1
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Ali M, Nair P, Capretta A, Brennan JD. In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes. Chembiochem 2024:e202400085. [PMID: 38574237 DOI: 10.1002/cbic.202400085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.
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Affiliation(s)
- Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Parameswaran Nair
- Division of Respirology, McMaster University, and, Firestone Institute of Respiratory Health at St. Joseph's Health Care, Hamilton, ON, L8N 4A6, Canada
| | - Alfredo Capretta
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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2
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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3
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Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
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Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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4
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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5
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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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6
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A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm. Sci Rep 2019; 9:8224. [PMID: 31160698 PMCID: PMC6546695 DOI: 10.1038/s41598-019-44750-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/17/2019] [Indexed: 01/12/2023] Open
Abstract
Deoxyribozymes capable of catalyzing sequence-specific RNA cleavage have found broad applications in biotechnology, DNA computing and environmental sensing. Among these, deoxyribozyme 8–17 is the most common small DNA motif capable of catalyzing RNA cleavage. However, the extent to which other DNA molecules with similar catalytic motifs exist remains elusive. Here we report a novel RNA-cleaving deoxyribozyme called 10–12opt that functions with an equally small catalytic motif and an unusually short binding arm. This deoxyribozyme contains a 14-nucleotide catalytic core that preferentially catalyzes RNA cleavage at UN dinucleotide junctions (kobs = 0.9 h−1 for UU cleavage). Surprisingly, the left binding arm contains only three nucleotides and forms two canonical base pairs with the RNA substrate. Mutational analysis reveals that a riboguanosine residue 3-nucleotide downstream of cleavage site must not form canonical base pairing for the optimal catalysis, and this nucleobase likely participates in catalysis with its carbonyl O6 atom. Furthermore, we demonstrate that deoxyribozyme 10–12opt can be utilized to cleave certain microRNA sequences which are not preferentially cleaved by 8–17. Together, these results suggest that this novel RNA-cleaving deoxyribozyme forms a distinct catalytic structure than 8–17 and that sequence space may contain additional examples of DNA molecules that can cleave RNA at site-specific locations.
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7
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Liu M, Zhang Q, Kannan B, Botton GA, Yang J, Soleymani L, Brennan JD, Li Y. Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 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
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Balamurali Kannan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Gianluigi A. Botton
- Department of Materials Science and Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Jie Yang
- School of Biomedical Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Leyla Soleymani
- School of Biomedical Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - John D. Brennan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
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8
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Liu M, Zhang Q, Kannan B, Botton GA, Yang J, Soleymani L, Brennan JD, Li Y. Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors. Angew Chem Int Ed Engl 2018; 57:12440-12443. [PMID: 30043544 DOI: 10.1002/anie.201806489] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 11/08/2022]
Abstract
Micrometer-sized functional nucleic acid (FNA) superstructures (denoted as 3D DNA) were examined as a unique class of biorecognition elements to produce highly functional bioactive paper surfaces. 3D DNA containing repeating sequences of either a DNA aptamer or DNAzyme was created from long-chain products of rolling circle amplification followed by salt aging. The resulting 3D DNA retained its original spherical shape upon inkjet printing and adhered strongly to the paper surface via physisorption. 3D DNA paper sensors showed resistance to degradation by nucleases, suppressed nonspecific protein adsorption, and provided a much higher surface density of functional DNA relative to monomeric FNAs, making such species ideally suited for development of paper-based biosensors.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, 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.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Qiang Zhang
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Balamurali Kannan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Gianluigi A Botton
- Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Jie Yang
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
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9
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Li H, Wang M, Shi T, Yang S, Zhang J, Wang HH, Nie Z. A DNA-Mediated Chemically Induced Dimerization (D-CID) Nanodevice for Nongenetic Receptor Engineering To Control Cell Behavior. Angew Chem Int Ed Engl 2018; 57:10226-10230. [PMID: 29944203 DOI: 10.1002/anie.201806155] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 12/31/2022]
Abstract
Small-molecule regulation is a powerful switching tool to manipulate cell signal transduction for a desired function; however, most available methods usually require genetic engineering to endow cells with responsiveness to user-defined small molecules. Herein, we demonstrate a nongenetic approach for small-molecule-controlled receptor activation and consequent cell behavior manipulation that is based on DNA-mediated chemically induced dimerization (D-CID). D-CID uses a programmable chemical-responsive DNA nanodevice to trigger DNA strand displacement and induce the activation of c-Met, a tyrosine kinase receptor cognate for hepatocyte growth factor, through dimerization. Through the use of various functional nucleic acids, including aptamers and DNAzymes, as recognition modules, the versatility of D-CID in inducing c-Met signaling upon addition of various small-molecular or ionic cues, including ATP, histidine, and Zn2+ , is demonstrated. Moreover, owing its multi-input properties, D-CID can be used to manipulate the behaviors of multiple cell populations simultaneously in a selective and programmable fashion.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Tianhui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Jinghui Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
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10
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Li H, Wang M, Shi T, Yang S, Zhang J, Wang HH, Nie Z. A DNA-Mediated Chemically Induced Dimerization (D-CID) Nanodevice for Nongenetic Receptor Engineering To Control Cell Behavior. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806155] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Tianhui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Jinghui Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
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11
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Liu M, Yin Q, McConnell EM, Chang Y, Brennan JD, Li Y. DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification. Chemistry 2018; 24:4473-4479. [PMID: 29240289 DOI: 10.1002/chem.201705338] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Indexed: 01/10/2023]
Abstract
Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template. DFA begins with a stimulus-dependent RCA reaction, producing tandemly linked RCDs in long-chain DNA products. These RCDs cleave an RNA-containing DNA sequence to form additional primers that hybridize to the circular DNA molecule, giving rise to DNA assemblies that act as the new inputs for RCA. The RCA reaction and the cleavage event keep on feeding each other autonomously, resulting in exponential growth of repetitive DNA sequences that can be easily detected. This method can be used for the detection of both nucleic acid based targets and non-nucleic acid analytes. In this article, we discuss the conceptual framework of the feedback amplification approach, the essential features of this method as well as remaining challenges and possible solutions.
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Affiliation(s)
- Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, P. R. China
| | - Qingxin Yin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, P. R. China
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, P. R. China
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
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12
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Serendipitous Discovery of a Guanine-rich DNA Molecule with a Highly Stable Structure in Urea. Sci Rep 2018; 8:1935. [PMID: 29386529 PMCID: PMC5792554 DOI: 10.1038/s41598-018-20248-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/15/2018] [Indexed: 11/16/2022] Open
Abstract
We have made an accidental discovery of an unusual, single-stranded, guanine-rich DNA molecule that is capable of adopting a folded structure in 7 M urea (7MU) known to denature nucleic acid structures. The folding of this molecule requires Na+ and Mg2+ and the folded structure remains stable when subjected to denaturing (7MU) polyacrylamide gel electrophoresis. Results from sequence mutagenesis, DNA methylation, and circular dichroism spectroscopy studies suggest that this molecule adopts an intramolecular guanine-quadruplex structure with 5 layers of guanine tetrads. Our finding indicates that DNA has the ability to create extremely stable structural folds despite its limited chemical repertoire, making it possible to develop DNA-based systems for unconventional applications.
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13
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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: 184] [Impact Index Per Article: 26.3] [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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14
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15
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Liu M, Zhang Q, Chang D, Gu J, Brennan JD, Li Y. A DNAzyme Feedback Amplification Strategy for Biosensing. Angew Chem Int Ed Engl 2017; 56:6142-6146. [PMID: 28370773 DOI: 10.1002/anie.201700054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - John D. Brennan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
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16
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Hsieh PY, Monsur Ali M, Tram K, Jahanshahi-Anbuhi S, Brown CL, Brennan JD, Filipe CDM, Li Y. RNA Protection is Effectively Achieved by Pullulan Film Formation. Chembiochem 2017; 18:502-505. [PMID: 28090736 DOI: 10.1002/cbic.201600643] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 11/05/2022]
Abstract
RNA is a functionally versatile polymer but suffers from susceptibility to spontaneous and RNase-catalyzed degradation. This vulnerability makes it difficult to preserve RNA for extended periods of time, thus limiting its use in various contexts, including practical applications as functional nucleic acids. Here we present a simple method to preserve RNA by pullulan (a complex sugar produced by Aureobasidium pullulans fungus) film formation. This strategy can markedly suppress both spontaneous and RNase degradation. Importantly, the pullulan film readily dissolves in aqueous solution, thus allowing retrieval of fully functional RNA species. In order to illustrate the advantage of this protective method in a practical application, we engineered a simple paper sensor containing a bacteria-detecting RNA-cleaving DNAzyme. This detection capability of the device was unchanged after storage at room temperature for six months.
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Affiliation(s)
- Ping-Yao Hsieh
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - M Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Kha Tram
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada)
| | - Christine L Brown
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada)
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada)
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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17
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Tram K, Manochehry S, Feng Q, Chang D, Salena BJ, Li Y. Colorimetric Detection of Bacteria Using Litmus Test. J Vis Exp 2016. [PMID: 27685457 DOI: 10.3791/54546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
There are increasing demands for simple but still effective methods that can be used to detect specific pathogens for point-of-care or field applications. Such methods need to be user-friendly and produce reliable results that can be easily interpreted by both specialists and non-professionals. The litmus test for pH is simple, quick, and effective as it reports the pH of a test sample via a simple color change. We have developed an approach to take advantage of the litmus test for bacterial detection. The method exploits a bacterium-specific RNA-cleaving DNAzyme to achieve two functions: recognizing a bacterium of interest and providing a mechanism to control the activity of urease. Through the use of magnetic beads immobilized with a DNAzyme-urease conjugate, the presence of bacteria in a test sample is relayed to the release of urease from beads to solution. The released urease is transferred to a test solution to hydrolyze urea into ammonia, resulting in an increase of pH that can be visualized using the classic litmus test.
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Affiliation(s)
- Kha Tram
- Department of Biochemistry and Biomedical Sciences, McMaster University
| | - Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster University
| | - Qian Feng
- Department of Chemistry and Chemical Biology, McMaster University
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University;
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18
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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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Tomita Y, Morita Y, Suga H, Fujiwara D. DNA module platform for developing colorimetric aptamer sensors. Biotechniques 2016; 60:285-92. [PMID: 27286805 DOI: 10.2144/000114425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/11/2016] [Indexed: 11/23/2022] Open
Abstract
Here we present a DNA module platform for developing simple aptamer sensors based on a microarray format combined with secondary structure prediction in silico. The platform comprises four parts: (i) aptamer, (ii) joint module, (iii) terminal stem, and (iv) a DNAzyme that catalyzes a redox reaction controlled by a structural change induced by aptamer/target binding. First, we developed a joint module, capable of sensing a conformational change in the aptamer region, that was linked to the signal transmission activity of a DNAzyme as the reporter in a concentration-dependent manner with the AMP aptamer. This module design was then used to generate an arginine sensor simply by replacing the AMP aptamer region with a previously reported arginine aptamer. Using this DNA module platform, we were also able to customize a microarray containing >10,000 sequences designed by in silico secondary structure prediction and successfully identify a new aptamer against patulin. Our results show that the DNA module platform can be used to readily devise sensors based on known aptamers as well as create new aptamer sensors by array-based screening.
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Affiliation(s)
- Yasuyuki Tomita
- Central Laboratories for Key Technologies, KIRIN Company, Ltd, Yokohama, Japan
| | - Yuji Morita
- Central Laboratories for Key Technologies, KIRIN Company, Ltd, Yokohama, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Daisuke Fujiwara
- Central Laboratories for Key Technologies, KIRIN Company, Ltd, Yokohama, Japan
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20
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Adornetto G, Porchetta A, Palleschi G, Plaxco KW, Ricci F. A general approach to the design of allosteric, transcription factor-regulated DNAzymes. Chem Sci 2015; 6:3692-3696. [PMID: 28706715 PMCID: PMC5496187 DOI: 10.1039/c5sc00228a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/09/2015] [Indexed: 12/26/2022] Open
Abstract
Here we explore a general strategy for the rational design of nucleic acid catalysts that can be allosterically activated by specific nucleic-acid binding proteins. To demonstrate this we have combined a catalytic DNAzyme sequence and the consensus sequence recognized by specific transcription factors to create a construct exhibiting two low-energy conformations: a more stable conformation lacking catalytic activity and lacking the transcription factor binding site, and a less stable conformation that is both catalytically active and competent to bind the transcription factor. The presence of the target transcription factor pushes the equilibrium between these states towards the latter conformation, concomitantly activating catalysis. To demonstrate this we have designed and characterized two peroxidase-like DNAzymes whose activities are triggered upon binding either TATA binding protein or the microphthalmia-associated transcription factor. Our approach augments the current tool kit for the allosteric control of DNAzymes and ribozymes and, because transcription factors control many key biological functions, could have important clinical and diagnostic applications.
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Affiliation(s)
- G Adornetto
- Dipartimento di Scienze e Tecnologie Chimiche University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy .
| | - A Porchetta
- Dipartimento di Scienze e Tecnologie Chimiche University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy .
- Consorzio Interuniversitario Biostrutture e Biosistemi "INBB" , Rome 00136 , Italy
| | - G Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy .
- Consorzio Interuniversitario Biostrutture e Biosistemi "INBB" , Rome 00136 , Italy
| | - K W Plaxco
- Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , USA
- Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , USA
| | - F Ricci
- Dipartimento di Scienze e Tecnologie Chimiche University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy .
- Consorzio Interuniversitario Biostrutture e Biosistemi "INBB" , Rome 00136 , Italy
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21
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Torabi SF, Wu P, McGhee CE, Chen L, Hwang K, Zheng N, Cheng J, Lu Y. In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing. Proc Natl Acad Sci U S A 2015; 112:5903-8. [PMID: 25918425 PMCID: PMC4434688 DOI: 10.1073/pnas.1420361112] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Over the past two decades, enormous progress has been made in designing fluorescent sensors or probes for divalent metal ions. In contrast, the development of fluorescent sensors for monovalent metal ions, such as sodium (Na(+)), has remained underdeveloped, even though Na(+) is one the most abundant metal ions in biological systems and plays a critical role in many biological processes. Here, we report the in vitro selection of the first (to our knowledge) Na(+)-specific, RNA-cleaving deoxyribozyme (DNAzyme) with a fast catalytic rate [observed rate constant (ko(bs)) ∼ 0.1 min(-1)], and the transformation of this DNAzyme into a fluorescent sensor for Na(+) by labeling the enzyme strand with a quencher at the 3' end, and the DNA substrate strand with a fluorophore and a quencher at the 5' and 3' ends, respectively. The presence of Na(+) catalyzed cleavage of the substrate strand at an internal ribonucleotide adenosine (rA) site, resulting in release of the fluorophore from its quenchers and thus a significant increase in fluorescence signal. The sensor displays a remarkable selectivity (>10,000-fold) for Na(+) over competing metal ions and has a detection limit of 135 µM (3.1 ppm). Furthermore, we demonstrate that this DNAzyme-based sensor can readily enter cells with the aid of α-helical cationic polypeptides. Finally, by protecting the cleavage site of the Na(+)-specific DNAzyme with a photolabile o-nitrobenzyl group, we achieved controlled activation of the sensor after DNAzyme delivery into cells. Together, these results demonstrate that such a DNAzyme-based sensor provides a promising platform for detection and quantification of Na(+) in living cells.
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Affiliation(s)
| | | | | | | | | | - Nan Zheng
- Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jianjun Cheng
- Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Departments of Biochemistry, Chemistry, and Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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22
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Tram K, Xia J, Gysbers R, Li Y. An Efficient Catalytic DNA that Cleaves L-RNA. PLoS One 2015; 10:e0126402. [PMID: 25946137 PMCID: PMC4422682 DOI: 10.1371/journal.pone.0126402] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/01/2015] [Indexed: 12/22/2022] Open
Abstract
Many DNAzymes have been isolated from synthetic DNA pools to cleave natural RNA (D-RNA) substrates and some have been utilized for the design of aptazyme biosensors for bioanalytical applications. Even though these biosensors perform well in simple sample matrices, they do not function effectively in complex biological samples due to ubiquitous RNases that can efficiently cleave D-RNA substrates. To overcome this issue, we set out to develop DNAzymes that cleave L-RNA, the enantiomer of D-RNA, which is known to be completely resistant to RNases. Through in vitro selection we isolated three L-RNA-cleaving DNAzymes from a random-sequence DNA pool. The most active DNAzyme exhibits a catalytic rate constant ~3 min-1 and has a structure that contains a kissing loop, a structural motif that has never been observed with D-RNA-cleaving DNAzymes. Furthermore we have used this DNAzyme and a well-known ATP-binding DNA aptamer to construct an aptazyme sensor and demonstrated that this biosensor can achieve ATP detection in biological samples that contain RNases. The current work lays the foundation for exploring RNA-cleaving DNAzymes for engineering biosensors that are compatible with complex biological samples.
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Affiliation(s)
- Kha Tram
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jiaji Xia
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rachel Gysbers
- Department of Biochemistry and Biomedical Sciences and Origins Institute, McMaster University, Hamilton, Ontario, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, and Origins Institute, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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23
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Abstract
Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Fax: 217-244-3186; Tel: 217-333-2619
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Fax: 217-244-3186; Tel: 217-333-2619
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24
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Torabi SF, Lu Y. Functional DNA nanomaterials for sensing and imaging in living cells. Curr Opin Biotechnol 2014; 28:88-95. [PMID: 24468446 DOI: 10.1016/j.copbio.2013.12.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/17/2013] [Accepted: 12/25/2013] [Indexed: 12/25/2022]
Abstract
Recent developments in integrating high selectivity of functional DNA, such as DNAzymes and aptamers, with efficient DNA delivery into cells by gold nanoparticles or superior near-infrared optical properties of upconversion nanoparticles are reviewed. Their applications in sensing and imaging small organic metabolites, toxins, metal ions, pH, DNA, RNA, proteins, and pathogens are summarized. The advantages and future directions of these functional DNA materials are discussed.
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Affiliation(s)
- Seyed-Fakhreddin Torabi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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25
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Ali MM, Li F, Zhang Z, Zhang K, Kang DK, Ankrum JA, Le XC, Zhao W. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev 2014; 43:3324-41. [DOI: 10.1039/c3cs60439j] [Citation(s) in RCA: 650] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Nesterova IV, Elsiddieg SO, Nesterov EE. Design and evaluation of an i-motif-based allosteric control mechanism in DNA-hairpin molecular devices. J Phys Chem B 2013; 117:10115-21. [PMID: 23941235 DOI: 10.1021/jp405230g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molecular devices designed to assess and manipulate biologically relevant conditions with required accuracy and precision play an essential role in life sciences research. Incorporating allosteric regulation mechanism is an attractive strategy toward more efficient artificial sensing and switching systems. Herein, we report on a new principle of regulating switching parameters of a DNA-based molecular device based on allosteric interaction between spatially separated hairpin stem and a tetraplexed fragment (i.e., i-motif). We characterized thermodynamic and kinetic effects arising from interaction between functional domains of the device and demonstrated the potential of applying the allosteric control principle for rational design of sensors and switches with precisely defined operational characteristics.
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Affiliation(s)
- Irina V Nesterova
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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27
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Abstract
The vast majority of deoxyribozyme-based sensors are designed using modified RNA-cleaving deoxyribozymes and detect analytes that act as allosteric regulators of their catalytic activity. These sensors are susceptible to background signals due to catalytic activity in the absence of target or contaminant molecules that cleave the RNA substrate, mimicking the deoxyribozyme reaction. In this manuscript, we introduce a novel system that avoids these problems by using the analyte as the substrate for a deoxyribozyme catalyzed self-phosphorylation reaction. This reaction creates a modified deoxyribozyme product that can be circularized and subjected to massive signal amplification by rolling circle amplification, leading to a sensor system with high sensitivity and low background, which can be coupled to numerous reporter systems. As an example of the potential of this system, we used the self-phosphorylating deoxyribozyme Dk2 to detect as little as 25 nM GTP even in the presence of 1 mM ATP, a potential contaminant. To demonstrate the adaptive properties of this system, we appended another DNA sequence to Dk2, which, once amplified by RCA, codes for a fluorescence generating deoxyribozyme. This two-deoxyribozyme system was able to report the presence of GTP from 4 μM to 1 mM, with specificity over other NTP molecules. Using this model system, we were able to show that small molecule modifying deoxyribozymes can be converted to analyte sensors by coupling their catalytic activity to signal amplification and reporting.
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Affiliation(s)
- Simon A McManus
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1 Canada
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28
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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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29
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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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30
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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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31
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Wang RE, Zhang Y, Cai J, Cai W, Gao T. Aptamer-based fluorescent biosensors. Curr Med Chem 2012; 18:4175-84. [PMID: 21838688 DOI: 10.2174/092986711797189637] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 01/24/2023]
Abstract
Selected from random pools of DNA or RNA molecules through systematic evolution of ligands by exponential enrichment (SELEX), aptamers can bind to target molecules with high affinity and specificity, which makes them ideal recognition elements in the development of biosensors. To date, aptamer-based biosensors have used a wide variety of detection techniques, which are briefly summarized in this article. The focus of this review is on the development of aptamer-based fluorescent biosensors, with emphasis on their design as well as properties such as sensitivity and specificity. These biosensors can be broadly divided into two categories: those using fluorescently-labeled aptamers and others that employ label-free aptamers. Within each category, they can be further divided into "signal-on" and "signal-off" sensors. A number of these aptamer-based fluorescent biosensors have shown promising results in biological samples such as urine and serum, suggesting their potential applications in biomedical research and disease diagnostics.
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Affiliation(s)
- R E Wang
- Department of Chemistry, Washington University in St. Louis, MO, USA
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32
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Zou R, Lou X, Ou H, Zhang Y, Wang W, Yuan M, Guan M, Luo Z, Liu Y. Highly specific triple-fragment aptamer for optical detection of cocaine. RSC Adv 2012. [DOI: 10.1039/c2ra20307c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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33
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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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34
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Abstract
Aptamers are useful for allosteric regulation because they are nucleic acid-based structures in which ligand binding induces conformational changes that may alter the function of a connected oligonucleotide at a distant site. Through this approach, a specific input is efficiently converted into an altered output. This property makes these biomolecules ideally suited to function as sensors or switches in biochemical assays or inside living cells. The ability to select oligonucleotide-based recognition elements in vitro in combination with the availability of nucleic acids with enzymatic activity has led to the development of a wide range of engineered allosteric aptasensors and aptazymes. Here, we discuss recent progress in the screening, design and diversity of these conformational switching oligonucleotides. We cover their application in vitro and for regulating gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Jan L Vinkenborg
- Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit, Laboratory of Chemical Biology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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35
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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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36
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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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37
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Functional Nucleic Acids for Fluorescence-Based Biosensing Applications. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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38
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Sun C, Liu X, Feng K, Jiang J, Shen G, Yu R. An aptazyme-based electrochemical biosensor for the detection of adenosine. Anal Chim Acta 2010; 669:87-93. [PMID: 20510908 DOI: 10.1016/j.aca.2010.04.057] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 04/23/2010] [Accepted: 04/26/2010] [Indexed: 11/29/2022]
Abstract
In this work, an aptazyme-based electrochemical biosensor for the detection of adenosine is reported. Aptazyme activity was modulated by appending an "inhibitor" oligonucleotide strand containing a 32-base adenosine aptamer to the 8-17 DNAzyme. In the absence of adenosine, the DNAzyme could not form appropriate catalytic structure due to the binding with the inhibitor strand. Upon adenosine binding to the aptamer, the inhibitor strand was dissociated from the DNAzyme sequence. This allowed the DNAzyme to open and bind with the hairpin substrate, and DNAzyme activity was thereby induced, cleaving the substrate at its ribonucleotide site in the presence of Pb(2+). Cleavage of the substrate yields two single-stranded products, one of which was ferrocene-tagged and acted as the signal probe. The thiolated probe modified on the gold electrode could capture the signal probe. As a result, the ferrocene (Fc) moiety was brought in close proximity to the electrode surface and the Faradaic current was observed. This electrochemical biosensor was proved to have a wide dynamic range from 5 nM to 2000 nM with a detection limit of 5 nM. The fabricated sensor is shown to exhibit high sensitivity and desirable selectivity, which might be promising for the rational construction of aptazyme-based biosensors and the determination of adenosine in clinical examination.
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Affiliation(s)
- Chenhu Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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Zhao Z, Xu L, Shi X, Tan W, Fang X, Shangguan D. Recognition of subtype non-small cell lung cancer by DNA aptamers selected from living cells. Analyst 2009; 134:1808-14. [PMID: 19684903 DOI: 10.1039/b904476k] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In this work, we have developed new aptamer probes for non-small cell lung cancer (NSCLC) by directing the aptamer selection process against the living cells of adenocarcinoma, the most common subtype of NSCLC. A panel of single-stranded DNA (ssDNA) aptamers were generated and evaluated for adenocarcinoma cell recognition. The aptamers bound to the adenocarcinoma cells with dissociation constants in the nanomolar range and the binding of the selected aptamers to the adenocarcinoma cells were significantly stronger than the other cancerous lung cells as well as other types of cancer cells. Moreover, the application of the aptamers to the clinical tissue section samples showed the differentiation of adenocarcinoma from normal lung tissue and other subtypes of lung cancer. The aptamers are expected to be new molecular probes for the investigation of the molecular bases of different NSCLC subtypes and their biological heterogeneity, which is valuable for advancing NSCLC diagnosis and treatment.
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Affiliation(s)
- Zilong Zhao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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Ali MM, Li Y. Colorimetric sensing by using allosteric-DNAzyme-coupled rolling circle amplification and a peptide nucleic acid-organic dye probe. Angew Chem Int Ed Engl 2009; 48:3512-5. [PMID: 19360817 DOI: 10.1002/anie.200805966] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Target detection by the naked eye: The action of an RNA-cleaving allosteric DNAzyme in response to ligand binding was coupled to a rolling circle amplification process to generate long single-stranded DNA molecules for colorimetric sensing (see scheme). Upon hybridization of the resulting DNA with a complementary PNA sequence in the presence of a duplex-binding dye, the color of the dye changed from blue to purple.
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Affiliation(s)
- M Monsur Ali
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
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Ali M, Li Y. Colorimetric Sensing by Using Allosteric-DNAzyme-Coupled Rolling Circle Amplification and a Peptide Nucleic Acid-Organic Dye Probe. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805966] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Berg J, Hung YP, Yellen G. A genetically encoded fluorescent reporter of ATP:ADP ratio. Nat Methods 2009; 6:161-6. [PMID: 19122669 PMCID: PMC2633436 DOI: 10.1038/nmeth.1288] [Citation(s) in RCA: 359] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2008] [Accepted: 11/17/2008] [Indexed: 11/09/2022]
Abstract
We constructed a fluorescent sensor of adenylate nucleotides by combining a circularly permuted variant of GFP with a bacterial regulatory protein, GlnK1, from Methanococcus jannaschii. The sensor's affinity for Mg-ATP was <100 nM, as seen for other members of the bacterial PII regulator family, a surprisingly high affinity given that normal intracellular ATP concentration is in the millimolar range. ADP bound the same site of the sensor as Mg-ATP, competing with it, but produced a smaller change in fluorescence. At physiological ATP and ADP concentrations, the binding site is saturated, but competition between the two substrates causes the sensor to behave as a nearly ideal reporter of the ATP:ADP concentration ratio. This principle for sensing the ratio of two analytes by competition at a high-affinity site probably underlies the normal functioning of PII regulatory proteins. The engineered sensor, Perceval, can be used to monitor the ATP:ADP ratio during live-cell imaging.
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Affiliation(s)
- Jim Berg
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, Massachusetts 02115, USA
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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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