Journal ArticleProc Natl Acad Sci U S A · September 20, 2016
Topoisomerase 3β (Top3β) can associate with the mediator protein Tudor domain-containing protein 3 (TDRD3) to participate in two gene expression processes of transcription and translation. Despite the apparent importance of TDRD3 in binding with Top3β and ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · May 2008
The ribozyme self-cleavage site in the antigenomic sequence of hepatitis delta virus (HDV) RNA is 33-nt downstream of the poly(A) site for the delta antigen mRNA. An HDV antigenomic ribozyme precursor RNA that included the upstream poly(A) processing site ...
Full textLink to itemCite
Journal ArticleJ Am Chem Soc · December 5, 2007
The glmS ribozyme is a catalytic riboswitch that is activated for endonucleolytic cleavage by the coenzyme glucosamine-6-phosphate. Using kinetic assays and X-ray crystallography, we identify an active-site mutation of a conserved guanine that abolishes ca ...
Full textLink to itemCite
Journal ArticleJ Mol Biol · October 12, 2007
The glmS ribozyme is a catalytic RNA that self-cleaves at its 5'-end in the presence of glucosamine 6-phosphate (GlcN6P). We present structures of the glmS ribozyme from Thermoanaerobacter tengcongensis that are bound with the cofactor GlcN6P or the inhibi ...
Full textLink to itemCite
Journal ArticleBiochemistry · May 1, 2007
The two ribozymes of hepatitis delta virus (HDV) cleave faster in divalent metal ions than in monovalent cations, and a variety of divalent metal ions can act as catalysts in supporting these higher rates. Although the ribozymes are closely related in sequ ...
Full textLink to itemCite
Journal ArticleBiochemistry · September 26, 2006
Activity of the two ribozymes from hepatitis delta virus in monovalent salts was examined and compared to activity in Mg2+. Both ribozymes self-cleaved in high concentrations of monovalent cations, and an active site cytosine was required for cleavage acti ...
Full textLink to itemCite
Journal ArticleRNA · July 2006
In the ribozyme from the hepatitis delta virus (HDV) genomic strand RNA, a cytosine side chain is proposed to facilitate proton transfer in the transition state of the reaction and, thus, act as a general acid-base catalyst. Mutation of this active-site cy ...
Full textLink to itemCite
Journal ArticleCurr Top Microbiol Immunol · 2006
The self-cleaving RNA sequences, or ribozymes, in the genomic and antigenomic strands of hepatitis delta virus (HDV) RNA fold into structures that are similar to each other but distinct from those of small ribozymes associated with the RNA replicons that i ...
Full textLink to itemCite
Journal ArticleRNA · December 2005
The recently described glmS ribozyme is a self-cleaving RNA sequence found in the 5' noncoding region of the transcript of the gene for glucosamine-6-phosphate (GlcN6P) synthase in many Gram-positive bacteria. This ribozyme is associated with the GlcN6P ri ...
Full textLink to itemCite
Journal ArticleAnnu Rev Biochem · 2002
The hepatitis delta virus (HDV) ribozymes are self-cleaving RNA sequences critical to the replication of a small RNA genome. A recently determined crystal structure together with biochemical and biophysical studies provides new insight into the possible ca ...
Full textLink to itemCite
Journal ArticleCell Mol Life Sci · January 2002
In the hepatitis delta virus, ribozymes are encoded in both the genomic strand RNA and its complement, the antigenomic strand. The two ribozymes are similar in sequence and structure, are most active in the presence of divalent cation and catalyze RNA clea ...
Full textLink to itemCite
Journal ArticleEMBO J · September 3, 2001
Hepatitis delta virus (HDV) ribozymes employ multiple catalytic strategies to achieve overall rate enhancement of RNA cleavage. These strategies include general acid-base catalysis by a cytosine side chain and involvement of divalent metal ions. Here we us ...
Full textLink to itemCite
Journal ArticleProc Natl Acad Sci U S A · February 13, 2001
Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that pr ...
Full textLink to itemCite
Journal ArticleJ Mol Biol · February 2, 2001
Self-cleavage of the genomic and antigenomic ribozymes from hepatitis delta virus (HDV) requires divalent cation for optimal activity. Recently, the HDV genomic ribozyme has been shown to be active in NaCl in the absence of added divalent metal ion at low ...
Full textLink to itemCite
Journal ArticleBiochemistry · August 8, 2000
A minimal kinetic mechanism for a trans-acting ribozyme derived from the HDV antigenomic RNA self-cleaving element was established from steady-state, pre-steady-state, single-turnover, and binding kinetics. Rate constants for individual steps, including su ...
Full textLink to itemCite
Journal ArticleScience · October 1, 1999
Ribozymes use a number of the same catalytic strategies as protein enzymes. However, general base catalysis by a ribozyme has not been demonstrated. In the hepatitis delta virus antigenomic ribozyme, imidazole buffer rescued activity of a mutant with a cyt ...
Full textLink to itemCite
Journal ArticleRNA · September 1999
The natural substrate cleaved by the hepatitis delta virus (HDV) ribozyme contains a 3',5'-phosphodiester linkage at the cleavage site; however, a 2',5'-linked ribose-phosphate backbone can also be cleaved by both trans-acting and self-cleaving forms of th ...
Full textLink to itemCite
Journal ArticleProc Natl Acad Sci U S A · September 20, 2016
Topoisomerase 3β (Top3β) can associate with the mediator protein Tudor domain-containing protein 3 (TDRD3) to participate in two gene expression processes of transcription and translation. Despite the apparent importance of TDRD3 in binding with Top3β and ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · May 2008
The ribozyme self-cleavage site in the antigenomic sequence of hepatitis delta virus (HDV) RNA is 33-nt downstream of the poly(A) site for the delta antigen mRNA. An HDV antigenomic ribozyme precursor RNA that included the upstream poly(A) processing site ...
Full textLink to itemCite
Journal ArticleJ Am Chem Soc · December 5, 2007
The glmS ribozyme is a catalytic riboswitch that is activated for endonucleolytic cleavage by the coenzyme glucosamine-6-phosphate. Using kinetic assays and X-ray crystallography, we identify an active-site mutation of a conserved guanine that abolishes ca ...
Full textLink to itemCite
Journal ArticleJ Mol Biol · October 12, 2007
The glmS ribozyme is a catalytic RNA that self-cleaves at its 5'-end in the presence of glucosamine 6-phosphate (GlcN6P). We present structures of the glmS ribozyme from Thermoanaerobacter tengcongensis that are bound with the cofactor GlcN6P or the inhibi ...
Full textLink to itemCite
Journal ArticleBiochemistry · May 1, 2007
The two ribozymes of hepatitis delta virus (HDV) cleave faster in divalent metal ions than in monovalent cations, and a variety of divalent metal ions can act as catalysts in supporting these higher rates. Although the ribozymes are closely related in sequ ...
Full textLink to itemCite
Journal ArticleBiochemistry · September 26, 2006
Activity of the two ribozymes from hepatitis delta virus in monovalent salts was examined and compared to activity in Mg2+. Both ribozymes self-cleaved in high concentrations of monovalent cations, and an active site cytosine was required for cleavage acti ...
Full textLink to itemCite
Journal ArticleRNA · July 2006
In the ribozyme from the hepatitis delta virus (HDV) genomic strand RNA, a cytosine side chain is proposed to facilitate proton transfer in the transition state of the reaction and, thus, act as a general acid-base catalyst. Mutation of this active-site cy ...
Full textLink to itemCite
Journal ArticleCurr Top Microbiol Immunol · 2006
The self-cleaving RNA sequences, or ribozymes, in the genomic and antigenomic strands of hepatitis delta virus (HDV) RNA fold into structures that are similar to each other but distinct from those of small ribozymes associated with the RNA replicons that i ...
Full textLink to itemCite
Journal ArticleRNA · December 2005
The recently described glmS ribozyme is a self-cleaving RNA sequence found in the 5' noncoding region of the transcript of the gene for glucosamine-6-phosphate (GlcN6P) synthase in many Gram-positive bacteria. This ribozyme is associated with the GlcN6P ri ...
Full textLink to itemCite
Journal ArticleAnnu Rev Biochem · 2002
The hepatitis delta virus (HDV) ribozymes are self-cleaving RNA sequences critical to the replication of a small RNA genome. A recently determined crystal structure together with biochemical and biophysical studies provides new insight into the possible ca ...
Full textLink to itemCite
Journal ArticleCell Mol Life Sci · January 2002
In the hepatitis delta virus, ribozymes are encoded in both the genomic strand RNA and its complement, the antigenomic strand. The two ribozymes are similar in sequence and structure, are most active in the presence of divalent cation and catalyze RNA clea ...
Full textLink to itemCite
Journal ArticleEMBO J · September 3, 2001
Hepatitis delta virus (HDV) ribozymes employ multiple catalytic strategies to achieve overall rate enhancement of RNA cleavage. These strategies include general acid-base catalysis by a cytosine side chain and involvement of divalent metal ions. Here we us ...
Full textLink to itemCite
Journal ArticleProc Natl Acad Sci U S A · February 13, 2001
Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that pr ...
Full textLink to itemCite
Journal ArticleJ Mol Biol · February 2, 2001
Self-cleavage of the genomic and antigenomic ribozymes from hepatitis delta virus (HDV) requires divalent cation for optimal activity. Recently, the HDV genomic ribozyme has been shown to be active in NaCl in the absence of added divalent metal ion at low ...
Full textLink to itemCite
Journal ArticleBiochemistry · August 8, 2000
A minimal kinetic mechanism for a trans-acting ribozyme derived from the HDV antigenomic RNA self-cleaving element was established from steady-state, pre-steady-state, single-turnover, and binding kinetics. Rate constants for individual steps, including su ...
Full textLink to itemCite
Journal ArticleScience · October 1, 1999
Ribozymes use a number of the same catalytic strategies as protein enzymes. However, general base catalysis by a ribozyme has not been demonstrated. In the hepatitis delta virus antigenomic ribozyme, imidazole buffer rescued activity of a mutant with a cyt ...
Full textLink to itemCite
Journal ArticleRNA · September 1999
The natural substrate cleaved by the hepatitis delta virus (HDV) ribozyme contains a 3',5'-phosphodiester linkage at the cleavage site; however, a 2',5'-linked ribose-phosphate backbone can also be cleaved by both trans-acting and self-cleaving forms of th ...
Full textLink to itemCite
Journal ArticleRNA · June 1999
The crystal structure of a genomic hepatitis delta virus (HDV) ribozyme 3' cleavage product predicts the existence of a 2 bp duplex, P1.1, that had not been previously identified in the HDV ribozymes. P1.1 consists of two canonical C-G base pairs stacked b ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · February 1, 1999
In the ribozyme of hepatitis delta virus antigenomic RNA, two short duplexes, P2 and P2a, stabilize the active self-cleaving structure. However, P2a also promotes kinetic trapping of non-native structures. A bulged adenosine (A14) separates P2a and P2; thi ...
Full textLink to itemCite
Journal ArticleJ Mol Biol · June 5, 1998
The antigenomic RNA of hepatitis delta virus (HDV) can form a short duplex, P2a, in which a four-nucleotide sequence within the self-cleaving domain pairs with a sequence just outside the previously defined 3'-boundary of the ribozyme. Both sequences that ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · October 15, 1997
The two ribozymes found in hepatitis delta virus RNA form related but non-identical secondary structures and display similar cleavage properties in vitro. Three of the non-duplex elements hypothesized to contribute nucleotides to the catalytic core vary sl ...
Full textLink to itemCite
Journal ArticleEur J Biochem · August 1, 1997
Hepatitis delta virus (HDV) is a small single-stranded RNA satellite of hepatitis B virus. Although it is a human pathogen, it shares a number of features with a subset of the small plant satellite RNA viruses, including self-cleaving sequences in the geno ...
Full textLink to itemCite
Journal ArticleBiotechnology Advances · January 1, 1997
Nucleic acid molecule having an RNA substrate cleaving enzymatic activity which cleaves a separate RNA substrate at a cleavage site. The nucleic acid molecule includes an RNA substrate binding portion which base pairs with the RNA substrate only 3′ of the ...
Full textCite
Journal ArticleBiotechnology Advances · January 1, 1997
RNA enzymes or ribozymes can act as endoribonucleases, catalyzing the cleavage of RNA molecules with a sequence specificity of cleavage greater than that of known ribonucleases and approaching that of the DNA restriction endonucleases, thus serving as RNA ...
Full textCite
Journal ArticleJ Biol Chem · October 18, 1996
A circularly permuted self-splicing group I intron from Anabaena was used to generate covalently closed circular trans-acting ribozymes in Escherichia coli. The RNA component of Bacillus subtilis RNaseP and an artificial trans-acting hepatitis delta virus ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · October 1, 1996
Linear TAR RNA has previously been used as a decoy to inhibit HIV-1 transcription in vitro and HIV-1 replication in vivo. A 48 nucleotide circular RNA containing the stem, bulge and loop of the HIV-1 TAR element was synthesized using the self-splicing acti ...
Full textLink to itemCite
Journal ArticleBiochemistry · September 3, 1996
Self-cleaving sequences or ribozymes from the hepatitis delta virus (HDV) genomic RNA and its complement form similar secondary structures that suggest a core region and potential active site composed of "single-stranded" sequences. However, there is littl ...
Full textLink to itemCite
Journal ArticleRNA · June 1996
Correct ligation of exons in pre-mRNA splicing requires splice site juxtaposition (splice site pairing), usually involving a 5' splice site and a downstream 3' splice site. Splicing of a 5' splice site to an upstream 3' splice site, however, is predicted t ...
Link to itemCite
Journal ArticleNucleic Acids Res · April 1, 1996
The secondary structures proposed for the cis-acting hepatitis delta virus (HDV) ribozymes contain four duplex regions, three sequences joining the duplexes and two hairpin loops. The core and active site of the ribozyme could be formed by portions of the ...
Full textLink to itemCite
Journal ArticleSAAS Bull Biochem Biotechnol · 1996
An Anabaena group I intron was circularly permuted at loop 5, loop 6 and loop 8, and tested for self-splicing activity. Precursor RNAs from these constructs spliced efficiently and produced circular exons in vitro. Using group I permuted-intron-exon sequen ...
Link to itemCite
Journal ArticleRNA · December 1995
A non-Watson-Crick G.G interaction within the core region of the hepatitis delta virus (HDV) antigenomic ribozyme is required for optimal rates of self-cleavage activity. Base substitutions for either one or both G's revealed that full activity was obtaine ...
Link to itemCite
Journal ArticleNucleic Acids Symp Ser · 1995
Circular exon sequences can be generated by splicing permuted intron-exon (PIE) sequences. The Anabaena pre-tRNA group I self-splicing PIE sequence was modified to generate circular forms of the HIV-TAR and the high affinity region of the HIV-RRE (RBE). RN ...
Link to itemCite
Journal ArticleNucleic Acids Symp Ser · 1995
A circular form of Bacillus subtilis ribonuclease P RNA (C-P RNA) was generated in vitro by splicing permuted intron-exon (PIE) sequences containing the P RNA sequence. Steady-state cleavage of pre-tRNA(Asp) catalyzed by circular P RNA is slightly faster t ...
Link to itemCite
Journal ArticleNucleic Acids Symp Ser · 1995
Circular exon sequences can be generated by splicing permuted intron-exon (PIE) sequences. The Anabaena pre-tRNA group I self-splicing PIE sequence was modified to generate circular forms of the HIV-TAR and the high affinity region of the HIV-RRE (RBE). RN ...
Link to itemCite
Journal ArticleTrends Biochem Sci · June 1994
Hepatitis delta virus (HDV) contains two self-cleaving RNA sequences (ribozymes) that may naturally function as such in human cells. A pseudo-knot-containing structural motif, which is distinct from the well-characterized secondary structures of self-cleav ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · September 11, 1993
A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · August 25, 1993
Three models for the secondary structure of the hepatitis delta virus (HDV) antigenomic self-cleaving RNA element were tested by site-directed mutagenesis. Two models in which bases 5' to the cleavage site are paired with sequence at the 3' end of the elem ...
Full textLink to itemCite
Journal ArticleProg Clin Biol Res · 1993
Specific features of a model for the secondary structure of the self-cleaving RNA sequences (ribozymes) of hepatitis delta virus were rigorously tested. Using a self-cleaving form of the antigenomic sequence, mutations were made in the 5' and 3' sequences ...
Link to itemCite
Journal ArticleBiochemistry · December 1, 1992
A model for the secondary structure of the self-cleaving RNA from hepatitis delta virus was tested. Specific base changes were introduced in each of four regions with the potential for base-pairing (stems I-IV), and for each variant sequence, a rate consta ...
Full textLink to itemCite
Journal ArticleJ Mol Biol · November 20, 1992
The length of the small subunit ribosomal DNA (SSU rDNA) differs significantly among individuals from natural populations of the ascomycetous lichen complex Cladonia chlorophaea. The sequence of the 3' region of the SSU rDNA from two individuals, chosen to ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · October 25, 1992
Circularly permuted group I intron precursor RNAs, containing end-to-end fused exons which interrupt half-intron sequences, were generated and tested for self-splicing activity. An autocatalytic RNA can form when the primary order of essential intron seque ...
Full textLink to itemCite
Journal ArticleBiochemistry · January 14, 1992
A self-cleaving RNA sequence from hepatitis delta virus was modified to produce a ribozyme capable of catalyzing the cleavage of RNA in an intermolecular (trans) reaction. The delta-derived ribozyme cleaved substrate RNA at a specific site, and the sequenc ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · October 11, 1991
The two sequences that define the self-cleaving elements from the genomic and antigenomic RNA of hepatitis delta virus were folded into secondary structures with similar features. Evidence in support of the two models was obtained from limited ribonuclease ...
Full textLink to itemCite
Journal ArticleScience · April 19, 1991
For self-splicing of Tetrahymena ribosomal RNA precursor, guanosine binding is required for 5' splice-site cleavage and exon ligation. Whether these two reactions use the same or different guanosine-binding sites has been debated. A double mutation in a pr ...
Full textLink to itemCite
Journal ArticleNature · April 4, 1991
Hepatitis delta virus genomic and antigenomic RNAs contain a self-cleavage site hypothesized to function in processing the viral RNA during replication. Self-cleavage requires only a divalent cation and is mediated at the genomic site by a sequence of less ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · December 11, 1990
The sequence requirements for self-cleavage of hepatitis delta virus genomic RNA were examined using precursor RNAs which were labeled at either the 5' or 3' ends and progressively deleted from the unlabeled end. In the presence of 50% formamide, which enh ...
Full textLink to itemCite
Journal ArticleBiochemistry · September 4, 1990
Self-cleavage of a polyribonucleotide containing an autocleaving sequence from the genomic strand of hepatitis delta virus was enhanced by conditions that destabilized RNA structure. Self-cleavage of the transcripts used in this study required Mg2+ (or ano ...
Full textLink to itemCite
Journal ArticleScience · March 18, 1988
A catalytic RNA (ribozyme) derived from an intervening sequence (IVS) RNA of Tetrahymena thermophila will catalyze an RNA polymerization reaction in which pentacytidylic acid (C5) is extended by the successive addition of mononucleotides derived from a gua ...
Full textLink to itemCite
Journal ArticleCell · September 11, 1987
Circularization and reverse circularization of the Tetrahymena thermophila rRNA intervening sequence resemble the first and second steps in splicing, respectively. However, site-specific base substitutions show that different nucleotides are involved in se ...
Full textLink to itemCite
Journal ArticleNature · December 4, 1986
A shortened form of the Tetrahymena self-splicing ribosomal RNA intervening sequence acts as an endoribonuclease, catalysing the cleavage of large RNA molecules by a mechanism involving guanosine transfer. The sequence specificity approaches that of the DN ...
Full textLink to itemCite
Journal ArticleCell · October 24, 1986
The specificity of reactions catalyzed by the Tetrahymena pre-rRNA intervening sequence (IVS) was studied using site-specific mutagenesis. Two sequences required for 5' splice-site selection during self-splicing were defined. Single-base changes in either ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · December 9, 1985
The sequence of the cloned Tetrahymena ribosomal RNA intervening sequence (IVS) was altered at the site to which circularization normally occurs. The alterations caused circularization to shift to other sites, usually a nearby position which followed three ...
Full textLink to itemCite
Journal ArticleJ Mol Biol · December 15, 1984
Eukaryotic type 1 DNA topoisomerases break single-stranded DNA at specific sites. A preferred site for rat liver topoisomerase breakage in single-stranded phi X174 DNA was located within a region of the DNA with the potential for duplex formation. To inves ...
Full textLink to itemCite
Journal ArticleBiochim Biophys Acta · July 18, 1984
Properties of strand breakage in duplex and single-stranded DNA by the wheat germ type 1 DNA topoisomerase were investigated. Strand breakage in duplex DNA is dependent upon the use of denaturing conditions to inactivate the enzyme and terminate the reacti ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · April 11, 1984
The site specificities of the type 1 DNA topoisomerases (topo 1) from rat liver and wheat germ were investigated. The nucleotide sequence at break sites on duplex SV40 DNA were determined for 245 wheat germ topo 1 sites and 223 rat liver topo 1 sites over ...
Full textLink to itemCite
Journal ArticleProc Natl Acad Sci U S A · May 1981
Circular single strands of bacteriophage phi X174 DNA are broken by rat liver DNA nicking-closing enzyme (type 1 topoisomerase) in low salt (50 mM KCl) at 37 degrees C, generating linear strands containing covalently bound enzyme [Been, M. D. & Champoux, J ...
Full textLink to itemCite
Journal ArticleNucleic Acids Res · December 20, 1980
The DNA nicking-closing enzyme (type I topoisomerase) from rat liver nuclei breaks single-stranded DNA. The broken strand contains a 5'-hydroxyl and tightly bound protein. The stability of this protein-DNA complex to high salt, alkali and detergent suggest ...
Full textLink to itemCite