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Nucleic acid-cleaving catalytic DNA for sensing and therapeutics. Talanta 2020; 211:120709. [PMID: 32070594 DOI: 10.1016/j.talanta.2019.120709] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/21/2022]
Abstract
DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.
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Mattioli EJ, Bottoni A, Calvaresi M. DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1. J Chem Inf Model 2019; 59:1547-1553. [DOI: 10.1021/acs.jcim.8b00815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Edoardo Jun Mattioli
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
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3
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Liu M, Chang D, Li Y. Discovery and Biosensing Applications of Diverse RNA-Cleaving DNAzymes. Acc Chem Res 2017; 50:2273-2283. [PMID: 28805376 DOI: 10.1021/acs.accounts.7b00262] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors. This Account begins with the description of an accidental discovery on the sequence adaptability of a small DNAzyme known as "8-17", when we performed 16 parallel selections to search for DNAzymes that targeted each and every possible dinucleotide junction of RNA for cleavage. DNAzyme 8-17 dominated all the selection pools targeting purine-containing junctions. In-depth sequence analysis revealed that 8-17 could manifest itself in many sequence options defined by the requirement of four absolutely conserved nucleotides. This study also exposed the fact that 8-17 had poor activity toward pyrimidine-pyrimidine junctions. With this information in hand, we proceeded to the discovery of diverse non-8-17 DNAzymes that exhibited robust catalytic activity under physiological conditions. These DNAzymes were found to universally interact with their substrates through two Watson-Crick binding arms and have a catalytic core of varying length and secondary-structure complexity. RNA-cleaving DNAzymes were also isolated to function at acidic conditions (pH 3-5), and these molecules exhibited intriguing pH profiles, with the highest activity precisely matching the pH used for their selection. Interestingly, these DNAzymes appear to use non-Watson-Crick interactions in defining their structures. More recently, we have embarked on the development of ligand-responsive RNA-cleaving fluorogenic DNAzymes that can recognize specific bacterial pathogens, such as Escherichia coli and Clostridium difficile, using a method that does not require a priori identification of a specific biomarker. Instead, the crude extracellular mixture as a whole is used as the target to drive the DNAzyme isolation. High recognition specificity can be achieved with a double-selection approach in which a DNA library is negatively selected against the cellular mixture prepared from unintended bacteria, followed by positive selection against the same mixture derived from a specific species or strain of bacterial pathogen. Finally, we have shown that DNAzymes' compatibility with DNA replication can benefit the design of amplification mechanisms that uniquely link the action of RNA-cleaving DNAzymes to rolling circle amplification, an isothermal DNA amplification technique. These methods are well suited for translating the target-binding and cleavage activity of an analyte-activated RNA-cleaving DNAzyme into the production of massive amounts of DNA amplicons to achieve ultrahigh detection sensitivity. Given the high chemical stability of DNA, our ability to discover catalytic DNA sequences by simultaneously evaluating as many as 1016 different DNA sequences, the accessibility to diverse RNA-cleaving DNAzymes in a single DNA pool, and the availability of methods for designing simple biosensors that incorporate RNA-cleaving DNAzymes, we believe we are moving closer to employing RNA-cleaving DNAzymes for exciting applications, such as point of care diagnostics or field detection of environmental toxins.
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Affiliation(s)
- Meng Liu
- Department
of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute
of Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- School
of Environmental Science and Technology, Key Laboratory of Industrial
Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
| | - Dingran Chang
- Department
of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute
of Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Yingfu Li
- Department
of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute
of Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
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4
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Zhang W, Feng Q, Chang D, Tram K, Li Y. In vitro selection of RNA-cleaving DNAzymes for bacterial detection. Methods 2016; 106:66-75. [DOI: 10.1016/j.ymeth.2016.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/23/2022] Open
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5
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Gao J, Shimada N, Maruyama A. Enhancement of deoxyribozyme activity by cationic copolymers. Biomater Sci 2015. [DOI: 10.1039/c4bm00256c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cationic copolymer enhanced DNAzyme activity.
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Affiliation(s)
- Jueyuan Gao
- Graduate School of Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Naohiko Shimada
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Atsushi Maruyama
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Yokohama
- Japan
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6
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Examination of bacterial inhibition using a catalytic DNA. PLoS One 2014; 9:e115640. [PMID: 25531274 PMCID: PMC4274092 DOI: 10.1371/journal.pone.0115640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/26/2014] [Indexed: 12/25/2022] Open
Abstract
Determination of accurate dosage of existing antibiotics and discovery of new antimicrobials or probiotics entail simple but effective methods that can conveniently track bacteria growth and inhibition. Here we explore the application of a previously reported fluorogenic E. coli-specific DNAzyme (catalytic DNA), RFD-EC1, as a molecular probe for monitoring bacterial inhibition exerted by antibiotics and for studying bacterial competition as a result of cohabitation. Because the DNAzyme method provides a convenient way to monitor the growth of E. coli, it is capable of determining the minimal inhibitory concentration (MIC) of antibiotics much faster than the conventional optical density (OD) method. In addition, since the target for RFD-EC1 is an extracellular protein molecule from E. coli, RFD-EC1 is able to identify pore-forming antibiotics or compounds that can cause membrane leakage. Finally, RFD-EC1 can be used to analyse the competition of cohabitating bacteria, specifically the inhibition of growth of E. coli by Bacillus subtilis. The current work represents the first exploration of a catalytic DNA for microbiological applications and showcases the utility of bacteria-sensing fluorogenic DNAzymes as simple molecular probes to facilitate antibiotic and probiotic research.
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Lighting Up RNA-Cleaving DNAzymes for Biosensing. J Nucleic Acids 2012; 2012:958683. [PMID: 23209883 PMCID: PMC3503364 DOI: 10.1155/2012/958683] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/03/2012] [Indexed: 01/02/2023] Open
Abstract
The development of the in vitro selection technique has allowed the isolation of functional nucleic acids, including catalytic DNA molecules (DNAzymes), from random-sequence pools. The first-ever catalytic DNA obtained by this technique in 1994 is a DNAzyme that cleaves RNA. Since then, many other RNase-like DNAzymes have been reported from multiple in vitro selection studies. The discovery of various RNase DNAzymes has in turn stimulated the exploration of these enzymatic species for innovative applications in many different areas of research, including therapeutics, biosensing, and DNA nanotechnology. One particular research topic that has received considerable attention for the past decade is the development of RNase DNAzymes into fluorescent reporters for biosensing applications. This paper provides a concise survey of the most significant achievements within this research topic.
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Abstract
Outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses each and every year. Prevention of such outbreaks and minimization of the impact of an ongoing epidemic place an ever-increasing demand for analytical methods that can accurately identify culprit pathogens at the earliest stage. Although there is a large array of effective methods for pathogen detection, none of them can satisfy all the following five premier requirements embodied for an ideal detection method: high specificity (detecting only the bacterium of interest), high sensitivity (capable of detecting as low as a single live bacterial cell), short time-to-results (minutes to hours), great operational simplicity (no need for lengthy sampling procedures and the use of specialized equipment), and cost effectiveness. For example, classical microbiological methods are highly specific but require a long time (days to weeks) to acquire a definitive result.(1) PCR- and antibody-based techniques offer shorter waiting times (hours to days), but they require the use of expensive reagents and/or sophisticated equipment.(2-4) Consequently, there is still a great demand for scientific research towards developing innovative bacterial detection methods that offer improved characteristics in one or more of the aforementioned requirements. Our laboratory is interested in examining the potential of DNAzymes as a novel class of molecular probes for biosensing applications including bacterial detection.(5) DNAzymes (also known as deoxyribozymes or DNA enzymes) are man-made single-stranded DNA molecules with the capability of catalyzing chemical reactions.(6-8) These molecules can be isolated from a vast random-sequence DNA pool (which contains as many as 10(16) individual sequences) by a process known as "in vitro selection" or "SELEX" (systematic evolution of ligands by exponential enrichment).(9-16) These special DNA molecules have been widely examined in recent years as molecular tools for biosensing applications.(6-8) Our laboratory has established in vitro selection procedures for isolating RNA-cleaving fluorescent DNAzymes (RFDs; Fig. 1) and investigated the use of RFDs as analytical tools.(17-29) RFDs catalyze the cleavage of a DNA-RNA chimeric substrate at a single ribonucleotide junction (R) that is flanked by a fluorophore (F) and a quencher (Q). The close proximity of F and Q renders the uncleaved substrate minimal fluorescence. However, the cleavage event leads to the separation of F and Q, which is accompanied by significant increase of fluorescence intensity. More recently, we developed a method of isolating RFDs for bacterial detection.(5) These special RFDs were isolated to "light up" in the presence of the crude extracellular mixture (CEM) left behind by a specific type of bacteria in their environment or in the media they are cultured (Fig. 1). The use of crude mixture circumvents the tedious process of purifying and identifying a suitable target from the microbe of interest for biosensor development (which could take months or years to complete). The use of extracellular targets means the assaying procedure is simple because there is no need for steps to obtain intracellular targets. Using the above approach, we derived an RFD that cleaves its substrate (FS1; Fig. 2A) only in the presence of the CEM produced by E. coli (CEM-EC).(5) This E. coli-sensing RFD, named RFD-EC1 (Fig. 2A), was found to be strictly responsive to CEM-EC but nonresponsive to CEMs from a host of other bacteria (Fig. 3). Here we present the key experimental procedures for setting up E. coli detection assays using RFD-EC1 and representative results.
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Affiliation(s)
- Sergio D Aguirre
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
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9
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Li Y. Advancements in using reporter DNAzymes for identifying pathogenic bacteria at speed and with convenience. Future Microbiol 2012; 6:973-6. [PMID: 21958136 DOI: 10.2217/fmb.11.79] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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10
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Nelson KE, Ihms HE, Mazumdar D, Bruesehoff PJ, Lu Y. The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme. Chembiochem 2012; 13:381-91. [PMID: 22250000 PMCID: PMC3299816 DOI: 10.1002/cbic.201100724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Indexed: 11/12/2022]
Abstract
DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co(2+) over Pb(2+) compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co(2+) over Pb(2+) to levels observed in clone 11. A comparison of these sequences' secondary structures and Co(2+) selectivities suggested that metastable structures affect metal ion selectivity. The Co(2+) selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal-ion selectivity is required in rationally designed DNAzymes and DNAzyme-based biosensors.
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Affiliation(s)
- Kevin E. Nelson
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Pediatrics, Primary Children’s Medical Center, University of Utah, 100 North Mario Capecchi Drive, Salt Lake City, UT 84113 (USA)
| | - Hannah E. Ihms
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Debapriya Mazumdar
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Peter J. Bruesehoff
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Yi Lu
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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11
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Abstract
Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules that have the ability to catalyze a chemical reaction. Currently, DNAzymes have to be isolated from random-sequence DNA libraries by a process known as in vitro selection (IVS) because no naturally occurring DNAzyme has been discovered. Several IVS studies have led to the isolation of many RNA-cleaving DNAzymes (RNase DNAzymes), which catalyze the transesterification of a phosphodiester linkage in an RNA substrate, resulting in its cleavage. An RNase DNAzyme and its substrate can be modified with a pair of donor and acceptor fluorophores (or a fluorophore and quencher pair) to create a fluorescence-signaling system (a signaling DNAzyme) where the RNA-cleaving activity of the DNAzyme is reported through the generation of a fluorescent signal. A signaling DNAzyme can be further coupled with an aptamer (a target-binding nucleic acid sequence) to generate a fluorogenic aptazyme in which the aptamer-target interaction confers an allosteric control of the coupled RNA-cleaving and fluorescence-signaling activity of the DNAzyme. Fluorogenic aptazymes can be exploited as valuable molecular tools for biosensing applications. In this chapter, we provide both a detailed description of methods for isolation of signaling DNAzymes by IVS and general approaches for rational engineering of fluorogenic aptazymes for target detection.
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Ali MM, Aguirre SD, Lazim H, Li Y. Fluorogenic DNAzyme Probes as Bacterial Indicators. Angew Chem Int Ed Engl 2011; 50:3751-4. [DOI: 10.1002/anie.201100477] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Indexed: 12/19/2022]
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13
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Ali MM, Aguirre SD, Lazim H, Li Y. Fluorogenic DNAzyme Probes as Bacterial Indicators. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100477] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Burke DH, Rhee SS. Assembly and activation of a kinase ribozyme. RNA (NEW YORK, N.Y.) 2010; 16:2349-2359. [PMID: 20935068 PMCID: PMC2995397 DOI: 10.1261/rna.2302810] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 08/30/2010] [Indexed: 05/30/2023]
Abstract
RNA activities can be regulated by modulating the relative energies of all conformations in a folding landscape; however, it is often unknown precisely how peripheral elements perturb the overall landscape in the absence of discrete alternative folds (inactive ensemble). This work explores the effects of sequence and secondary structure in governing kinase ribozyme activity. Kin.46 catalyzes thiophosphoryl transfer from ATPγS onto the 5' hydroxyl of polynucleotide substrates, and is regulated 10,000-fold by annealing an effector oligonucleotide to form activator helix P4. Transfer kinetics for an extensive series of ribozyme variants identified several dispensable internal single-stranded segments, in addition to a potential pseudoknot at the active site between segments J1/4 and J3/2 that is partially supported by compensatory rescue. Standard allosteric mechanisms were ruled out, such as formation of discrete repressive structures or docking P4 into the rest of the ribozyme via backbone 2' hydroxyls. Instead, P4 serves both to complete an important structural element (100-fold contribution to the reaction relative to a P4-deleted variant) and to mitigate nonspecific, inhibitory effects of the single-stranded tail (an additional 100-fold contribution to the apparent rate constant, k(obs)). Thermodynamic activation parameters ΔH(‡) and ΔS(‡), calculated from the temperature dependence of k(obs), varied with tail length and sequence. Inhibitory effects of the unpaired tail are largely enthalpic for short tails and are both enthalpic and entropic for longer tails. These results refine the structural view of this kinase ribozyme and highlight the importance of nonspecific ensemble effects in conformational regulation by peripheral elements.
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Affiliation(s)
- Donald H Burke
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, Missouri 65211, USA.
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15
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McManus SA, Li Y. The structural diversity of deoxyribozymes. Molecules 2010; 15:6269-84. [PMID: 20877222 PMCID: PMC6257715 DOI: 10.3390/molecules15096269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/23/2010] [Accepted: 09/02/2010] [Indexed: 11/16/2022] Open
Abstract
When not constrained to long double-helical arrangements, DNA is capable of forming structural arrangements that enable specific sequences to perform functions such as binding and catalysis under defined conditions. Through a process called in vitro selection, numerous catalytic DNAs, known as deoxyribozymes or DNAzymes, have been isolated. Many of these molecules have the potential to act as therapeutic agents and diagnostic tools. As such, a better understanding of the structural arrangements present in these functional DNAs will aid further efforts in the development and optimization of these useful molecules. Structural characterization of several deoxyribozymes through mutagenesis, in vitro re-selection, chemical probing and circular dichroism has revealed many distinct and elaborate structural classes. Deoxyribozymes have been found to contain diverse structural elements including helical junctions, pseudoknots, triplexes, and guanine quadruplexes. Some of these studies have further shown the repeated isolation of similar structural motifs in independent selection experiments for the same type of chemical reaction, suggesting that some structural motifs are well suited for catalyzing a specific chemical reaction. To investigate the extent of structural diversity possible in deoxyribozymes, a group of kinase deoxyribozymes have been extensively characterized. Such studies have discovered some interesting structural features of these DNAzymes while revealing some novel DNA structures.
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Affiliation(s)
- Simon A. McManus
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada; E-Mail:
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada; E-Mail:
- Department of Chemistry and Chemical Biology, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-905-528-9140 ext. 22462
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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17
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Abstract
BACKGROUND Although catalytic RNA enzymes (CRzs) are naturally occurring in many organisms, their DNA counterparts (CDzs) were developed by in vitro selection/evolution from random sequence libraries. OBJECTIVE To provide a brief overview of how CDzs have been selected in vitro, and of their properties and functions, as well as their possible future utility. METHODS We concentrated on examples of 'direct' selection of CDzs. Many CDzs have been used in biological settings, for example downregulation of target mRNAs, while many more recent applications use CDzs in biosensor and nanotechnology settings. CONCLUSIONS Although much work has concentrated on using CDzs for regulating gene expression, their potential as nucleic acid medicines has diminished substantially, supplanted by simple antisense oligonucleotides and, more recently, by small interfering RNAs (siRNAs). It seems unlikely that CDzs will have clinical utility. In contrast, they are likely to have significant potential in the sensor/nanotechnology arena.
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Affiliation(s)
- Weihua Pan
- Department of Pathology, Pennsylvania State University, Gittlen Cancer Research Foundation, Hershey Medical Center, Hershey, PA 17033, USA
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19
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Chiuman W, Li Y. Simple fluorescent sensors engineered with catalytic DNA 'MgZ' based on a non-classic allosteric design. PLoS One 2007; 2:e1224. [PMID: 18030352 PMCID: PMC2077808 DOI: 10.1371/journal.pone.0001224] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2007] [Accepted: 10/30/2007] [Indexed: 11/20/2022] Open
Abstract
Most NAE (nucleic acid enzyme) sensors are composed of an RNA-cleaving catalytic motif and an aptameric receptor. They operate by activating or repressing the catalytic activity of a relevant NAE through the conformational change in the aptamer upon target binding. To transduce a molecular recognition event to a fluorescence signal, a fluorophore-quencher pair is attached to opposite ends of the RNA substrate such that when the NAE cleaves the substrate, an increased level of fluorescence can be generated. However, almost all NAE sensors to date harbor either NAEs that cannot accommodate a fluorophore-quencher pair near the cleavage site or those that can accept such a modification but require divalent transition metal ions for catalysis. Therefore, the signaling magnitude and the versatility of current NAE sensors might not suffice for analytical and biological applications. Here we report an RNA-cleaving DNA enzyme, termed ‘MgZ’, which depends on Mg2+ for its activity and can accommodate bulky dye moieties next to the cleavage site. MgZ was created by in vitro selection. The selection scheme entailed acidic buffering and ethanol-based reaction stoppage to remove selfish DNAs. Characterization of MgZ revealed a three-way junction structure, a cleavage rate of 1 min−1, and 26-fold fluorescence enhancement. Two ligand-responsive NAE sensors were rationally designed by linking an aptamer sequence to the substrate of MgZ. In the absence of the target, the aptamer-linked substrate is locked into a conformation that prohibits MgZ from accessing the substrate. In the presence of the target, the aptamer releases the substrate, which induces MgZ-mediated RNA cleavage. The discovery of MgZ and the introduction of the above NAE sensor design strategy should facilitate future efforts in sensor engineering.
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Affiliation(s)
- William Chiuman
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * To whom correspondence should be addressed. E-mail:
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20
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Ali MM, Kandadai SA, Li Y. Characterization of pH3DZ1 — An RNA-cleaving deoxyribozyme with optimal activity at pH 3. CAN J CHEM 2007. [DOI: 10.1139/v07-017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We previously described a cis-acting RNA-cleaving deoxyribozyme known as pH3DZ1 that exhibits optimal catalytic activity at pH 3.0 (Zhongjie Liu, Shirley H. Mei, John D. Brennan, and Yingfu Li. J. Am. Chem. Soc. 125, 7539 (2003)). This DNA catalyst was made of a 99-nucleotide (nt) catalytic domain covalently linked to a 23-nt DNA–RNA chimeric substrate containing a single ribonucleotide as the cleavage site. In the present work, we conducted an extensive sequence examination of this deoxyribozyme via nucleotide truncation and reselection experiments, with a goal to minimize its size and identify the nucleotides that are crucial to its catalytic function. A trans-acting deoxyribozyme that can process an external substrate was also successfully designed. Stretches of 30 and 17 nucleotides from the 5′ and 3′ ends of the trans catalyst, respectively, were found to be completely dispensable; in contrast, few nucleotides could be deleted internally without producing a detrimental effect. The reselection experiment led to the discovery of 7 and 5 absolutely conserved nucleotides located at the 5′ and 3′ ends of the minimized catalyst, respectively, separated by a 31-nt element in which 14 highly conserved nucleotides were scattered among 17 variable nucleotides. The shortened deoxyribozyme and the original catalyst showed a similar pH profile with the optimal activity at pH 3; however, the minimized deoxyribozyme still exhibited strong catalytic activity at pH 2.5, while the full-length catalyst was barely active at this pH. Finally, it was found that this deoxyribozyme generated two cleavage fragments, one with 2′,3′-cyclic phosphate and the other with 5′-OH.Key words: DNA, deoxyribozyme, RNA cleavage, in vitro selection, catalysis.
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