A Versatile Endoribonuclease Mimic Made of DNA: Characteristics and Applications of the 8–17 RNA‐Cleaving DNAzyme

Enzymes play a crucial role in all living organisms by accelerating the rates of a myriad of biochemical reactions that are necessary to sustain life. Although the vast majority of known enzymes are made of protein, in recent years it has become increasingly apparent that other molecular formats, like nucleic acids, can also serve in this capacity. DNAzymes (also known as deoxyribozymes) are synthetic enzymes made of short, single strands of deoxyribonucleic acid. These DNA‐based enzymes offer the prospect of significant commercial utility, because they are exceptionally stable and can be produced very easily and inexpensively. The study of one particular DNAzyme, known as “8–17”, has enhanced our understanding of DNAzyme‐mediated catalysis. Moreover, the function of 8–17 has been regarded with special importance because it can catalyze sequence‐specific cleavage of RNA, a reaction that has broad implications in biotechnology and biomedical fields. In this review, we explore the creation, characterization, and application of the 8–17 RNA‐cleaving DNAzyme.

[1]  G. F. Joyce,et al.  A general purpose RNA-cleaving DNA enzyme. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Yi Lu,et al.  A lead-dependent DNAzyme with a two-step mechanism. , 2003, Biochemistry.

[3]  Jing Li,et al.  A highly sensitive and selective catalytic DNA biosensor for lead ions [9] , 2000 .

[4]  S. Silverman In vitro selection, characterization, and application of deoxyribozymes that cleave RNA , 2005, Nucleic acids research.

[5]  Zhiwei Zhu,et al.  Electrochemical DNAzyme sensor for lead based on amplification of DNA-Au bio-bar codes. , 2008, Analytical chemistry.

[6]  M. Famulok,et al.  The Ca2+ Ion as a Cofactor for a Novel RNA-Cleaving Deoxyribozyme† , 1996 .

[7]  S. Silverman,et al.  Deoxyribozymes with 2'-5' RNA ligase activity. , 2003, Journal of the American Chemical Society.

[8]  D. Stefanovic,et al.  Deoxyribozyme-based half-adder. , 2003, Journal of the American Chemical Society.

[9]  S. Silverman,et al.  Deoxyribozymes: selection design and serendipity in the development of DNA catalysts. , 2009, Accounts of chemical research.

[10]  Marcel Hollenstein,et al.  A highly selective DNAzyme sensor for mercuric ions. , 2008, Angewandte Chemie.

[11]  S. Silverman,et al.  DNA and RNA can be equally efficient catalysts for carbon-carbon bond formation. , 2008, Journal of the American Chemical Society.

[12]  Yi Lu,et al.  Immobilization of DNAzyme catalytic beacons on PMMA for Pb2+ detection. , 2008, Lab on a chip.

[13]  Yingfu Li,et al.  Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection. , 2004, Biochemistry.

[14]  Yong Liu,et al.  Local rather than global folding enables the lead-dependent activity of the 8-17 deoxyribozyme: evidence from contact photo-crosslinking. , 2010, Journal of molecular biology.

[15]  Yingfu Li,et al.  Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates , 2006, Nucleic acids research.

[16]  D. Crothers,et al.  RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. , 1996, RNA.

[17]  Yi Lu,et al.  A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. , 2003, Journal of the American Chemical Society.

[18]  Kevin W Plaxco,et al.  Electrochemical detection of parts-per-billion lead via an electrode-bound DNAzyme assembly. , 2007, Journal of the American Chemical Society.

[19]  Alessio Peracchi,et al.  Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme. , 2004, Nucleic acids research.

[20]  J Li,et al.  In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. , 2000, Nucleic acids research.

[21]  Yi Lu,et al.  Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions. , 2009, Journal of the American Chemical Society.

[22]  J. Piccirilli,et al.  General acid catalysis by the hepatitis delta virus ribozyme , 2005, Nature chemical biology.

[23]  A mutational analysis of the 8-17 deoxyribozyme core. , 2005, Journal of molecular biology.

[24]  Whitney E. Purtha,et al.  General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages. , 2005, Journal of the American Chemical Society.

[25]  W. Scott,et al.  The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. , 1998, Chemistry & biology.

[26]  Stephen P. Fox,et al.  Sustained Polymeric Delivery of Gene Silencing Antisense ODNs, siRNA, DNAzymes and Ribozymes: In Vitro and In Vivo Studies , 2004, Journal of drug targeting.

[27]  G. F. Joyce,et al.  Perfectly Complementary Nucleic Acid Enzymes , 2003, Journal of Molecular Evolution.

[28]  R R Breaker,et al.  An amino acid as a cofactor for a catalytic polynucleotide. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[29]  D. Perrin,et al.  Bridging the gap between proteins and nucleic acids: a metal-independent RNAseA mimic with two protein-like functionalities. , 2001, Journal of the American Chemical Society.

[30]  D. Sen,et al.  A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. , 2002, Journal of molecular biology.

[31]  M. Famulok,et al.  Characterization and divalent metal-ion dependence of in vitro selected deoxyribozymes which cleave DNA/RNA chimeric oligonucleotides. , 1997, Journal of molecular biology.

[32]  Yi Lu,et al.  A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity , 2007, Proceedings of the National Academy of Sciences.

[33]  Yi Lu,et al.  Dissecting metal ion-dependent folding and catalysis of a single DNAzyme. , 2007, Nature chemical biology.

[34]  Stephen P. Fox,et al.  Gene Silencing Nucleic Acids Designed by Scanning Arrays: Anti-EGFR Activity of siRNA, Ribozyme and DNA Enzymes Targeting a Single Hybridization-accessible Region using the Same Delivery System , 2003, Journal of drug targeting.

[35]  Yi Lu,et al.  Adenosine-dependent assembly of aptazyme-functionalized gold nanoparticles and its application as a colorimetric biosensor. , 2004, Analytical chemistry.

[36]  Yingfu Li,et al.  Understanding DNA-based catalysis one molecule at a time. , 2007, Nature chemical biology.

[37]  Yi Lu,et al.  Immobilization of a catalytic DNA molecular beacon on Au for Pb(II) detection. , 2005, Analytical chemistry.

[38]  Improving metal ion specificity during in vitro selection of catalytic DNA. , 2002, Combinatorial chemistry & high throughput screening.

[39]  Juewen Liu,et al.  Proofreading and error removal in a nanomaterial assembly. , 2005, Angewandte Chemie.

[40]  S. Asano,et al.  Comparison of the specificities and catalytic activities of hammerhead ribozymes and DNA enzymes with respect to the cleavage of BCR-ABL chimeric L6 (b2a2) mRNA. , 1997, Nucleic acids research.

[41]  Alistair G. Rust,et al.  Ensembl 2002: accommodating comparative genomics , 2003, Nucleic Acids Res..

[42]  Darko Stefanovic,et al.  Behavior of polycatalytic assemblies in a substrate-displaying matrix. , 2006, Journal of the American Chemical Society.

[43]  A. Banerjea,et al.  Inhibition of HIV-1 gene expression by novel DNA enzymes targeted to cleave HIV-1 TAR RNA: potential effectiveness against all HIV-1 isolates. , 2003, Molecular therapy : the journal of the American Society of Gene Therapy.

[44]  DNAzyme catalytic beacon sensors that resist temperature-dependent variations. , 2009, Chemical communications.

[45]  Darko Stefanovic,et al.  Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. , 2006, Biochemistry.

[46]  J. Macdonald,et al.  Deoxyribozyme-based ligase logic gates and their initial circuits. , 2005, Journal of the American Chemical Society.

[47]  M. Hollenstein,et al.  A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+) , 2009, Nucleic acids research.

[48]  Yingfu Li,et al.  In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine–pyrimidine junctions , 2008, Nucleic acids research.

[49]  Yi Lu,et al.  Surface immobilization of catalytic beacons based on ratiometric fluorescent DNAzyme sensors: a systematic study. , 2007, Langmuir : the ACS journal of surfaces and colloids.

[50]  E. Southern,et al.  A simple and cost-effective method for producing small interfering RNAs with high efficacy. , 2003, Nucleic acids research.

[51]  S. Silverman,et al.  Deoxyribozymes: useful DNA catalysts in vitro and in vivo , 2008, Cellular and Molecular Life Sciences.

[52]  Juewen Liu,et al.  Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli. , 2006, Organic & biomolecular chemistry.

[53]  Juewen Liu,et al.  Colorimetric Cu2+ detection with a ligation DNAzyme and nanoparticles. , 2007, Chemical communications.

[54]  Yi Lu,et al.  Rational design of "turn-on" allosteric DNAzyme catalytic beacons for aqueous mercury ions with ultrahigh sensitivity and selectivity. , 2007, Angewandte Chemie.

[55]  R R Breaker,et al.  A DNA enzyme that cleaves RNA. , 1994, Chemistry & biology.

[56]  Y. Aoyama,et al.  Amplified nucleic acid sensing using programmed self-cleaving DNAzyme. , 2003, Journal of the American Chemical Society.

[57]  R. Kane,et al.  Highly active and stable DNAzyme-carbon nanotube hybrids. , 2005, Journal of the American Chemical Society.

[58]  Jing Li,et al.  DNAzyme-based colorimetric sensing of lead (Pb2+) using unmodified gold nanoparticle probes , 2008, Nanotechnology.

[59]  Yingfu Li,et al.  Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. , 2004, Chemistry & biology.

[60]  Yi Lu,et al.  Stimuli-responsive disassembly of nanoparticle aggregates for light-up colorimetric sensing. , 2005, Journal of the American Chemical Society.

[61]  Yi Lu,et al.  In Vitro Selection of High Temperature Zn2+-Dependent DNAzymes , 2005, Journal of Molecular Evolution.

[62]  J. Cowan,et al.  Metallobiochemistry of RNA. Co(NH3)6(3+) as a probe for Mg2+(aq) binding sites. , 1993, Journal of inorganic biochemistry.

[63]  S. Silverman,et al.  In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3'-5' to 2'-5'. , 2003, Journal of the American Chemical Society.

[64]  Juewen Liu,et al.  Miniaturized lead sensor based on lead-specific DNAzyme in a nanocapillary interconnected microfluidic device. , 2005, Environmental science & technology.

[65]  L. M. Alvarez-Salas,et al.  Cleavage of HPV-16 E6/E7 mRNA mediated by modified 10-23 deoxyribozymes. , 2009, Oligonucleotides.

[66]  Milan N Stojanovic,et al.  Molecular computing with deoxyribozymes. , 2008, Progress in nucleic acid research and molecular biology.

[67]  S. Silverman,et al.  Deoxyribozymes that synthesize branched and lariat RNA. , 2003, Journal of the American Chemical Society.

[68]  K. Taira,et al.  Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity. , 1998, Nucleic acids research.

[69]  Yi Lu,et al.  Incorporation of a DNAzyme into Au-coated nanocapillary array membranes with an internal standard for Pb(ii) sensing. , 2006, The Analyst.

[70]  K. Entian,et al.  Analysis of 2'-O-methylated nucleosides and pseudouridines in ribosomal RNAs using DNAzymes. , 2007, Analytical biochemistry.

[71]  Kee Suk Ryu,et al.  A modular microfluidic architecture for integrated biochemical analysis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[72]  S. Nakano,et al.  General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. , 2000, Science.

[73]  Nam Ki Lee,et al.  Folding of 8-17 deoxyribozyme studied by three-color alternating-laser excitation of single molecules. , 2007, Journal of the American Chemical Society.

[74]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[75]  A. Ferré-D’Amaré,et al.  Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA. , 1996, Nucleic acids research.

[76]  Ronald R. Breaker,et al.  Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group , 1999 .

[77]  S. Benner,et al.  Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. , 2004, Biochemistry.

[78]  Juewen Liu,et al.  FRET study of a trifluorophore-labeled DNAzyme. , 2002, Journal of the American Chemical Society.

[79]  Juewen Liu,et al.  Accelerated color change of gold nanoparticles assembled by DNAzymes for simple and fast colorimetric Pb2+ detection. , 2004, Journal of the American Chemical Society.

[80]  S. Silverman,et al.  Rational modification of a selection strategy leads to deoxyribozymes that create native 3'-5' RNA linkages. , 2004, Journal of the American Chemical Society.

[81]  Y. Aoyama,et al.  Locked TASC probes for homogeneous sensing of nucleic acids and imaging of fixed E. coli cells. , 2005, Organic & biomolecular chemistry.

[82]  S. Silverman,et al.  Directing the outcome of deoxyribozyme selections to favor native 3'-5' RNA ligation. , 2005, Biochemistry.

[83]  Adam Roth,et al.  Ribozyme speed limits. , 2003, RNA.

[84]  D. Sen,et al.  Electron hole flow patterns through the RNA-cleaving 8-17 deoxyribozyme yield unusual information about its structure and folding. , 2007, Chemistry & biology.

[85]  Yingfu Li,et al.  Structure-switching signaling aptamers. , 2003, Journal of the American Chemical Society.

[86]  DNA and DNAzyme-mediated 2D colloidal assembly. , 2008, Journal of the American Chemical Society.

[87]  D. Lilley,et al.  Nucleobase catalysis in the hairpin ribozyme. , 2006, RNA.

[88]  W. Tan,et al.  Engineering a unimolecular DNA-catalytic probe for single lead ion monitoring. , 2009, Journal of the American Chemical Society.

[89]  A. Peracchi Preferential Activation of the 8–17 Deoxyribozyme by Ca 2+ Ions , 2000, The Journal of Biological Chemistry.

[90]  Yingfu Li,et al.  Enzymatic cleavage of nucleic acids on gold nanoparticles: a generic platform for facile colorimetric biosensors. , 2008, Small.

[91]  Scott K. Silverman,et al.  DNA-catalyzed sequence-specific hydrolysis of DNA , 2009, Nature chemical biology.

[92]  M. Famulok,et al.  Ca2+-Ionen als Cofaktoren für ein neuartiges RNA-spaltendes Desoxyribozym† , 1996 .

[93]  S. Silverman,et al.  Mimicking the first step of RNA splicing: an artificial DNA enzyme can synthesize branched RNA using an oligonucleotide leaving group as a 5'-exon analogue. , 2005, Biochemistry.

[94]  Yingfu Li,et al.  DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides , 2008, Nucleic acids research.

[95]  Yong Liu,et al.  A contact photo-cross-linking investigation of the active site of the 8-17 deoxyribozyme. , 2008, Journal of molecular biology.

[96]  A. Feldman,et al.  A new and efficient DNA enzyme for the sequence-specific cleavage of RNA. , 2001, Journal of molecular biology.

[97]  Yi Lu,et al.  Probing metal binding in the 8-17 DNAzyme by TbIII luminescence spectroscopy. , 2008, Chemistry.

[98]  Peter F M Choong,et al.  DNAzyme technology and cancer therapy: cleave and let die , 2008, Molecular Cancer Therapeutics.

[99]  Yi Lu,et al.  Improving fluorescent DNAzyme biosensors by combining inter- and intramolecular quenchers. , 2003, Analytical chemistry.

[100]  Yingfu Li,et al.  Sequence-function relationships provide new insight into the cleavage site selectivity of the 8–17 RNA-cleaving deoxyribozyme , 2008, Nucleic acids research.

[101]  Yi Lu,et al.  A DNAzyme catalytic beacon sensor for paramagnetic Cu2+ ions in aqueous solution with high sensitivity and selectivity. , 2007, Journal of the American Chemical Society.

[102]  C. Geyer,et al.  Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. , 1997, Chemistry & biology.

[103]  Darko Stefanovic,et al.  Deoxyribozyme-based logic gates. , 2002, Journal of the American Chemical Society.

[104]  Yingfu Li,et al.  Biologically inspired synthetic enzymes made from DNA. , 2009, Chemistry & biology.

[105]  S. Silverman,et al.  Characterization of deoxyribozymes that synthesize branched RNA. , 2003, Biochemistry.

[106]  The Advantages of Being Locked , 2007, Journal of Biological Chemistry.

[107]  Yi Lu,et al.  Label‐Free Colorimetric Detection of Lead Ions with a Nanomolar Detection Limit and Tunable Dynamic Range by using Gold Nanoparticles and DNAzyme , 2008 .

[108]  S. Silverman,et al.  Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects. , 2008, Chemical communications.

[109]  Juewen Liu,et al.  Metal-dependent global folding and activity of the 8-17 DNAzyme studied by fluorescence resonance energy transfer. , 2007, Journal of the American Chemical Society.

[110]  A. Peracchi,et al.  A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe. , 2002, Nucleic acids research.

[111]  Yi Lu,et al.  Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb(2+) and adenosine with high sensitivity, selectivity, and tunable dynamic range. , 2009, Journal of the American Chemical Society.

[112]  Y. Roupioz,et al.  Toward an RNaseA mimic: A DNAzyme with imidazoles and cationic amines. , 2002, Journal of the American Chemical Society.

[113]  R. Breaker,et al.  A common speed limit for RNA-cleaving ribozymes and deoxyribozymes. , 2003, RNA.

[114]  Zhenyu Lin,et al.  A sensitive and specific electrochemiluminescent sensor for lead based on DNAzyme. , 2009, Chemical communications.

[115]  A. Feldman,et al.  A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes. , 2002, Nucleic acids research.

[116]  G. F. Joyce,et al.  Mechanism and utility of an RNA-cleaving DNA enzyme. , 1998, Biochemistry.

[117]  Yong Liu,et al.  Light-regulated catalysis by an RNA-cleaving deoxyribozyme. , 2004, Journal of molecular biology.

[118]  Razvan Nutiu,et al.  Structure-switching allosteric deoxyribozymes , 2004 .

[119]  Yingfu Li,et al.  Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection , 2006, Nucleic acids research.