Epub 2008 Jul 25. The hairpin ribozyme is a small catalytic RNA that has been reengineered resulting in a number of variants with extended or even new functions. The hairpin ribozyme is one of four known natural catalytic RNAs that carry out sequence-specific cleavage of RNA. Together, the results of these experiments present a highly congruent picture of the catalytic cycle, i.e. The minimal hairpin ribozyme-substrate complex folds into a secondary structure that includes two domains, each consisting of two short base pairedhelices separated by an internal loop. The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics. These reactions are important for processing the large multimeric RNA molecules that are generated by rolling circle replication. Please enable it to take advantage of the complete set of features! NLM USA.gov. The combinatorial approach simultaneou … a molecule rearranging its own structure. Hairpin ribozyme Last updated April 18, 2020 Secondary structure of a minimal hairpin ribozyme with substrate RNA bound. Would you like email updates of new search results? In the hairpin ribozyme, metal ions or metal-bound water would function to organize the tertiary structure of the ribozyme–substrate complex in a manner that facilitates catalysis by the RNA where a specific nucleotide (e.g. The hairpin ribozyme is one of a number of small catalytic RNAs that are excellent paradigms for RNA structure-function analysis and have potential also as therapeutic agents. Catalán P, Elena SF, Cuesta JA, Manrubia S. Viruses. The hairpin ribozyme is a small catalytic RNA that has been reengineered resulting in a number of variants with extended or even new functions. The hairpin ribozyme is a naturally occurring RNA that catalyzes sequence‐specific cleavage and ligation of RNA. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. One strand of stem A harbours the scissile bond. The hairpin ribozyme is a small catalytic RNA with a unique two-domain structure. covalent joining of RNA fragments ending with a 2',3'-cyclic phosphate and a 5'-hydroxyl group to generate the ordinary 3'-5' phosphodiester linkage used in both RNA and DNA. Two independent NMR structures have been determined for the hairpin ribozyme. This ribozyme is a relatively small RNA molecule (50 nucleotides, 17 kDa) derived from the minus strand of the satellite RNA associated with tobacco ringspot virus (16–18). In this structure, the bases of loop A form a series of four non-canonical pairs resulting in an extended helix. Results and Discussion. Here we present the solution structure of the loop B domain of the hairpin ribozyme, which contains most of the catalytically essential nucleotides. Studies of this reaction in multiple ribozymes have served to establish that the reaction chemistry (catalytic mechanism) is an endogenous property of the RNA molecule itself and is not mediated by metal ions, as is true for some protein enzymes and some other ribozymes. The hairpin ribozyme is a small section of RNA that can act as a ribozyme. [11][12], The minimal hairpin ribozyme-substrate complex folds into a secondary structure that includes two domains, each consisting of two short base paired helices separated by an internal loop. Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme. Hairpin ribozyme lacking a substrate moiety, comprising at least six bases in helix 2 and able to base-pair with a separate substrate RNA, wherein the said ribozyme comprises one or more bases 3' of helix 3 able to base-pair with the said substrate RNA to form a helix 5 and wherein the said ribozyme can cleave and/or ligate said separate RNA(s) in trans. 41 Hairpin Ribozyme Structure 42 Formation of the Active Structure. It has been the subject of extensive biochemical and structural studies, perhaps the most detailed for any catalytic RNA to date. Search for more papers by this author. [15] In order for catalysis to occur, the two domains lie parallel to one another in a fold that resembles a paperclip. Biol. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors. The arrow shows the cleavage site. 2018 Apr 25;118(8):4177-4338. doi: 10.1021/acs.chemrev.7b00427. J. Mol. Tertiary structure stabilization promotes hairpin ribozyme ligation. Donor (Cy3) and acceptor (Cy5) fluorophores were attached to the 5′ termini of the A and B arms, respectively (Fig. The underlined target bases (NGUC) are not base-paired with the ribozyme. The hairpin ribozyme is a small catalytic RNA with a unique two-domain structure. Here we present the solution structure of the loop B domain of the hairpin ribozyme… The VS ribozyme [3] is embedded within a cir- The hairpin ribozyme is a small catalytic motif that catalyzes a reversible, site-specific RNA cleavage reaction essential for the propagation of plant RNA replicons, and is an important model system for understanding biological catalysis by RNA (Figure 1A; Fedor, 2000). It is of particular biochemical interest because, unlike ‘classic’ ribozymes, such as the group I intron, it appears not to employ metal ions as catalytic cofactors. The arrow indicates cleavage-ligation site. Uppercase letters indicate ribozyme; lowercase letters indicate substrate. 2019 May 9;11(5):425. doi: 10.3390/v11050425. 2002). These reactions are self-processing, i.e. Circles represent individual nucleotides and lines indicate canonical (Watson-Crick) base pairs. G8) would assume the role of … HHS (A ) The double‐labeled ribozyme–substrate complex utilized for energy transfer measurements.The two‐strand hairpin ribozyme (Rz, capital letters) binds the 14‐nucleotide substrate (S, small letters) to form the A domain comprising helices 1 and 2, and … Hairpins recognize the sequence NNYNGUCNNNNNN, where N is any nucleotide and Y is a pyrimidine. hairpin ribozyme ribozyme hairpin Prior art date 1992-07-02 Legal status (The legal status is an assumption and is not a legal conclusion. The RNA substrate is bound in domain A through Watson-Crick base pairs in H1 and H2. PubMed Abstract: The hairpin ribozyme is an RNA enzyme that performs site-specific phosphodiester bond cleavage between nucleotides A-1 and G+1 within its cognate substrate.  |  hairpin ribozymes are found in opposite strands of the satel- lite RNA of tobacco ringspot virus (sTRSV) and related sequences [l], whereas the HDV ribozyme [Z] is necessary for replication of a unique human pathogen, the hepatitis delta virus. Exploration of the interactions between the two domains has begun only recently.  |  [8] Using these artificially derived sequences, a trans-acting ribozyme was developed that can catalyze the cleavage of multiple substrate molecules. The hairpin ribozyme belongs to the family of small catalytic RNAs that cleave RNA substrates in a reversible reaction that generates 2',3'-cyclic phosphate and 5'-hydroxyl termini. An uncleavable substrate analog was used to obtain the initial-state structure, and an RNA-vanadate complex to mimic the intermediate or transition-state (Rupert and Ferré-D'Amaré 2001; Rupert et al. Typically, ribozymes possess nucleotide sequences that are complementary to a target RNA of interest; other sequences adopt a three-dimensional fold (e.g., hammerhead or hairpin) that positions a catalytic machinery close to a fissile bond in the target RNA … Abstract The past few years have seen exciting advances in understanding the structure and function of catalytic RNA. 17. The hairpin ribozyme from satellite RNAs of plant viruses is 50 nucleotides long, and can cleave itself internally, or, in a truncated form, can cleave other RNA strands in a transesterification reaction. OSTI.GOV Conference: Structural studies on an internal loop from a hairpin ribozyme Title: Structural studies on an internal loop from a hairpin ribozyme Full Record Nature 410:780–786 PubMed CrossRef Google Scholar Sharmeen L, Kuo MY-P, Dinter-Gottlieb G, Taylor J (1988) Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. Crystal structures of several ribozymes have provided detailed insight into the folds of RNA molecules. [16], The structure and activity of the hairpin ribozyme has been explored using a wide range of complementary experimental methods, including nucleotide replacement, functional group substitution, combinatorial selection, fluorescence spectroscopy, covalent crosslinking, NMR analysis and x-ray crystallography. 1 Coronavirus: Find the latest articles and preprints Domain B (helix 3 – loop B – helix 4) is larger and contains the primary catalytic determinants of the ribozyme. Self-cleaving hairpin ribozyme construct. These RNA catalysts may have pharmaceutical applications. Here, we utilize these data to assess the functional relevance of the available hairpin ribozyme structures. Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, Burlington 05405. Kinetics of tertiary structure formation in the hairpin ribozyme–substrate complex can be monitored by FRET. 2017 Apr 24;22(4):678. doi: 10.3390/molecules22040678. Additionally, G8, A38, and A9 have been suggested to play roles in the catalysis by deprotonating the 2'-OH of A-1, stabilizing the developing negative charge of the pentacoordinate phosphate oxygens, and protonating the 5'-O leaving group of G+1. The active site of the ribozyme results from docking of two irregular double helices. Thus, manipulation of the hairpin ribozyme structure has allowed for activity control by external effectors, namely oligonucleotides, flavine mononucleotide, and adenine. structure of a hairpin-ribozyme-inhibitor complex at a resolution of 2.4 A. Ceased Application number AU45130/93A Other versions AU4513093A (en 1a).The relative proximity of the two arms can be deduced by measuring the FRET efficiency between the fluorophores. [18], One area of particular interest has been the development of hairpin ribozymes for potential therapeutic use, for example by preventing the replication of pathogenic viruses. Hairpin ribozyme lacking a substrate moiety, comprising at least six bases in helix 2 and able to base-pair with a separate substrate RNA, wherein the … It was first identified in the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where it catalyzes self-cleavage and joining (ligation) reactions to process the products of rolling circle virus replication into linear and circular satellite RNA molecules. The hairpin ribozyme: structure, assembly and catalysis Nils G Walter and John M Burke∗ Recent studies of the hairpin ribozyme have revealed a distinct catalytic mechanism for this small RNA motif. HAIRPIN RIBOZYME STRUCTURES. A tertiary structure model of the hairpin ribozyme has been developed from published biochemical data and new cross-linking results (Earnshaw et al., 1997). ticular, such heterogeneous species have been To analyze homogeneity and electrophoretic mobility found to be inherent to its global structure as a of the two-strand hairpin ribozyme constructs, their 50 two-way junction (Esteban et al., 1997, 1998). Furthermore, in crystal structures of a ribozyme-inhibitor complex and a transition state mimic, it was shown that the three-dimensional architecture splays apart A-1 and G+1, positioning the 2'-OH of A-1 for an in-line nucleophilic attack on the scissile phosphate linkage. For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution. b: The consensus sequence and structure, where dots are any nucleotide, Y is a pyrimidine and R is a purine. An RNA hairpin is an essential secondary structure of RNA. 1999 Mar 5;286(4):1009-24. doi: 10.1006/jmbi.1999.2543. 2019 Feb 8;9(2):233. doi: 10.3390/nano9020233. This suggests there is no metal-catalyzed proton transfer or direct coordination to the RNA, but instead metals are only required for folding. Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes. Recent structure-function studies have begun to yield insights into the molecular bases of these unique features of the hairpin ribozyme. It consisted of four helical regions separated by single stranded or internal loop sequences. Here we show that freezing stimulates the self-ligation (circularization) of linear forms of the hairpin ribozyme (HPR) containing 2′,3′-cyclic phosphate and 5′-OH termini. The hairpin ribozyme has been identified in only 3 naturally occurring sequences: Smaller artificial versions of the hairpin ribozyme have been developed to enable a more detailed experimental analysis of the molecule. [9] Moreover, cleavage activity is still observed when Mg2+ is replaced by [Co(NH3)6]3+. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. This ribozyme is a relatively small RNA molecule (50 nucleotides, 17 kDa) derived from the minus strand of the satellite RNA associated with tobacco ringspot virus ( It has been the subject of extensive biochemical and structural studies, perhaps the most detailed for any catalytic RNA to date. One strand of stem A harbours the scissile bond. Nature, Volume 354, November 28, 1991 (28.11.91), JOHN M. BURKE et al. The RCSB PDB also provides a variety of tools and resources. In the laboratory, a functional interaction between the two domains is promoted by the addition of cations, whose positive charge suffices to overcome the electrostatic repulsion of the negatively charged RNA backbone. At the end of the replication cycle, these large intermediates of satellite RNA replication are processed down to unit length molecules (circular or linear) before they can be packaged by viruses and carried to other cells for further rounds of replication.[1]. Prevention and treatment information (HHS). [22], Natural and artificial versions of the hairpin ribozyme, Targeted RNA cleavage and antiviral activity, "Plant pathogenic RNAs and RNA catalysis", "Nucleotide sequence and structural analysis of two satellite RNAs associated with chicory yellow mottle virus", "Catalytically active geometry in the reversible circularization of 'mini-monomer' RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA", "The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone", "Metal Ions Play a Passive Role in the Hairpin Ribozyme Catalysed Reaction", "Transition state stabilization by a catalytic RNA", "Water in the active site of an all-RNA hairpin ribozyme and the effects of Gua8 base variants on the geometry of phosphoryl transfer", "Reconstitution of hairpin ribozyme activity following separation of functional domains", "Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme", "A hairpin ribozyme inhibits expression of diverse strains of human immunodeficiency virus type 1", "Inhibition of HIV-1 replication by RNA targeted against the LTR region", "Combinatorial Screening and Intracellular Antiviral Activity of Hairpin Ribozymes Directed against Hepatitis B Virus", "Inhibition of viral replication by ribozyme: mutational analysis of the site and mechanism of antiviral activity", "The hairpin ribozyme: from crystal structure to function", https://en.wikipedia.org/w/index.php?title=Hairpin_ribozyme&oldid=951505998, Creative Commons Attribution-ShareAlike License, satellite RNA of chicory yellow mottle virus (sCYMV), This page was last edited on 17 April 2020, at 14:26. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. J Mol Biol. The secondary structure of the hairpin ribozyme contains two independently folding domains, called A (green) and B (yellow). A. Berzal‐Herranz. The RCSB PDB also provides a variety of tools and resources. 2019 Oct 10;47(18):9480-9494. doi: 10.1093/nar/gkz737. It is of particular biochemical interest because, unlike 'classic' ribozymes, such as the group I intron, it appears not to employ metal ions as catalytic cofactors. Structure and function of the hairpin ribozyme. Many ribozymes have either a hairpin – or hammerhead – shaped active center and a unique secondary structure that allows them to cleave other RNA molecules at specific sequences. The hairpin ribozyme, like the hammerhead ribozyme, is found within RNA satellites of plant viruses, where it performs a reversible self-cleavage reaction to … It is now possible to make ribozymes that will specifically cleave any RNA molecule. [17], Hairpin ribozymes have been modified in such a way that they can be used to target cleavage of other RNA molecules. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The two domains are covalently joined via a phosphodiester linka… The active site of this natural RNA results from the docking of two irregular helices: stems A and B. The hairpin ribozyme is a better ligase than it is a nuclease while the hammerhead reaction favors cleavage over ligation of bound products by nearly 200-fold. Hairpin ribozyme Structure and Catalysis. Fedor, M. J. The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects. Figure 1. These studies have been facilitated by the ability of the functional complex to self-assemble from segments made by solid phase chemical RNA synthesis, permitting the incorporation of a wide variety of modified nucleotides that are not naturally found in RNA. The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The hairpin ribozyme folds in solution and catalyzes self-cleavage or ligation via a specific two-domain structure. Like the hammerhead ribozyme it is found in RNA satellites of plant viruses. In vitro selection experiments have been used to isolate active variants of the 50 nt hairpin catalytic RNA motif following randomization of individual ribozyme … The hairpin ribozyme is an RNA motif that catalyzes RNA processing reactions essential for replication of the satellite RNA molecules in which it is embedded. The hairpin ribozyme is one of four known natural catalytic RNAs that carry out sequence-specific cleavage of RNA. : "Novel Guanosine Requirement for Catalysis by the Hairpin Ribozyme", see p. 320-322. The solution structure of loop A from the hairpin ribozyme found in the minus strand of tobacco ringspot virus satellite has been determined by NMR spectroscopy. Hairpin ribozyme structure. Inner-sphere coordinated metal ions are not required, as the inert metal ion complex cobalt hexammine promotes catalysis.
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