online1 May 2002Published inissue 8 December 1992https://pubs.acs.org/doi/10.1021/bi00163a012https://doi.org/10.1021/bi00163a012research-articleACS PublicationsRequest reuse permissionsArticle Views469Altmetric-Citations126LEARN ABOUT...

RNAs adopt defined structures to perform biological activities, and conformational transitions among alternative are critical virtually all RNA-mediated processes ranging from metabolite-activation of bacterial riboswitches pre-mRNA splicing viral replication in eukaryotes. Mechanistic analysis an RNA folding reaction a context is challenging because many steps usually intervene between assembly functional structure execution function. We developed system probe mechanisms secondary exchange...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics and Thermodynamics of Intermolecular Catalysis by Hairpin RibozymesLisa A. Hegg Martha J. FedorCite this: Biochemistry 1995, 34, 48, 15813–15828Publication Date (Print):December 5, 1995Publication History Published online1 May 2002Published inissue 5 December 1995https://doi.org/10.1021/bi00048a027RIGHTS & PERMISSIONSArticle Views273Altmetric-Citations78LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum full text article...

The hairpin ribozyme catalyzes a reversible RNA cleavage reaction that participates in processing intermediates of viral satellite replication plants. A minimal consists two helix−loop−helix segments. These segments associate noncoaxially the active folded structure way brings catalytically important loop nucleotides into close proximity. Tobacco Ringspot Virus assembles context four-way helical junction. Recent physical characterization structures using fluorescence resonance energy...

Conversion of the positioned nucleosome array characteristic repressed GAL1-GAL10 promoter region to more accessible conformation induced state was found depend on upstream activation sequence, GAL4 protein, a positive regulator transcription, and galactose, inducing agent. The effect protein-upstream sequence complex structure adjacent chromatin required no other sequences. Although sequences protected by histones in became micrococcal nuclease (methidiumpropyl-EDTA)iron(II) cleavage...

We investigated the structure of adenovirus deoxyribonucleic acid (DNA)-protein complexes in nuclei infected cells by using micrococcal nuclease. Parental (infecting) DNA was digested into multimers which had a unit fragment size that indistinguishable from nucleosomal repeat cellular chromatin. This pattern maintained parenteral throughout infection. Similar repeating units were detected hamster nonpermissive for human and pretreated with n-butyrate. Late infection, digestion viral...

The glmS ribozyme is the first natural self-cleaving known to require a cofactor. d-glucosamine-6-phosphate (GlcN6P) cofactor has been proposed serve as general acid, but its role in catalytic mechanism not established conclusively. We surveyed GlcN6P-like molecules for their ability support self-cleavage of and found strong correlation between pH dependence cleavage reaction intrinsic acidity cofactors. For cofactors with low binding affinities, contribution rate enhancement was...

The fluorescent nucleotide analogue 8-azaguanosine-5'-triphosphate (8azaGTP) is prepared easily by in vitro enzymatic synthesis methods. 8azaGTP an efficient substrate for T7 RNA polymerase and incorporated specifically opposite cytosine the transcription template, as expected a nucleobase with same Watson−Crick hydrogen bonding face guanine. 8-Azaguanine (8azaG) oligonucleotides also recognized guanine during ribonuclease T1 digestion. Moreover, replacement of 8azaG does not alter melting...

Active-site guanines that occupy similar positions have been proposed to serve as general base catalysts in hammerhead, hairpin, and glmS ribozymes, but no specific roles for these demonstrated conclusively. Structural studies place G33(N1) of the ribozyme Bacillus anthracis within hydrogen-bonding distance 2′-OH nucleophile. Apparent pKa values determined from pH dependence cleavage kinetics wild-type mutant ribozymes do not support a role G33, or any other active-site guanine, catalysis....

Understanding how self-cleaving ribozymes mediate catalysis is crucial in light of compelling evidence that human and bacterial gene expression can be regulated through RNA self-cleavage. The hairpin ribozyme catalyzes reversible phosphodiester bond cleavage a mechanism does not require divalent metal cations. Previous structural biochemical implicated the amidine group an active site adenosine, A38, pH-dependent step catalysis. We developed way to determine microscopic pK(a) values based on...