Scholars@Duke
Michael Douglas Been

Michael Douglas Been

Professor Emeritus of Biochemistry
Biochemistry
Duke Box 3711, Durham, NC 27710
151-B Nanaline H Duke, Durham, NC 27708

Selected Publications

DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3.

Journal Article Proc 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 text Link to item Cite

The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme.

Journal Article Nucleic 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 text Link to item Cite

Essential role of an active-site guanine in glmS ribozyme catalysis.

Journal Article J 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 text Link to item Cite

Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme.

Journal Article J 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 text Link to item Cite

A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes.

Journal Article Biochemistry · 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 text Link to item Cite

HDV ribozyme activity in monovalent cations.

Journal Article Biochemistry · 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 text Link to item Cite

Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme.

Journal Article RNA · 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 text Link to item Cite

HDV ribozymes.

Journal Article Curr 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 text Link to item Cite

A pseudoknot in the 3' non-core region of the glmS ribozyme enhances self-cleavage activity.

Journal Article RNA · 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 text Link to item Cite

Catalytic strategies of the hepatitis delta virus ribozymes.

Journal Article Annu 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 text Link to item Cite

Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus.

Journal Article Cell 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 text Link to item Cite

Energetic contribution of non-essential 5' sequence to catalysis in a hepatitis delta virus ribozyme.

Journal Article EMBO 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 text Link to item Cite

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage.

Journal Article Proc 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 text Link to item Cite

A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion.

Journal Article J 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 text Link to item Cite

Kinetic scheme for intermolecular RNA cleavage by a ribozyme derived from hepatitis delta virus RNA.

Journal Article Biochemistry · 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 text Link to item Cite

Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme.

Journal Article Science · 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 text Link to item Cite

Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement.

Journal Article RNA · 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 text Link to item Cite

A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes.

Journal Article RNA · 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 text Link to item Cite

A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduceskinetic trapping of inactive conformations.

Journal Article Nucleic 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 text Link to item Cite

A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation.

Journal Article J 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 text Link to item Cite

Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus.

Journal Article Nucleic 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 text Link to item Cite

Self-cleaving ribozymes of hepatitis delta virus RNA.

Journal Article Eur 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 text Link to item Cite

Enzymatic RNA molecules

Journal Article Biotechnology 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 text Cite

RNA ribozyme polymerases, dephosphorylases, restriction endoribonucleases and methods

Journal Article Biotechnology 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 text Cite

Circular ribozymes generated in Escherichia coli using group I self-splicing permuted intron-exon sequences.

Journal Article J 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 text Link to item Cite

A small circular TAR RNA decoy specifically inhibits Tat-activated HIV-1 transcription.

Journal Article Nucleic 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 text Link to item Cite

Hepatitis delta virus ribozymes fold to generate a solvent-inaccessible core with essential nucleotides near the cleavage site phosphate.

Journal Article Biochemistry · 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 text Link to item Cite

Exon circularization in mammalian nuclear extracts.

Journal Article RNA · 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 item Cite

Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage.

Journal Article Nucleic 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 text Link to item Cite

Circularizing ribozymes and decoy-competitors by autocatalytic splicing in vitro and in vivo.

Journal Article SAAS 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 item Cite

Optimal self-cleavage activity of the hepatitis delta virus RNA is dependent on a homopurine base pair in the ribozyme core.

Journal Article RNA · 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 item Cite

Generation of nuclease resistant circular RNA decoys for HIV-Tat and HIV-Rev by autocatalytic splicing.

Journal Article Nucleic 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 item Cite

Generation and characterization of circular Bacillus subtilis RNase P RNA; activation by RNase P protein.

Journal Article Nucleic 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 item Cite

Generation of nuclease resistant circular RNA decoys for HIV-Tat and HIV-Rev by autocatalytic splicing.

Journal Article Nucleic 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 item Cite

Cis- and trans-acting ribozymes from a human pathogen, hepatitis delta virus.

Journal Article Trends 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 text Link to item Cite

A circular trans-acting hepatitis delta virus ribozyme.

Journal Article Nucleic 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 text Link to item Cite

Assessment of disparate structural features in three models of the hepatitis delta virus ribozyme.

Journal Article Nucleic 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 text Link to item Cite

Experimental evidence for the secondary structure of the hepatitis delta virus ribozyme.

Journal Article Prog 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 item Cite

Secondary structure of the self-cleaving RNA of hepatitis delta virus: applications to catalytic RNA design.

Journal Article Biochemistry · 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 text Link to item Cite

Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus.

Journal Article J 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 text Link to item Cite

Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons.

Journal Article Nucleic 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 text Link to item Cite

Cleavage of oligoribonucleotides by a ribozyme derived from the hepatitis delta virus RNA sequence.

Journal Article Biochemistry · 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 text Link to item Cite

Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures.

Journal Article Nucleic 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 text Link to item Cite

The self-cleaving domain from the genomic RNA of hepatitis delta virus: Sequence requirements and the effects of denaturant

Journal Article Nucleic Acids Research · April 25, 1991 The publishers wish to apologize for an error which occurred during printing of this article. Some text was inadvertantly omitted from the legend to figure 1 during translation. The correct legend is published below. © 1991 Oxford University Press. ... Full text Cite

Group I intron self-splicing with adenosine: evidence for a single nucleoside-binding site.

Journal Article Science · 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 text Link to item Cite

A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA.

Journal Article Nature · 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 text Link to item Cite

The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant.

Journal Article Nucleic 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 text Link to item Cite

Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions.

Journal Article Biochemistry · 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 text Link to item Cite

RNA as an RNA polymerase: net elongation of an RNA primer catalyzed by the Tetrahymena ribozyme.

Journal Article Science · 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 text Link to item Cite

Selection of circularization sites in a group I IVS RNA requires multiple alignments of an internal template-like sequence.

Journal Article Cell · 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 text Link to item Cite

The Tetrahymena ribozyme acts like an RNA restriction endonuclease.

Journal Article Nature · 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 text Link to item Cite

One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity.

Journal Article Cell · 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 text Link to item Cite

Sites of circularization of the Tetrahymena rRNA IVS are determined by sequence and influenced by position and secondary structure.

Journal Article Nucleic 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 text Link to item Cite

Breakage of single-stranded DNA by eukaryotic type 1 topoisomerase occurs only at regions with the potential for base-pairing.

Journal Article J 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 text Link to item Cite

DNA strand breakage by wheat germ type 1 topoisomerase.

Journal Article Biochim 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 text Link to item Cite

Nucleotide sequence preference at rat liver and wheat germ type 1 DNA topoisomerase breakage sites in duplex SV40 DNA.

Journal Article Nucleic 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 text Link to item Cite

DNA breakage and closure by rat liver type 1 topoisomerase: separation of the half-reactions by using a single-stranded DNA substrate.

Journal Article Proc 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 text Link to item Cite

Breakage of single-stranded DNA by rat liver nicking-closing enzyme with the formation of a DNA-enzyme complex.

Journal Article Nucleic 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 text Link to item Cite