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Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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2
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Zhou W, Zhang Y, Huang PJJ, Ding J, Liu J. A DNAzyme requiring two different metal ions at two distinct sites. Nucleic Acids Res 2015; 44:354-63. [PMID: 26657636 PMCID: PMC4705669 DOI: 10.1093/nar/gkv1346] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na+ and a trivalent lanthanide (e.g. Ce3+), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na+-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb3+ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na+-binding. The Na+ dissociation constants of Ce13d measured from the cleavage activity assay, Tb3+ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce3+ might be replaced by G23 in NaA43. Ce3+ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G23 competes favorably with low concentration Ce3+ (below 1 μM). The G23-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes.
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Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yupei Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Juewen Liu
- School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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3
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Qi X, Xia T. Structure, dynamics, and mechanism of the lead-dependent ribozyme. Biomol Concepts 2015; 2:305-14. [PMID: 25962038 DOI: 10.1515/bmc.2011.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/06/2011] [Indexed: 12/24/2022] Open
Abstract
Leadzyme is a small catalytic RNA that was identified by in vitro selection for Pb2+-dependent cleavage from a tRNA library. Leadzyme employs a unique two-step Pb2+-specific mechanism to cleave within its active site. NMR and crystal structures of the active site revealed different folding patterns, but neither features the in-line alignment for attack by the 2'-OH nucleophilic group. These experimentally determined structures most likely represent ground states and are catalytically inactive. There are significant dynamics of the active site and the motif samples multiple conformations at the ground states. Various metal ion binding sites have been identified, including one that may be occupied by a catalytic Pb2+. Based on functional group analysis, a computational model of the transition state has been proposed. This model features a unique base triple that is consistent with sequence and functional group requirements for catalysis. This structure is likely only populated transiently, but imposing appropriate conformational constraints may significantly stabilize this state thereby promoting catalysis. Other ions may inhibit the cleavage by competing for the Pb2+ binding site, or by stabilizing the ground state thereby suppressing its transition to the catalytically active conformation. Some rare earth ions can enhance the reaction via an unknown mechanism. Because of its unique chemistry and dynamic behavior, leadzyme can continue to serve as an excellent model system for teaching us RNA biology and chemistry.
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4
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Abstract
Lanthanides represent a group of very important but challenging analytes for biosensor development. These 15 elements are very similar in their chemical properties. So far, limited success has been realized using the rational ligand design approach. My laboratory has successfully accomplished the task of carrying out combinatorial selection to isolate lanthanide-dependent RNA-cleaving DNAzymes. We report two new DNAzymes, each discovered in a different selection condition and both are highly specific to lanthanides. When both DNAzymes are used together, it is possible to identify the last few heavy lanthanides. Upon introducing a phosphorothioate modification, one of the abovementioned DNAzymes becomes highly active with many toxic heavy metals. With the selection of more DNAzymes with different activity patterns cross the lanthanide series, a sensor array might be produced for identifying each ion. This article is a minireview of the current developments on this topic and some of the historical aspects. It reflects the main content of the Fred Beamish Award presentation delivered at the 2014 Canadian Society for Chemistry Conference in Vancouver. Future directions in this area are also discussed.
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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5
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Huang PJJ, Vazin M, Matuszek Ż, Liu J. A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect. Nucleic Acids Res 2014; 43:461-9. [PMID: 25488814 PMCID: PMC4288186 DOI: 10.1093/nar/gku1296] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In vitro selection of RNA-cleaving DNAzymes was performed using three heavy lanthanide ions (Ln3+): Ho3+, Er3+ and Tm3+. The resulting sequences were aligned together and about half of the library contained a new family of DNAzyme. These DNAzymes have a simple loop structure, and they are active only with the seven heavy Ln3+. Among the tested non-lanthanide ions, only Y3+ induced cleavage and even Pb2+ failed to cleave, suggesting a very high specificity. A representative DNAzyme, Tm7, has a sigmoidal metal binding curve with a Hill coefficient of 3, indicating that three metal ions are involved in the catalytic step. Its pH-rate profile has a slope of 1, suggesting a single deprotonation step is involved in the rate-limiting step. Tm7 has a cleavage rate of 1.6 min−1 at pH 7.8 with 10 μM Er3+. Phosphorothioate substitution at the cleavage junction completely inhibits the activity, which cannot be rescued by Cd2+ alone, or by a mixture of Er3+ and Cd2+, suggesting that two interacting metal ions are involved in direct bonding to both non-bridging oxygen atoms. A new model involving three lanthanide ions is proposed based on this study. A biosensor is engineered using Tm7 to detect Dy3+ down to 14 nM.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Żaneta Matuszek
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
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6
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Lin WTD, Huang PJJ, Pautler R, Liu J. The group trend of lanthanides binding to DNA and DNAzymes with a complex but symmetric pattern. Chem Commun (Camb) 2014; 50:11859-62. [DOI: 10.1039/c4cc05551a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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7
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Huang PJJ, Lin J, Cao J, Vazin M, Liu J. Ultrasensitive DNAzyme Beacon for Lanthanides and Metal Speciation. Anal Chem 2014; 86:1816-21. [PMID: 24383540 DOI: 10.1021/ac403762s] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Po-Jung Jimmy Huang
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jenny Lin
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jing Cao
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Mahsa Vazin
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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8
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Javadi-Zarnaghi F, Höbartner C. Lanthanide cofactors accelerate DNA-catalyzed synthesis of branched RNA. J Am Chem Soc 2013; 135:12839-48. [PMID: 23895365 DOI: 10.1021/ja406162z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most deoxyribozymes (DNA catalysts) require metal ions as cofactors for catalytic activity, with Mg(2+), Mn(2+), and Zn(2+) being the most represented activators. Trivalent transition-metal ions have been less frequently considered. Rare earth ions offer attractive properties for studying metal ion binding by biochemical and spectroscopic methods. Here we report the effect of lanthanide cofactors, in particular terbium (Tb(3+)), for DNA-catalyzed synthesis of 2',5'-branched RNA. We found up to 10(4)-fold increased ligation rates for the 9F7 deoxribozyme using 100 μM Tb(3+) and 7 mM Mg(2+), compared to performing the reaction with 7 mM Mg(2+) alone. Combinatorial mutation interference analysis (CoMA) was used to identify nucleotides in the catalytic region of 9F7 that are essential for ligation activity with different metal ion combinations. A minimized version of the DNA enzyme sustained high levels of Tb(3+)-assisted activity. Sensitized luminescence of Tb(3+) bound to DNA in combination with DMS probing and DNase I footprinting results supported the CoMA data. The accelerating effect of Tb(3+) was confirmed for related RNA-ligating deoxyribozymes, pointing toward favorable activation of internal 2'-OH nucleophiles. The results of this study offer fundamental insights into nucleotide requirements for DNA-catalyzed RNA ligation and will be beneficial for practical applications that utilize 2',5'-branched RNA.
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Affiliation(s)
- Fatemeh Javadi-Zarnaghi
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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9
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Giel-Pietraszuk M, Barciszewski J. Hydrostatic and osmotic pressure study of the RNA hydration. Mol Biol Rep 2012; 39:6309-18. [PMID: 22314910 PMCID: PMC3310992 DOI: 10.1007/s11033-012-1452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 01/23/2012] [Indexed: 11/17/2022]
Abstract
The tertiary structure of nucleic acids results from an equilibrium between electrostatic interactions of phosphates, stacking interactions of bases, hydrogen bonds between polar atoms and water molecules. Water interactions with ribonucleic acid play a key role in its structure formation, stabilization and dynamics. We used high hydrostatic pressure and osmotic pressure to analyze changes in RNA hydration. We analyzed the lead catalyzed hydrolysis of tRNAPhe from S. cerevisiae as well as hydrolytic activity of leadzyme. Pb(II) induced hydrolysis of the single phosphodiester bond in tRNAPhe is accompanied by release of 98 water molecules, while other molecule, leadzyme releases 86.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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10
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Hou AX, Xue Z, Liu Y, Qu SS. Microcalorimetric study of the action of Yb3+ ion on the growth of Staphylococcus aureus. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20030210909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Kadakkuzha BM, Zhao L, Xia T. Conformational distribution and ultrafast base dynamics of leadzyme. Biochemistry 2009; 48:3807-9. [PMID: 19301929 DOI: 10.1021/bi900256q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The dynamic nature of ribozymes represents a significant challenge in elucidating their structure-dynamics-function relationship. Here, using femtosecond time-resolved spectroscopy and other biophysical tools, we demonstrate that the active site of leadzyme does not have a unique structure, but rather samples an ensemble of conformations that undergo picosecond structural changes. Various base modifications have a profound context-dependent impact on the catalysis.
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Affiliation(s)
- Beena M Kadakkuzha
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75083-0688, USA
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12
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13
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Knobloch B, Suliga D, Okruszek A, Sigel RKO. Acid-base and metal-ion binding properties of the RNA dinucleotide uridylyl-(5'-->3')-[5']uridylate (pUpU3-). Chemistry 2006; 11:4163-70. [PMID: 15861476 DOI: 10.1002/chem.200500013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It is well known that Mg2+ and other divalent metal ions bind to the phosphate groups of nucleic acids. Subtle differences in the coordination properties of these metal ions to RNA, especially to ribozymes, determine whether they either promote or inhibit catalytic activity. The ability of metal ions to coordinate simultaneously with two neighboring phosphate groups is important for ribozyme structure and activity. However, such an interaction has not yet been quantified. Here, we have performed potentiometric pH titrations to determine the acidity constants of the protonated dinucleotide H2(pUpU)-, as well as the binding properties of pUpU3- towards Mg2+, Mn2+, Cd2+, Zn2+, and Pb2+. Whereas Mg2+, Mn2+, and Cd2+ only bind to the more basic 5'-terminal phosphate group, Pb2+, and to a certain extent also Zn2+, show a remarkably enhanced stability of the [M(pUpU)]- complex. This can be attributed to the formation of a macrochelate by bridging the two phosphate groups within this dinucleotide by these metal ions. Such a macrochelate is also possible in an oligonucleotide, because the basic structural units are the same, despite the difference in charge. The formation degrees of the macrochelated species of [Zn(pUpU)]- and [Pb(pUpU)]- amount to around 25 and 90 %, respectively. These findings are important in the context of ribozyme and DNAzyme catalysis, and explain, for example, why the leadzyme could be selected in the first place, and why this artificial ribozyme is inhibited by other divalent metal ions, such as Mg2+.
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Affiliation(s)
- Bernd Knobloch
- Institute of Inorganic Chemistry, University of Zürich, Switzerland
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14
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Paxon TL, Brown TS, Lin HYN, Brancato SJ, Roddy ES, Bevilacqua PC, Ewing AG. Continuous monitoring of enzyme reactions on a microchip: application to catalytic RNA self-cleavage. Anal Chem 2006; 76:6921-7. [PMID: 15571342 DOI: 10.1021/ac0491758] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic analysis of RNA enzymes, or ribozymes, typically involves the tedious process of collecting and quenching reaction time points and then fractionating by polyacrylamide gel electrophoresis (PAGE). As a way to automate and simplify this process, continuous analysis of a ribozyme reaction is demonstrated here using completely automated capillary sample introduction onto a microfabricated device with laser-induced fluorescence detection. The method of injection is extremely reproducible thereby standardizing data analysis. A 30-nucleotide ribozyme model, the self-cleaving lead-dependent ribozyme, or "leadzyme", which cleaves into a 24-mer and a 6-mer in the presence of Pb(2+), was end-labeled with fluorescein (FAM) and used to demonstrate the potential of this technique. After manually initiating the cleavage reaction by Pb(2+) addition, reaction samples were automatically injected directly into the parallel separation lanes of the chip via a capillary at predetermined time intervals, thus eliminating the need for additional sample-handling steps. The FAM-labeled leadzyme starting material and products were monitored for 60 min in order to ascertain kinetic information. The effect of lead acetate concentration on cleavage rates was also studied, and the results are in agreement with rates determined by conventional hand-mixing/PAGE analysis. This work demonstrates, through the use of a simple ribozyme model, the potential of this method to provide valuable kinetic information for other, more complex, biologically relevant RNA and protein enzymes.
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Affiliation(s)
- Tracy L Paxon
- Department of Chemistry and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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15
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Kawakami J, Wang ZM, Fujiki H, Izumi S, Sugimoto N. Introduction of Peptide Functions into DNA by Nucleic Acid Peptides, NAPs. CHEM LETT 2004. [DOI: 10.1246/cl.2004.1554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Affiliation(s)
- L David
- Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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17
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Abstract
A novel 24-residue peptide (L2-G), Ile-Arg-Met-Lys-Ile-Gly-Val-Met-Phe-Gly-Asn-Pro-Glu-Thr-Thr-Thr-Gly-Gly-Asn-Ala-Leu-Lys-Phe-Tyr, derived from RecA can discriminate a single-stranded DNA (ssDNA) from a double-stranded DNA (dsDNA) and a new developed support with this peptide recognizes not dsDNA but ssDNA. The 24-mer peptide with L2 and helix G amino acids of Escherichia coli RecA protein showed the ssDNA binding property with more than 1000 times affinity difference for the dsDNA. However, truncated 15-mer peptide showed no ssDNA binding activity. In the ssDNA binding, L2-G changed its conformation with the perturbation of an alpha-helix structure. The ssDNA binding and the DNA discrimination property of this peptide were due to almost all L2 and helix G amino acids, respectively. This result is useful to design synthetic peptides as functional materials for DNA recognition.
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Affiliation(s)
- N Sugimoto
- Department of Chemistry, Faculty of Science, and High Technology Research Center, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
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18
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Doherty EA, Doudna JA. Ribozyme structures and mechanisms. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:457-75. [PMID: 11441810 DOI: 10.1146/annurev.biophys.30.1.457] [Citation(s) in RCA: 156] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The past few years have seen exciting advances in understanding the structure and function of catalytic RNA. Crystal structures of several ribozymes have provided detailed insight into the folds of RNA molecules. Models of other biologically important RNAs have been constructed based on structural, phylogenetic, and biochemical data. However, many questions regarding the catalytic mechanisms of ribozymes remain. This review compares the structures and possible catalytic mechanisms of four small self-cleaving RNAs: the hammerhead, hairpin, hepatitis delta virus, and in vitro-selected lead-dependent ribozymes. The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron.
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Affiliation(s)
- E A Doherty
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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19
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Abstract
The past few years have seen exciting advances in understanding the structure and function of catalytic RNA. Crystal structures of several ribozymes have provided detailed insight into the folds of RNA molecules. Models of other biologically important RNAs have been constructed based on structural, phylogenetic, and biochemical data. However, many questions regarding the catalytic mechanisms of ribozymes remain. This review compares the structures and possible catalytic mechanisms of four small self-cleaving RNAs: the hammerhead, hairpin, hepatitis delta virus, and in vitro-selected lead-dependent ribozymes. The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron.
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Affiliation(s)
- E A Doherty
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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20
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Metzler DE, Metzler CM, Sauke DJ. Transferring Groups by Displacement Reactions. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Da Costa CP, Sigel H. Lead(II)-binding properties of the 5'-monophosphates of adenosine (AMP2-), inosine (IMP2-), and guanosine (GMP2-) in aqueous solution. Evidence for nucleobase-lead(II) interactions. Inorg Chem 2000; 39:5985-93. [PMID: 11151499 DOI: 10.1021/ic0007207] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stability constants of the 1:1 complexes formed between Pb2+ and the nucleosides (Ns), adenosine and guanosine, as well as between the nucleotides (NMP2-), AMP2-, IMP2-, and GMP2-, were determined by potentiometric pH titrations in aqueous solution (25 degrees C; I = 0.1 M, NaNO3). Based on previously established log KPb(R-PO3)Pb versus pKH(R-PO3)H straight-line plots (R-PO3(2-) = simple phosphate monoester or phosphonate ligands where R is a noninteracting site), it is shown that the Pb(IMP) and Pb(GMP) complexes are more stable than is expected on the basis of the basicity of the phosphate group of IMP2- and GMP2-. This means that macrochelates are formed, where the phosphate-coordinated Pb2+ also interacts with N7 of the nucleobase residue. In contrast, the stability of the Pb(AMP) complex is governed by the basicity of the AMP2- phosphate group. These results agree with the observations made for the Pb(Ns)2+ complexes: Pb(adenosine)2+ is very unstable in contrast to Pb(guanosine)2+, the stability of which is very similar to the one of Pb(cytidine)2+ studied previously. The stability constants of the Pb(Ns)2+ complexes also allowed an evaluation of the structure in solution of the monoprotonated Pb(H;NMP)+ complexes, the stabilities of which were also determined. We were able to show that the proton is located at the phosphate group and Pb2+ at the N7/(C6)O site of H(GMP)-; in the case of H(AMP)- Pb2+ is probably about equally distributed between the adenine residue and the monoprotonated phosphate group. On the basis of the stability constants of these complexes and their structures in solution, it is possible to provide a series which reflects the decreasing affinity for Pb2+ of nucleobase residues in single-stranded nucleic acids: guanine approximately equal to cytosine > (hypoxanthine) > adenine > uracil approximately equal to thymine. The Pb2+ affinity of the phosphodiester linkage, -PO3(-)-, is similar to the one of the adenine residue, but is expected to be more significant due to its larger abundance. The relevance of these results for lead-activated ribozymes is briefly discussed.
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Affiliation(s)
- C P Da Costa
- Institute of Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
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22
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Hosaka H, Hosono K, Kawai G, Takai K, Takaku H. Self-cleavage of p2Sp1 RNA with Mg2+ and non-ionic detergent (Brij 58). J Inorg Biochem 2000; 82:215-9. [PMID: 11132630 DOI: 10.1016/s0162-0134(00)00164-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The precursor of an RNA molecule from T4-infected E. coli cells (p2Sp1 RNA) has the capacity to cleave itself at specific positions [(UpA (139-140) and CpA (170-171)], within a putative loop and stem structure. This sequence-specific cleavage requires at least a monovalent cation and non-ionic detergents. We studied the self-cleavage reaction of an RNA fragment (GUUUCGUACAAAC) (R1) with the sequence corresponding to the p2Sp1 RNA in the presence of Mg2+ and non-ionic detergents. It requires Mg2+ and is aided by a non-ionic detergent, Brij 58. The cleavage reaction is time, temperature, and pH-dependent. The cleavage occurs at the phosphodiester bond between UpA and CpA on the RNA fragment (GUUUCGUACAAAC) (R1). Furthermore, the maximum of cleavage of R1 occurs at a very low Mg2+ concentration (< or = 5 mM).
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Affiliation(s)
- H Hosaka
- Department of Industrial Chemistry and High Technology Research Center, Chiba Institute of Technology, Narashino, Japan
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23
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Hosono K, Hosaka H, Kawai G, Takai K, Takaku H. The stem hairpin loop structure of p2Sp1 RNA is required for RNA-cleaving activity. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:374-82. [PMID: 10673038 DOI: 10.1016/s0167-4781(99)00215-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
We studied the hairpin-loop structure of an RNA fragment (GUUUCGUACAAAC) (R13) with the sequence corresponding to the self-cleavage domain in the precursor of an RNA molecule from bacteriophage T4-infected Escherichia coli cells (p2Sp1 RNA). In order to determine the influence of the hairpin-loop structure on these sequence-specific cleavage reactions, we have synthesized oligoribonucleotides containing hairpin-loop, double-helical stem-loop, and single-stranded RNA structures. The cleavage was affected by the hairpin-loop structure. Furthermore, the helix-stem, which retains the thermodynamically extrastable stem hairpin-loop structures, is also important for the cleavage activity. However, the thermodynamically extrastable helix-stem structure reduced the cleavage activity of the adjacent UA and CA sequences at the helix-stem site. For the cleavage reactions of the RNA cleavage products, the R6 (ACAAAC), R7 (GUUUCGU), and R9 (GUUUCGUAC) mers from the parent RNA, R13 (GUUUCGUACAAAC), a very slight amount of cleavage product (2%) from the RNA 9 was observed, but no reaction occurred for the R6 and R7. We also describe the influences of the sequences (UA and CA) on the cleavage activity.
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Affiliation(s)
- K Hosono
- Department of Industrial Chemistry and High Technology Research Center, Chiba Institute of Technology, Narashino, Japan
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Baldwin GS, Sessions RB, Erskine SG, Halford SE. DNA cleavage by the EcoRV restriction endonuclease: roles of divalent metal ions in specificity and catalysis. J Mol Biol 1999; 288:87-103. [PMID: 10329128 DOI: 10.1006/jmbi.1999.2672] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The roles of divalent metal ions in DNA cleavage by the EcoRV endonuclease were studied by using Co2+ or Mn2+ as substitutes for the natural cofactor Mg2+. In steady-state experiments with a 12 bp oligonucleotide substrate, Co2+ yielded a similar turnover rate to that with Mg2+, but Mn2+ gave a slower rate. Single turnovers of EcoRV on this substrate were analysed by stopped-flow and quench-flow methods, to determine the rates for the formation of the ternary enzyme-DNA-metal complex, the hydrolysis of the phosphodiester bonds and the dissociation of the cleaved DNA. With Co2+, all three steps had similar rates to those with Mg2+. In contrast, Mn2+ gave a faster rate for phosphodiester hydrolysis than either Mg2+ or Co2+, but a slower rate for product dissociation, thus accounting for its low turnover rate. Single turnovers on plasmids also yielded faster rates for substrate hydrolysis with Mn2+ compared to Mg2+ and Co2+. Since Mn2+ gave the most rapid rates for the hydrolytic step, despite being less electronegative than Co2+, the function of the metal ion at the active site of EcoRV cannot be just the polarisation of the scissile phosphate. Moreover, the minimal scheme for the Co2+-catalysed reaction requires two metal ions for DNA cleavage. The metal ions seem to be involved in the precise positioning of both the substrate and the water that acts as the attacking nucleophile and in activating that water molecule. A model is presented to account for how two metal ions might fulfil these functions.
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Affiliation(s)
- G S Baldwin
- Department of Biochemistry School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK.
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Legault P, Hoogstraten CG, Metlitzky E, Pardi A. Order, dynamics and metal-binding in the lead-dependent ribozyme. J Mol Biol 1998; 284:325-35. [PMID: 9813121 DOI: 10.1006/jmbi.1998.2181] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The in vitro selected lead-dependent ribozyme is among the smallest and simplest of the known catalytic RNA motifs and has a unique metal ion specificity for divalent lead. The conformation and dynamics of this ribozyme are analyzed here by NMR and chemical probing experiments. Complete assignments of the 1H, 13C, and 15N resonances have been made, and the NMR chemical shift changes in the presence of Pb2+, Mg2+ or high concentrations of Na+ show that there is no significant structural change upon addition of either activating (Pb2+) or inhibitory (Mg2+) divalent ions. The 13C NMR relaxation data indicate substantial dynamic fluctuations on various time-scales for active-site residues in this ribozyme. The combination of chemical probing and NMR experiments reveals a picture of the active site for the lead-dependent ribozyme that has both ordered and dynamic features.
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Affiliation(s)
- P Legault
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO, 80309-0215, USA
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Hoogstraten CG, Legault P, Pardi A. NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis. J Mol Biol 1998; 284:337-50. [PMID: 9813122 DOI: 10.1006/jmbi.1998.2182] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The NMR solution structure of a lead-dependent ribozyme, known as the leadzyme, is presented. This ribozyme is among the smallest of the known catalytic RNAs, with an active site consisting of a six-nucleotide asymmetric internal loop. This loop has a roughly double-helical structure, including a protonated adenine-cytosine wobble base-pair, that positions the cytosine base 5' to the cleavage site in a double-helical conformation. The deviations from helical structure consist of two bulged guanosine residues, G7 and G9, where G7 is the residue 3' to the cleavage site. The scissile phosphate group of the leadzyme is not positioned for in-line nucleophilic attack. Therefore, a conformational rearrangement in the active site is required to reach the proposed transition state for this ribozyme. This is similar to previous observations in X-ray studies of the hammerhead ribozyme, and emphasizes the necessity for dynamic structural fluctuations in the catalytic mechanism of small ribozymes. A model for metal-binding in the leadzyme is proposed in which a lead ion binds to a bulged guanine base that is critical for leadzyme function.
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Affiliation(s)
- C G Hoogstraten
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Campus Box 215, Boulder, CO, 80309, USA
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Zhou DM, Taira K. The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA. Chem Rev 1998; 98:991-1026. [PMID: 11848922 DOI: 10.1021/cr9604292] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- De-Min Zhou
- Institute of Applied Biochemistry, University of Tsukuba, Tennoudai 1-1-1, Tsukuba Science City 305-8572, Japan, National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba Science City 305-8562, Japan, and National Institute of Bioscience & Human Technology, 1-1 Higashi, Tsukuba Science City 305-8566, Japan
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28
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Lott WB, Pontius BW, von Hippel PH. A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate. Proc Natl Acad Sci U S A 1998; 95:542-7. [PMID: 9435228 PMCID: PMC18456 DOI: 10.1073/pnas.95.2.542] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/1997] [Indexed: 02/05/2023] Open
Abstract
Evidence for a two-metal ion mechanism for cleavage of the HH16 hammerhead ribozyme is provided by monitoring the rate of cleavage of the RNA substrate as a function of La3+ concentration in the presence of a constant concentration of Mg2+. We show that a bell-shaped curve of cleavage activation is obtained as La3+ is added in micromolar concentrations in the presence of 8 mM Mg2+, with a maximal rate of cleavage being attained in the presence of 3 microM La3+. These results show that two-metal ion binding sites on the ribozyme regulate the rate of the cleavage reaction and, on the basis of earlier estimates of the Kd values for Mg2+ of 3.5 mM and > 50 mM, that these sites bind La3+ with estimated Kd values of 0.9 and > 37.5 microM, respectively. Furthermore, given the very different effects of these metal ions at the two binding sites, with displacement of Mg2+ by La3+ at the stronger (relative to Mg2+) binding site activating catalysis and displacement of Mg2+ by La3+ at the weaker (relative to Mg2+) (relative to Mg2+) binding site inhibiting catalysis, we show that the metal ions at these two sites play very different roles. We argue that the metal ion at binding site 1 coordinates the attacking 2'-oxygen species in the reaction and lowers the pKa of the attached proton, thereby increasing the concentration of the attacking alkoxide nucleophile in an equilibrium process. In contrast, the role of the metal ion at binding site 2 is to catalyze the reaction by absorbing the negative charge that accumulates at the leaving 5'-oxygen in the transition state. We suggest structural reasons why the Mg(2+)-La3+ ion combination is particularly suited to demonstrating these different roles of the two-metal ions in the ribozyme cleavage reaction.
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Affiliation(s)
- W B Lott
- Institute of Molecular Biology, University of Oregon, Eugene 97403-1229, USA
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Ohmichi T, Sugimoto N. Roles of 2′-Hydroxyls of Leadzyme on an RNA Cleavage. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1997. [DOI: 10.1246/bcsj.70.2743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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