Online citations, reference lists, and bibliographies.
Please confirm you are human
(Sign Up for free to never see this)
← Back to Search

Multi-metal-dependent Nucleic Acid Enzymes.

W. Zhou, J. Liu
Published 2018 · Chemistry, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy
Share
Nucleic acid enzymes (NAEs) are catalytically active RNA and DNA molecules. NAEs with RNA-cleaving activity are most extensively studied for applications in analytical chemistry, gene therapy and nanotechnology. Most NAEs require metal ions for activity. From a biochemical standpoint, these NAEs are reminiscent of metalloprotein enzymes with metal binding sites. While most NAEs require a single metal for the reaction, more and more recent examples have emerged that use two or even three metals for the reaction. The metal binding profile is sharper for these NAEs if they use the same metal ion due to cooperativity. Detailed studies have indicated examples of lanthanide and Ca2+ binding DNAzymes, where the metals interact with the non-bridging oxygen atoms in the scissile phosphate, and these DNAzymes often have a very strong thio effect that cannot be rescued by adding thiophilic metals. Another type uses multiple different metals, where one metal interacts with the scissile phosphate and the other binds to the catalytic loop for allosteric interactions. Such allosteric NAEs can also be obtained via rational design or intentional selection based on existing NAEs. These multi-metal NAEs might be useful as logic gates with metal ions as inputs. In this article, we review different types of NAEs based on their use of metal ions. The NAEs reviewed include ribozymes, DNAzymes and rationally designed aptazymes. Finally, their emerging applications are discussed, and some future research opportunities are proposed.
This paper references
10.1016/j.cbpa.2013.01.009
Chelators for investigating zinc metalloneurochemistry.
R. Radford (2013)
10.1093/NAR/29.9.1815
Recent advances in the elucidation of the mechanisms of action of ribozymes.
Y. Takagi (2001)
Proc
J. Liu (2007)
Chem
D. D. Vo (2016)
10.1093/nar/gki182
Engineered allosteric ribozymes that respond to specific divalent metal ions
M. Zivarts (2005)
10.1038/6700
Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis
J. Wedekind (1999)
Chem
F. Wang (2014)
Chem
J. Liu (2007)
10.1021/AC034924R
Improving fluorescent DNAzyme biosensors by combining inter- and intramolecular quenchers.
J. Liu (2003)
10.1021/ja407586u
DNA catalysts with tyrosine kinase activity.
S. Walsh (2013)
A
M. D. Been (1991)
Y
K. Schlosser (2008)
R
K. A. Harris (2015)
Angew
A. Ono (2004)
10.1002/cbic.200800632
Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme
A. K. Brown (2009)
10.1002/cbic.201600174
A Selective Na+ Aptamer Dissected by Sensitized Tb3+ Luminescence
W. Zhou (2016)
Anal
P.-J.J. Huang (2016)
10.1002/ANIE.200500703
A DNAzyme that walks processively and autonomously along a one-dimensional track.
Y. Tian (2005)
Chem
R. R. Breaker (1994)
10.1021/cr030183i
Functional nucleic acid sensors.
J. Liu (2009)
10.3390/molecules22010078
The Hammerhead Ribozyme: A Long History for a Short RNA
M. de la Peña (2017)
Chem
Z. Liu (2003)
10.1016/0022-2836(86)90387-6
New reactions of the ribosomal RNA precursor of Tetrahymena and the mechanism of self-splicing.
T. Inoue (1986)
10.1002/anie.200800960
A highly selective DNAzyme sensor for mercuric ions.
M. Hollenstein (2008)
10.1016/0092-8674(82)90414-7
Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena
K. Kruger (1982)
10.1093/NAR/GKL820
Self-splicing of a group IIC intron: 5′ exon recognition and alternative 5′ splicing events implicate the stem–loop motif of a transcriptional terminator
N. Toor (2006)
10.1039/b808686a
Specific interactions between silver(I) ions and cytosine-cytosine pairs in DNA duplexes.
A. Ono (2008)
A
J. L. Boots (2008)
A
M. Bonaccio (2004)
R
M. Pechlaner (2012)
10.1002/anie.201100477
Fluorogenic DNAzyme probes as bacterial indicators.
M. M. Ali (2011)
10.1038/361085A0
Metal ion catalysis in the Tetrahymena ribozyme reaction
J. Piccirilli (1993)
10.1021/acs.analchem.5b02810
Platinum(II)-Oligonucleotide Coordination Based Aptasensor for Simple and Selective Detection of Platinum Compounds.
Sheng Cai (2015)
Curr
B. Nawrot (2008)
Anal
R. Saran (2016)
10.1021/CR60273A002
Sites and thermodynamic quantities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and nucleotides.
R. Izatt (1971)
10.1039/b926003j
Ion-induced DNAzyme switches.
Simcha Shimron (2010)
10.1021/BI00211A013
Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism.
S. Dahm (1993)
10.1038/342391a0
The guanosine binding site of the Tetrahymena ribozyme
F. Michel (1989)
10.1073/PNAS.94.9.4262
A general purpose RNA-cleaving DNA enzyme.
S. Santoro (1997)
10.1039/c4cc09874a
Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications.
R. Orbach (2015)
G
H. Meng (2014)
Chem
E. L. Que (2008)
Nat
A. E. Palmer (2006)
3rd, J
S. W. Santoro (2000)
10.1039/b926910j
A highly selective lead sensor based on a classic lead DNAzyme.
T. Lan (2010)
10.1126/SCIENCE.1114994
Structural Evidence for a Two-Metal-Ion Mechanism of Group I Intron Splicing
M. Stahley (2005)
10.1021/cr900223a
In situ imaging of metals in cells and tissues.
Reagan L. McRae (2009)
10.1039/b718428j
DNAzymes for sensing, nanobiotechnology and logic gate applications.
I. Willner (2008)
10.1002/ANIE.200454172
Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions.
A. Ono (2004)
10.1021/acs.analchem.5b04904
An Ultrasensitive Light-up Cu(2+) Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate.
P. Huang (2016)
10.1038/86723
Immobilized RNA switches for the analysis of complex chemical and biological mixtures
Sukeerthi Seetharaman (2001)
10.1068/p4310ed
Q…
J. Koenderink (2014)
10.1021/bi4000673
Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme.
Pallavi Thaplyal (2013)
10.1074/jbc.273.10.5655
Role of the Dimeric Structure in Cu,Zn Superoxide Dismutase
A. Battistoni (1998)
10.1093/nar/gkr860
Establishing broad generality of DNA catalysts for site-specific hydrolysis of single-stranded DNA
Y. Xiao (2012)
10.1073/pnas.0607875104
A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity
J. Liu (2007)
10.1002/ANIE.200462443
An exceptionally selective lead(II)-regulatory protein from Ralstonia metallidurans: development of a fluorescent lead(II) probe.
P. Chen (2005)
10.1016/1074-5521(94)90014-0
A DNA enzyme that cleaves RNA.
R. Breaker (1994)
10.1039/c3an02117c
Selection of a DNA aptamer for cadmium detection based on cationic polymer mediated aggregation of gold nanoparticles.
Yuangen Wu (2014)
10.1002/ANIE.200461848
In vitro selection of structure-switching signaling aptamers.
Razvan Nutiu (2005)
Chem
H. Ueyama (2002)
Chem
K. P. Carter (2014)
Chem
Y. Xiao (2011)
Chem
H. Sigel (1993)
Chem
I. Willner (2008)
10.1039/c0cs00162g
Fluorescent DNA-based enzyme sensors.
Nan Dai (2011)
10.1021/acs.biochem.6b01131
A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity.
R. Saran (2017)
10.1039/c7ob01709j
Splitting a DNAzyme enables a Na+-dependent FRET signal from the embedded aptamer.
W. Zhou (2017)
10.1007/s13277-014-2477-9
Therapeutic potential of siRNA and DNAzymes in cancer
H. Karnati (2014)
Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.
H. Hofmann (1997)
Nat
M. Chandra (2009)
Anal
L. Li (2015)
Angew
M. M. Ali (2011)
Chem
L. Buttner (2014)
10.1021/acs.biochem.6b00132
In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage.
P. Huang (2016)
10.1126/SCIENCE.2200121
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
C. Tuerk (1990)
10.1093/nar/gkv1346
A DNAzyme requiring two different metal ions at two distinct sites
W. Zhou (2016)
10.1038/nsmb906
Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation
A. Serganov (2005)
10.1002/anie.201408333
Photocaged DNAzymes as a general method for sensing metal ions in living cells.
Kevin M. Hwang (2014)
10.1021/acschembio.5b00867
Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme.
X. Wang (2016)
10.1021/BI9913202
Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate.
S. Wang (1999)
10.1002/anie.201703540
Imaging Endogenous Metal Ions in Living Cells Using a DNAzyme-Catalytic Hairpin Assembly Probe.
Zhenkun Wu (2017)
Trends Biochem
S. K. Silverman (2016)
Mol
D. E. Weng (2005)
Nat
H.-K. Kim (2007)
Chem
H. K. Kim (2007)
10.1007/978-1-59745-033-1_4
In-line probing analysis of riboswitches.
E. E. Regulski (2008)
10.1021/BI00198A023
Properties of an in vitro selected Pb2+ cleavage motif.
T. Pan (1994)
L
C. Tuerk (1990)
10.1021/cr400546e
Fluorescent Sensors for Measuring Metal Ions in Living Systems
Kyle P. Carter (2014)
10.1039/C2SC01067D
Lanthanide ions as required cofactors for DNA catalysts.
V. Dokukin (2012)
10.1021/BI001089O
Kinetic characterization of the second step of group II intron splicing: role of metal ions and the cleavage site 2'-OH in catalysis.
P. M. Gordon (2000)
10.1021/acsnano.6b02558
Rapid and Label-Free Strategy to Isolate Aptamers for Metal Ions.
Hao Qu (2016)
10.1517/14712598.2015.1025048
DNA enzymes as potential therapeutics: towards clinical application of 10-23 DNAzymes
A. Fokina (2015)
10.1016/J.CHEMBIOL.2007.05.008
A second divalent metal ion in the group II intron reaction center.
P. M. Gordon (2007)
10.1146/ANNUREV.BIOPHYS.34.122004.184428
The structure-function dilemma of the hammerhead ribozyme.
K. Blount (2005)
Chem
R. M. Izatt (1971)
Chem
Y. Li (1999)
10.1021/cr900301e
Fluorescent analogs of biomolecular building blocks: design, properties, and applications.
Renatus W. Sinkeldam (2010)
10.1093/NAR/28.2.481
In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme.
J Li (2000)
10.1093/nar/gkn1070
A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+)
M. Hollenstein (2009)
Chem
J. Li (2000)
Proc
S.-F. Torabi (2015)
10.1002/cbic.201500690
An Efficient Lanthanide‐Dependent DNAzyme Cleaving 2′–5′‐Linked RNA
W. Zhou (2016)
O
T. Pan (1992)
G
S. W. Santoro (1998)
Nat
A. Serganov (2005)
Chem
H. Gu (2013)
Angew
J. Liu (2007)
10.1038/NCHEMBIO.2007.45
Dissecting metal ion-dependent folding and catalysis of a single DNAzyme.
H. Kim (2007)
10.1021/JA026892F
A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation.
H. Ueyama (2002)
10.1016/j.tibs.2016.04.010
Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes.
S. Silverman (2016)
Chem
R. McRae (2009)
10.1093/nar/gkv519
Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing
P. Huang (2015)
Chem
J. Liu (2009)
ACS Chem
X. Wang (2015)
ACS Comb
T. E. Velez (2012)
Nat
Z. Weinberg (2015)
Chem
B. Seelig (1999)
Mol
K. Furukawa (2015)
10.1002/9780470048672.WECB406
Nucleic Acid Enzymes (Ribozymes and Deoxyribozymes): In Vitro Selection and Application
S. Silverman (2008)
10.1021/ac5031557
Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe.
Shengnan He (2015)
10.1021/BI962030D
Role of Nd3+ and Pb2+ on the RNA cleavage reaction by a small ribozyme.
T. Ohmichi (1997)
10.1016/j.talanta.2016.04.005
Selection and characterization of DNA aptamers for the development of light-up biosensor to detect Cd(II).
H. Wang (2016)
10.1021/BI9812221
Mechanism and utility of an RNA-cleaving DNA enzyme.
S. Santoro (1998)
10.1021/acs.analchem.6b00327
A Silver DNAzyme.
R. Saran (2016)
Chem
A. Ono (2008)
At
H. Haraguchi (2004)
Anal
J. Liu (2003)
Anal
Z. J. Zhou (2015)
10.1016/j.cell.2012.09.033
Visualizing Group II Intron Catalysis through the Stages of Splicing
M. Marcia (2012)
10.1021/nn5015962
DNA Dendrimer: An Efficient Nanocarrier of Functional Nucleic Acids for Intracellular Molecular Sensing
Hong-Min Meng (2014)
O
S. C. Dahm (1993)
10.1021/cr400354z
From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures.
Fuan Wang (2014)
10.1021/cr200104q
Functionalized DNA nanostructures.
Ofer I. Wilner (2012)
10.1038/nchembio.201
DNA-catalyzed sequence-specific hydrolysis of DNA
M. Chandra (2009)
Chem
L. Lermer (2002)
10.1039/B308213J
Metallomics as integrated biometal science
H. Haraguchi (2004)
10.1021/ja400150v
A DNAzyme-gold nanoparticle probe for uranyl ion in living cells.
Peiwen Wu (2013)
10.1093/NAR/GKH250
Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme.
M. Bonaccio (2004)
10.1515/9783110685039-030
s ? ? ? ? ? ? ? ? ?
Hung-Yu Tseng (2005)
Chem
J. Chandrasekar (2015)
10.1039/c4cs00365a
Optical probes for the detection of protons, and alkali and alkaline earth metal cations.
Graham R. C. Hamilton (2015)
10.1021/BI992710R
Capping DNA with DNA.
Y. Li (2000)
10.1007/s00239-015-9715-7
Identification of the Same Na+-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions
Seyed-Fakhreddin Torabi (2015)
10.2174/138527208785161204
Effect of RP and SPPhosphorothioate Substitution at the Scissile Site on the Cleavage Activity of Deoxyribozyme 10-23
B. Nawrot (2008)
T
J. A. Piccirilli (1993)
Anal
S. He (2014)
Chem
R. W. Sinkeldam (2010)
10.1021/JA990592P
Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group
Y. Li (1999)
10.1016/S1074-5521(99)89008-5
A small catalytic RNA motif with Diels-Alderase activity.
B. Seelig (1999)
10.1053/j.gastro.2012.03.039
An RNA aptamer that binds carcinoembryonic antigen inhibits hepatic metastasis of colon cancer cells in mice.
Y. Lee (2012)
10.1128/MCB.15.8.4466
Stereochemical selectivity of group II intron splicing, reverse splicing, and hydrolysis reactions.
M. Podar (1995)
10.1038/346818A0
In vitro selection of RNA molecules that bind specific ligands
A. Ellington (1990)
10.1039/C5QI00125K
A comparison of two classic Pb2+-dependent RNA-cleaving DNAzymes
R. Saran (2016)
10.1038/42076
A second catalytic metal ion in a group I ribozyme
L. B. Weinstein (1997)
10.1126/SCIENCE.2017681
Group I intron self-splicing with adenosine: evidence for a single nucleoside-binding site.
M. Been (1991)
10.1177/001452469000101110
"J."
G.G. Stokes (1890)
Chem
P. Wu (2013)
Chem
W. L. Ward (2014)
10.1021/cr078203u
Metals in neurobiology: probing their chemistry and biology with molecular imaging.
E. L. Que (2008)
10.1021/ja100710j
Activation and deactivation of DNAzyme and antisense function with light for the photochemical regulation of gene expression in mammalian cells.
D. D. Young (2010)
V
L. Hunsicker-Wang (2009)
Inorg
K. Hwang (2016)
Angew
Z. Wu (2017)
10.1021/BI027332W
A lead-dependent DNAzyme with a two-step mechanism.
A. K. Brown (2003)
10.1021/JA01028A024
Interaction of metal ions with polynucleotides and related compounds. XII. The relative effect of various metal ions on DNA helicity.
G. Eichhorn (1968)
10.1016/j.biochi.2017.07.001
Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence.
R. Saran (2018)
10.1261/rna.1010808
Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme.
J. L. Boots (2008)
10.1021/JA047991R
Putting a brake on an autonomous DNA nanomotor.
Y. Chen (2004)
10.1007/978-94-007-2172-2_1
Characterization of metal ion-nucleic acid interactions in solution.
M. Pechlaner (2012)
10.1111/j.1365-2958.2008.06208.x
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism
E. E. Regulski (2008)
10.1021/CR0502605
Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry.
R. Sigel (2007)
Small RNA-divalent domains.
J. Ciesiołka (1996)
10.1021/acs.chemrev.7b00063
Metal Sensing by DNA.
W. Zhou (2017)
Angew
R. Nutiu (2005)
10.1021/JA0281232
An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling.
Shirley H. J. Mei (2003)
10.1039/c1cs15149e
Binding of metal ions by pyrimidine base pairs in DNA duplexes.
A. Ono (2011)
Y
A. K. Brown (2003)
N
T. Ohmichi (1997)
T
K. Kruger (1982)
Chem
M. Komiyama (1999)
Anal
S. Cai (2015)
Angew
C. Hobartner (2007)
Anal
P.-J.J. Huang (2014)
10.1074/JBC.275.16.11693
Preferential Activation of the 8–17 Deoxyribozyme by Ca 2+ Ions
A. Peracchi (2000)
10.1021/JA0383975
A general strategy to convert the MerR family proteins into highly sensitive and selective fluorescent biosensors for metal ions.
P. Chen (2004)
Selection of an RNA domain that binds Zn2+.
J. Ciesiołka (1995)
10.1016/j.aca.2015.06.036
A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins.
Zhaojuan Zhou (2015)
10.1021/ja503864v
Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work.
L. Buettner (2014)
10.1007/S00216-007-1735-8
Selection of fluorescent aptamer beacons that light up in the presence of zinc
Manjula T. Rajendran (2008)
10.1021/ja403585e
Small, highly active DNAs that hydrolyze DNA.
Hongzhou Gu (2013)
R
H. K. Karnati (2014)
G
X. Gao (2012)
T
N. Sugimoto (1996)
H
H. Qu (2016)
10.1021/acs.biochem.5b00691
Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates.
Mahsa Vazin (2015)
10.1016/j.cbpa.2009.11.024
Controlling ribozyme activity by metal ions.
Joachim Schnabl (2010)
10.1021/nl803887y
Sensing of UO22+ and design of logic gates by the application of supramolecular constructs of ion-dependent DNAzymes.
Michal Moshe (2009)
10.1093/nar/gku1296
A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect
P. Huang (2015)
10.1002/cbic.201500603
A New Na+‐Dependent RNA‐Cleaving DNAzyme with over 1000‐fold Rate Acceleration by Ethanol
W. Zhou (2016)
10.1021/JA0205075
Toward an RNaseA mimic: A DNAzyme with imidazoles and cationic amines.
L. Lermer (2002)
10.1006/JMBI.2001.5058
A new and efficient DNA enzyme for the sequence-specific cleavage of RNA.
A. Feldman (2001)
Chem
D. D. Young (2010)
Chem
G. R. Hamilton (2015)
Anal
P.-J.J. Huang (2014)
Chem
V. Dokukin (2012)
Angew
M. Hollenstein (2008)
10.1016/S0076-6879(09)68016-2
EPR methods to study specific metal-ion binding sites in RNA.
Laura M Hunsicker-Wang (2009)
Chem
S. M. Walsh (2013)
Nat
S. Seetharaman (2001)
10.1002/ANIE.200702006
Rational design of "turn-on" allosteric DNAzyme catalytic beacons for aqueous mercury ions with ultrahigh sensitivity and selectivity.
J. Liu (2007)
10.1021/ar900197y
A stability concept for metal ion coordination to single-stranded nucleic acids and affinities of individual sites.
R. Sigel (2010)
10.1021/ac403762s
Ultrasensitive DNAzyme beacon for lanthanides and metal speciation.
P. Huang (2014)
10.1021/BI00131A001
In vitro selection of RNAs that undergo autolytic cleavage with Pb2+.
T. Pan (1992)
10.1016/j.molcel.2015.02.009
Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters.
Kazuhiro Furukawa (2015)
O
T. Pan (1994)
R
M. Zivarts (2005)
10.1002/ANIE.200702217
Engineering a selective small-molecule substrate binding site into a deoxyribozyme.
C. Höbartner (2007)
10.1093/nar/gkw845
A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing
W. Zhou (2016)
10.1021/JA0021316
A highly sensitive and selective catalytic DNA biosensor for lead ions [9]
J. Li (2000)
Y
J. Li (2000)
Expert Opin
A. A. Fokina (2015)
Chem
R. K. Sigel (2007)
Anal
J. C. Achenbach (2005)
Chem
W. Zhou (2017)
Mol
M. Podar (1995)
Chem
P. M. Gordon (2007)
10.1021/ac5029962
In vitro selection of a new lanthanide-dependent DNAzyme for ratiometric sensing lanthanides.
P. Huang (2014)
10.1021/jacs.5b06308
Phosphoserine Lyase Deoxyribozymes: DNA-Catalyzed Formation of Dehydroalanine Residues in Peptides.
J. Chandrasekar (2015)
10.1261/rna.052514.115
Biochemical analysis of pistol self-cleaving ribozymes.
K. Harris (2015)
10.1158/1535-7163.MCT-04-0210
A phase I clinical trial of a ribozyme-based angiogenesis inhibitor targeting vascular endothelial growth factor receptor-1 for patients with refractory solid tumors
D. Weng (2005)
10.1515/9783486731620-002
I
John B. Shoven (1824)
10.1126/SCIENCE.7527587
The stereochemical course of group II intron self-splicing.
R. Padgett (1994)
Curr
R. J. Radford (2013)
Chem
A. Ono (2011)
10.1021/bi200585n
DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates.
On Yi Wong (2011)
Inorg
R. Saran (2016)
Chem
O. I. Wilner (2012)
Chem
S. H. Mei (2003)
Chem
T. Lan (2010)
Proc
J. M. Warnecke (1996)
10.18388/ABP.2006_3296
Iron-sulfur cluster proteins: electron transfer and beyond.
K. Brzóska (2006)
10.1038/nature16471
Crystal structure of a DNA catalyst
A. Ponce-Salvatierra (2016)
10.1039/9781849732512-00101
Importance of diffuse metal ion binding to RNA.
Zhi-Jie Tan (2011)
10.1002/cbic.201700184
Two Completely Different Mechanisms for Highly Specific Na+ Recognition by DNAzymes
W. Zhou (2017)
10.1016/J.ICA.2016.04.017
Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes.
Kevin M. Hwang (2016)
Y
J. Liu (2006)
Angew
K. Hwang (2014)
Chem
R. Orbach (2015)
Chem
S. Shimron (2010)
Chem
Y. Chen (2004)
Nat
J. E. Wedekind (1999)
Proc
S. W. Santoro (1997)
10.1016/0014-5793(96)00860-5
Site‐specific cleavage reaction catalyzed by leadzyme is enhanced by combined effect of lead and rare earth ions
N. Sugimoto (1996)
10.1002/cbic.201600708
An Exceptionally Selective DNA Cooperatively Binding Two Ca2+ Ions
W. Zhou (2017)
10.1021/ACSSENSORS.5B00306
In Vitro Selection in Serum: RNA-Cleaving DNAzymes for Measuring Ca2+ and Mg2+
W. Zhou (2016)
T
L. B. Weinstein (1997)
10.1002/chem.201505094
Oncogenic MicroRNAs Biogenesis as a Drug Target: Structure-Activity Relationship Studies on New Aminoglycoside Conjugates.
D. D. Vo (2016)
10.1039/C2AY05846D
Determination of magnesium ion in serum samples by a DNAzyme-based electrochemical biosensor
Xiaoyao Gao (2012)
10.1038/nchembio.69
Synthetic fluorescent sensors for studying the cell biology of metals.
D. W. Domaille (2008)
10.1002/cbic.200500264
The RNA‐Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme
A. Feldman (2006)
10.1021/acs.analchem.5b00204
Simultaneous imaging of Zn(2+) and Cu(2+) in living cells based on DNAzyme modified gold nanoparticle.
L. Li (2015)
Mol
C. R. Dass (2008)
Anal
M. Rajendran (2008)
10.1016/J.ACA.2004.03.080
Structure-switching allosteric deoxyribozymes
J. C. Achenbach (2004)
10.1039/c0cc04575f
Merely two mutations switch a DNA-hydrolyzing deoxyribozyme from heterobimetallic (Zn2+/Mn2+) to monometallic (Zn2+-only) behavior.
Y. Xiao (2011)
10.1021/co300111f
Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length.
Tania E Velez (2012)
10.1002/chem.201001171
Hg(II) ion specifically binds with T:T mismatched base pair in duplex DNA.
H. Torigoe (2010)
10.1021/JA0712625
Metal-dependent global folding and activity of the 8-17 DNAzyme studied by fluorescence resonance energy transfer.
H. Kim (2007)
10.1039/B605799C
Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli.
J. Liu (2006)
10.1021/ac501070a
Sensing parts-per-trillion Cd(2+), Hg(2+), and Pb(2+) collectively and individually using phosphorothioate DNAzymes.
P. Huang (2014)
10.1021/ac1009047
Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity.
X. Zhang (2010)
10.1017/S003358350500404X
Role of cofactors in metalloprotein folding.
C. Wilson (2004)
10.1073/pnas.1420361112
In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing
Seyed-Fakhreddin Torabi (2015)
10.1039/CS9932200255
Interactions of metal ions with nucleotides and nucleic acids and their constituents
H. Sigel (1993)
R
Y. F. Li (2000)
10.1074/JBC.M200977200
c-Jun Regulates Vascular Smooth Muscle Cell Growth and Neointima Formation after Arterial Injury
L. Khachigian (2002)
10.1056/NEJMoa1411776
Allergen-induced asthmatic responses modified by a GATA3-specific DNAzyme.
N. Krug (2015)
10.1021/JA035208+
Assemblage of signaling DNA enzymes with intriguing metal-ion specificities and pH dependences.
Z. Liu (2003)
Y
A. K. Brown (2009)
R
H. Wang (2016)
V
A. Ponce-Salvatierra (2016)
Chem
N. Dai (2011)
Angew
Y. Tian (2005)
Curr
J. Schnabl (2010)
Chem
J. Yin (2015)
Nat
D. W. Domaille (2008)
Acc
R. K. Sigel (2010)
10.1021/AC0351769
Adenosine-dependent assembly of aptazyme-functionalized gold nanoparticles and its application as a colorimetric biosensor.
J. Liu (2004)
10.1385/1-59745-069-3:275
Fluorescent DNAzyme biosensors for metal ions based on catalytic molecular beacons.
J. Liu (2006)
10.1093/nar/gkm1175
Sequence-function relationships provide new insight into the cleavage site selectivity of the 8–17 RNA-cleaving deoxyribozyme
K. Schlosser (2008)
10.1038/nprot.2006.172
Measuring calcium signaling using genetically targetable fluorescent indicators
A. Palmer (2006)
A
M. Marcia (2012)
10.1515/9783111548050-027
P ? ? ? ? ? ? ? % ? ? ? ?
Lesterol IN Pregnancy (1991)
K
Y. Takagi (2001)
10.4324/9780203379950-24
{m
Kaushalya Madhawa (2020)
10.1021/cr400476k
Nucleic Acid Catalysis: Metals, Nucleobases, and Other Cofactors
W. L. Ward (2014)
10.1039/A901621J
Hydrolysis of DNA and RNA by lanthanide ions: mechanistic studies leading to new applications
M. Komiyama (1999)
10.1021/JA993688S
RNA cleavage by a DNA enzyme with extended chemical functionality.
S. Santoro (2000)
10.1158/1535-7163.MCT-07-0510
DNAzyme technology and cancer therapy: cleave and let die
C. Dass (2008)
10.1021/acs.langmuir.6b00906
DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays.
Lingzi Ma (2016)
10.1073/PNAS.93.17.8924
Ribonuclease P (RNase P) RNA is converted to a Cd(2+)-ribozyme by a single Rp-phosphorothioate modification in the precursor tRNA at the RNase P cleavage site.
J. Warnecke (1996)
Chem
P. Chen (2004)
Acta Biochim
K. Brzoska (2006)
Annu
K. F. Blount (2005)
Chem
G. L. Eichhorn (1968)
10.1038/nchembio.1846
New classes of self-cleaving ribozymes revealed by comparative genomics analysis
Z. Weinberg (2015)
10.1021/JA0717358
A DNAzyme catalytic beacon sensor for paramagnetic Cu2+ ions in aqueous solution with high sensitivity and selectivity.
J. Liu (2007)
10.1039/c4cs00275j
Fluorescent probes and bioimaging: alkali metals, alkaline earth metals and pH.
J. Yin (2015)



This paper is referenced by
10.1039/d0dt00784f
Arsenic-nucleotides interactions: an experimental and computational investigation.
Giuseppe Cassone (2020)
10.1039/c9an02612f
Sensitivity of a classic DNAzyme for Pb2+ modulated by cations, anions and buffers.
W. Ren (2020)
10.3390/molecules24224134
Constructing Controllable Logic Circuits Based on DNAzyme Activity
F. Yang (2019)
10.3390/CATAL8110550
RNA-Cleaving DNAzymes: Old Catalysts with New Tricks for Intracellular and In Vivo Applications
Jingjing Zhang (2018)
10.1002/cbic.201700498
Ultrasensitive DNAzyme‐Based Ca2+ Detection Boosted by Ethanol and a Solvent‐Compatible Scaffold for Aptazyme Design
T. Yu (2018)
10.9734/jabb/2019/v22i430127
Impact of Metal Ion Substitution on the Activity and Stability of Saccharifying Raw Starch Digesting Amylase from Aspergillus carbonarius
T. N. Nwagu (2020)
10.1002/cbic.201800548
Global Folding of a Na+‐Specific DNAzyme Studied by FRET
Yan-Ping He (2019)
10.1039/d0ra06329k
Monitoring intracellular metal ion complexation with an acetylene-tagged ligand by Raman spectroscopy
Seiya Takemura (2020)
10.1016/j.isci.2020.101555
Insight into an Oxidative DNA-Cleaving DNAzyme: Multiple Cofactors, the Catalytic Core Map and a Highly Efficient Variant
Wenqian Yu (2020)
10.1002/cbic.201800322
An in Vitro–Selected DNAzyme Mutant Highly Specific for Na+ under Slightly Acidic Conditions
Lingzi Ma (2019)
10.1016/j.trac.2020.115811
Photoactivatable Fluorescent Probes for Spatiotemporal-Controlled Biosensing and Imaging
Z. Zou (2020)
10.1039/C8AY00373D
Screening of DNAzyme mutants for highly sensitive and selective detection of calcium in milk
T. Yu (2018)
10.1002/cbic.201900143
Probing Local Folding Allows Robust Metal Sensing Based on a Na+‐Specific DNAzyme
Yan-Ping He (2019)
10.1101/2020.10.28.359059
Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations and NMR Experiments
Zhengyue Zhang (2020)
10.1016/j.isci.2019.100815
Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology
Lingzi Ma (2020)
10.1002/anie.201915675
Target Self-enhanced Selectivity in Metal-specific DNAzymes.
P. Huang (2019)
10.1002/open.202000134
In vitro Selection of Chemically Modified DNAzymes
P. Huang (2020)
Semantic Scholar Logo Some data provided by SemanticScholar