1
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Pang H, Peng Y, Zhang R, Gao Z, Lai X, Li D, Zhao X, Wang Y, Pei H, Qiao B, Ji Y, Wu Q. A triggered DNA nanomachine with enzyme-free for the rapid detection of telomerase activity in a one-step method. Anal Chim Acta 2024; 1299:342420. [PMID: 38499416 DOI: 10.1016/j.aca.2024.342420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/08/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Telomerase is considered a biomarker for the early diagnosis and clinical treatment of cancer. The rapid and sensitive detection of telomerase activity is crucial to biological research, clinical diagnosis, and drug development. However, the main obstacles facing the current telomerase activity assay are the cumbersome and time-consuming procedure, the easy degradation of the telomerase RNA template and the need for additional proteases. Therefore, it is necessary to construct a new method for the detection of telomerase activity with easy steps, efficient reaction and strong anti-interference ability. RESULTS Herein, an efficient, enzyme-free, economical, sensitive, fluorometric detection method for telomerase activity in one-step, named triggered-DNA (T-DNA) nanomachine, was created based on target-triggered DNAzyme-cleavage activity and catalytic molecular beacon (CMB). Telomerase served as a switch and extended few numbers of (TTAGGG)n repeat sequences to initiate the signal amplification in the T-DNA nanomachine, resulting in a strong fluorescent signal. The reaction was a one-step method with a shortened time of 1 h and a constant temperature of 37 °C, without the addition of any protease. It also sensitively distinguished telomerase activity in various cell lines. The T-DNA nanomachine offered a detection limit of 12 HeLa cells μL-1, 9 SK-Hep-1 cells μL-1 and 3 HuH-7 cells μL-1 with a linear correlation detection range of 0.39 × 102-6.25 × 102 HeLa cells μL-1 for telomerase activity. SIGNIFICANCE In conclusion, our study demonstrated that the triggered-DNA nanomachine fulfills the requirements for rapid detection of telomerase activity in one-step under isothermal and enzyme-free conditions with excellent specificity, and its simple and stable structure makes it ideal for complex systems. These findings indicated the application prospect of DNA nanomachines in clinical diagnostics and provided new insights into the field of DNA nanomachine-based bioanalysis.
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Affiliation(s)
- Huajie Pang
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Yanan Peng
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Rui Zhang
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Zhijun Gao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Xiangde Lai
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Dongxia Li
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Xuan Zhao
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Yuanyuan Wang
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Hua Pei
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China
| | - Bin Qiao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China.
| | - Yuxiang Ji
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China; Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou, 571199, China.
| | - Qiang Wu
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China.
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Zhou G, Lu X, Yuan M, Li T, Li L. Enzymatic Cycle-Inspired Dynamic Biosensors Affording No False-Positive Identification. Anal Chem 2021; 93:15482-15492. [PMID: 34767335 DOI: 10.1021/acs.analchem.1c03502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is an urgent need for reliable biosensors to detect nucleic acid of interest in clinical samples. We propose that the accuracy of the present nucleic acid-sensing method can be advanced by avoiding false-positive identifications derived from nonspecific interactions (e.g., nonspecific binding, probe degradation). The challenge is to exploit biosensors that can distinguish false-positive from true-positive samples in nucleic acid screening. In the present study, by learning from the enzymatic cycle in nature, we raise an allostery tool displaying invertible positive/negative cooperativity for reversible or cyclic activity control of the biosensing probe. We demonstrate that the silencing and regeneration of a positive (or negative) allosteric effector can be carried out through toehold displacement or an enzymatic reaction. We, thus, have developed several dynamic biosensors that can repeatedly measure a single nucleic acid sample. The ability to distinguish a false-positive from a true-positive signal is ascribed to the nonspecific interaction presenting equivalent signal variations, while the specific target binding exhibits diverse signal variations according to repeated measurements. Given its precise identification, such consequent dynamic biosensors offer exciting opportunities in physiological and pathological diagnosis.
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Affiliation(s)
- Guobao Zhou
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Xing Lu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Mengmeng Yuan
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Tuqiang Li
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Lei Li
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
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3
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Tickner ZJ, Farzan M. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors. Pharmaceuticals (Basel) 2021; 14:ph14060554. [PMID: 34200913 PMCID: PMC8230432 DOI: 10.3390/ph14060554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation.
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Affiliation(s)
- Zachary J. Tickner
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Correspondence:
| | - Michael Farzan
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Emmune, Inc., Jupiter, FL 33458, USA
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4
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Inhibited aptazyme-based catalytic molecular beacon for amplified detection of adenosine. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2014.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Lee JW, Cho JH, Cho EJ. Aptamer-based optical switch for biosensors. ANALYTICAL SCIENCE AND TECHNOLOGY 2014. [DOI: 10.5806/ast.2014.27.3.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Huang J, He Y, Yang X, Wang K, Quan K, Lin X. Split aptazyme-based catalytic molecular beacons for amplified detection of adenosine. Analyst 2014; 139:2994-7. [DOI: 10.1039/c4an00454j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Oh SS, Plakos K, Xiao Y, Eisenstein M, Soh HT. In vitro selection of shape-changing DNA nanostructures capable of binding-induced cargo release. ACS NANO 2013; 7:9675-9683. [PMID: 24168267 PMCID: PMC3919467 DOI: 10.1021/nn404079v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Many biological systems employ allosteric regulatory mechanisms, which offer a powerful means of directly linking a specific binding event to a wide spectrum of molecular functionalities. There is considerable interest in generating synthetic allosteric regulators that can perform useful molecular functions for applications in diagnostics, imaging and targeted therapies, but generating such molecules through either rational design or directed evolution has proven exceptionally challenging. To address this need, we present an in vitro selection strategy for generating conformation-switching DNA nanostructures that selectively release a small-molecule payload in response to binding of a specific trigger molecule. As an exemplar, we have generated a DNA nanostructure that hybridizes with a separate 'cargo strand' containing an abasic site. This abasic site stably sequesters a fluorescent cargo molecule in an inactive state until the DNA nanostructure encounters an ATP trigger molecule. This ATP trigger causes the nanostructure to release the cargo strand, thereby liberating the fluorescent payload and generating a detectable fluorescent readout. Our DNA nanostructure is highly sensitive, with an EC50 of 30 μM, and highly specific, releasing its payload in response to ATP but not to other chemically similar nucleotide triphosphates. We believe that this selection approach could be generalized to generate synthetic nanostructures capable of selective and controlled release of other small-molecule cargos in response to a variety of triggers, for both research and clinical applications.
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Affiliation(s)
- Seung Soo Oh
- Materials Department, University of California, Santa Barbara, CA 93106
| | - Kory Plakos
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Yi Xiao
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Michael Eisenstein
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Hyongsok Tom Soh
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
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8
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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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9
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Reymond C, Beaudoin JD, Perreault JP. Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol Life Sci 2009; 66:3937-50. [PMID: 19718544 PMCID: PMC2777235 DOI: 10.1007/s00018-009-0124-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 01/12/2023]
Abstract
RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today's knowledge in the field.
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Affiliation(s)
- Cedric Reymond
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
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10
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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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11
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Furchak JRW, Yang P, Jennings C, Walter NG, Kennedy RT. Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection. Anal Chem 2008; 80:8195-201. [PMID: 18842060 DOI: 10.1021/ac801410k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A naturally occurring aptazyme, the glmS ribozyme, is adapted to an assay for glucosamine 6-phosphate, an effector molecule for the aptazyme. In the assay, binding of analyte allosterically activates aptazyme to cleave a fluorescently labeled oligonucleotide substrate. The extent of reaction, and hence analyte concentration, is detected by either fluorescence resonance energy transfer (FRET) or capillary electrophoresis with laser-induced fluorescence (CE-LIF). With FRET, assay signal is the rate of increase in FRET in presence of analyte. With CE-LIF, the assay signal is the peak height of cleavage product formed after a fixed incubation time. The assay has a linear response up to 100 (CE-LIF) or 500 microM (FRET) and detection limit of approximately 500 nM for glucosamine 6-phosphate under single-turnover conditions. When substrate is present in excess of the aptazyme, it is possible to amplify the signal by multiple turnovers to achieve a 13-fold improvement in sensitivity and detection limit of 50 nM. Successful signal amplification requires a temperature cycle to alternately dissociate cleaved substrate and allow fresh substrate to bind aptazyme. The results show that aptazymes have potential utility as analytical reagents for quantification of effector molecules.
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Affiliation(s)
- Jennifer R W Furchak
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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12
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Shen L, Chen Z, Li Y, He S, Xie S, Xu X, Liang Z, Meng X, Li Q, Zhu Z, Li M, Le XC, Shao Y. Electrochemical DNAzyme Sensor for Lead Based on Amplification of DNA−Au Bio-Bar Codes. Anal Chem 2008; 80:6323-8. [DOI: 10.1021/ac800601y] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Shen
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Zhong Chen
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Yihan Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Shali He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Shubao Xie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xiaodong Xu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Zhongwei Liang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xin Meng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Qing Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Zhiwei Zhu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Meixian Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - X. Chris Le
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Yuanhua Shao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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13
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Strohbach D, Turcu F, Schuhmann W, Müller S. Electrochemically Induced Modulation of the Catalytic Activity of a Reversible Redoxsensitive Riboswitch. ELECTROANAL 2008. [DOI: 10.1002/elan.200704173] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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15
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Nevoigt E, Fischer C, Mucha O, Matthäus F, Stahl U, Stephanopoulos G. Engineering promoter regulation. Biotechnol Bioeng 2007; 96:550-8. [PMID: 16964624 DOI: 10.1002/bit.21129] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Systems for easily controlled, conditional induction or repression of gene expression are indispensable tools in fundamental research and industrial-scale biotechnological applications. Both native and rationally designed inducible promoters have been widely used for this purpose. However, inherent regulation modalities or toxic, expensive or inconvenient inducers can impose limitations on their use. Tailored promoters with user-specified regulatory properties would permit sophisticated manipulations of gene expression. Here, we report a generally applicable strategy for the directed evolution of promoter regulation. Specifically, we applied random mutagenesis and a multi-stage flow cytometry screen to isolate mutants of the oxygen-responsive Saccharomyces cerevisiae DAN1 promoter. Two mutants were isolated which were induced under less-stringent anaerobiosis than the wild-type promoter enabling induction of gene expression in yeast fermentations simply by oxygen depletion during cell growth. Moreover, the engineered promoters showed a markedly higher maximal expression than the unmutated DAN1 promoter, under both fastidious anaerobiosis and microaerobisois.
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Affiliation(s)
- Elke Nevoigt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, Massachusetts 02139, USA
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16
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Rankin CJ, Fuller EN, Hamor KH, Gabarra SA, Shields TP. A simple fluorescent biosensor for theophylline based on its RNA aptamer. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 25:1407-24. [PMID: 17067962 DOI: 10.1080/15257770600919084] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Theophylline is a potent bronchodilator with a narrow therapeutic index. A simple fluorescent biosensor that detects clinically relevant theophylline concentrations has been developed using the well-characterized theophylline binding RNA aptamer. Hybridization of the RNA aptamer to a fluorescently labeled DNA strand (FL-DNA) yields a fluorescent RNA:DNA hybrid that is sensitive to theophylline. The biosensor retains the remarkable selectivity of the RNA aptamer for theophylline over caffeine and is sensitive to 0-2 muM theophylline, well below the clinically relevant concentration (5-20 mg/L or approximately 10-50 muM). Adding a dabcyl quenching dye to the 3'-terminus of the fluorescently labeled DNA strand yielded a dual-labeled DNA strand (FL-DNA-Q) and increased the dynamic range of this simple biosensor from 1.5-fold to 4-fold.
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Affiliation(s)
- C J Rankin
- Department of Chemistry and Biochemistry, University of North Carolina-Greensboro, Greensboro, North Carolina 92110, USA
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17
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Ferraz RM, Arís A, Villaverde A. Enhanced molecular recognition signal in allosteric biosensing by proper substrate selection. Biotechnol Bioeng 2006; 94:193-9. [PMID: 16538674 DOI: 10.1002/bit.20798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Among protein biosensors, those based on enzymatic responses to specific analytes offer convenient instruments for fast and ultra-fast molecular diagnosis, through the comparative analysis of the product formed in presence and in absence of the effector. We have explored here the performance of five beta-galactosidase substrates during the activation of a beta-galactosidase sensor by antibodies against the human immunodeficiency virus (HIV). Interestingly, the employed substrate determines the dynamic range of the allosteric signal and significantly influences the sensitivity of the senso-enzymatic reaction. While ortho-nitrophenyl beta-D-galactopyranoside allows the detection of a model anti-gp41 monoclonal antibody below 0.024 ng/microL, phenol red beta-D-galactopyranoside offers the most dynamic response with signal/background ratios higher than 12-fold and a detection limit around 0.071 ng/microL. The hydrolysis of both chromogenic substrates generates linear sensing responses to immune human sera and parallel time-course topologies of the allosteric reaction. Therefore, the obtained results stress the potential of chromogenic substrates versus those rendering quimioluminescent, amperometric, or fluorescent signals, for the further automatization, miniaturization, or adaptation of beta-galactosidase-based biosensing to high-throughput applications.
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Affiliation(s)
- Rosa María Ferraz
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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18
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Altschuh D, Oncul S, Demchenko AP. Fluorescence sensing of intermolecular interactions and development of direct molecular biosensors. J Mol Recognit 2006; 19:459-77. [PMID: 17089349 DOI: 10.1002/jmr.807] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Molecular biosensors are devices of molecular size that are designed for sensing different analytes on the basis of biospecific recognition. They should provide two coupled functions - the recognition (specific binding) of the target and the transduction of information about the recognition event into a measurable signal. The present review highlights the achievements and prospects in design and operation of molecular biosensors for which the transduction mechanism is based on fluorescence. We focus on the general strategy of fluorescent molecular sensing, construction of sensor elements, based on natural and designed biopolymers (proteins and nucleic acids). Particular attention is given to the coupling of sensing elements with fluorescent reporter dyes and to the methods for producing efficient fluorescence responses.
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Affiliation(s)
- Danièle Altschuh
- UMR 7175 CNRS/ULP, ESBS, Parc d'Innovation, Bld S. Brant, BP 10413, 67412 Illkirch Cedex, France.
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Penchovsky R, Breaker RR. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat Biotechnol 2005; 23:1424-33. [PMID: 16244657 DOI: 10.1038/nbt1155] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Accepted: 09/04/2005] [Indexed: 01/03/2023]
Abstract
Allosteric RNAs operate as molecular switches that alter folding and function in response to ligand binding. A common type of natural allosteric RNAs is the riboswitch; designer RNAs with similar properties can be created by RNA engineering. We describe a computational approach for designing allosteric ribozymes triggered by binding oligonucleotides. Four universal types of RNA switches possessing AND, OR, YES and NOT Boolean logic functions were created in modular form, which allows ligand specificity to be changed without altering the catalytic core of the ribozyme. All computationally designed allosteric ribozymes were synthesized and experimentally tested in vitro. Engineered ribozymes exhibit >1,000-fold activation, demonstrate precise ligand specificity and function in molecular circuits in which the self-cleavage product of one RNA triggers the action of a second. This engineering approach provides a rapid and inexpensive way to create allosteric RNAs for constructing complex molecular circuits, nucleic acid detection systems and gene control elements.
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Affiliation(s)
- Robert Penchovsky
- Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520-8103, USA
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Alper H, Fischer C, Nevoigt E, Stephanopoulos G. Tuning genetic control through promoter engineering. Proc Natl Acad Sci U S A 2005; 102:12678-83. [PMID: 16123130 PMCID: PMC1200280 DOI: 10.1073/pnas.0504604102] [Citation(s) in RCA: 639] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene function is typically evaluated by sampling the continuum of gene expression at only a few discrete points corresponding to gene knockout or overexpression. We argue that this characterization is incomplete and present a library of engineered promoters of varying strengths obtained through mutagenesis of a constitutive promoter. A multifaceted characterization of the library, especially at the single-cell level to ensure homogeneity, permitted quantitative assessment correlating the effect of gene expression levels to improved growth and product formation phenotypes in Escherichia coli. Integration of these promoters into the chromosome can allow for a quantitative accurate assessment of genetic control. To this end, we used the characterized library of promoters to assess the impact of phosphoenolpyruvate carboxylase levels on growth yield and deoxy-xylulose-P synthase levels on lycopene production. The multifaceted characterization of promoter strength enabled identification of optimal expression levels for ppc and dxs, which maximized the desired phenotype. Additionally, in a strain preengineered to produce lycopene, the response to deoxy-xylulose-P synthase levels was linear at all levels tested, indicative of a rate-limiting step, unlike the parental strain, which exhibited an optimum expression level, illustrating that optimal gene expression levels are variable and dependent on the genetic background of the strain. This promoter library concept is illustrated as being generalizable to eukaryotic organisms (Saccharomyces cerevisiae) and thus constitutes an integral platform for functional genomics, synthetic biology, and metabolic engineering endeavors.
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Affiliation(s)
- Hal Alper
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, MA 02139, USA
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Abstract
RNA and DNA molecules can form complex, three-dimensional folded structures that have surprisingly sophisticated functions, including catalysing chemical reactions and controlling gene expression. Although natural nucleic acids make occasional use of these advanced functions, the true potential for sophisticated function by these biological polymers is far greater. An important challenge for biochemists is to take RNA and DNA beyond their proven use as polymers that form double-helical structures. Molecular engineers are beginning to harness the power of nucleic acids that form more complex three-dimensional structures, and apply them as tools for exploring biological systems and as therapeutics.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, P. O. Box 208103, New Haven, Connecticut 06520-8103, USA.
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Abstract
Rational design, usually guided by computational prediction, and selection from libraries of variants of natural proteins have been used with success in the engineering of novel non-natural receptors. Many of these engineered protein binders will find use in biotechnological, diagnostic and medical applications, sometimes in the place of natural antibodies.
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Affiliation(s)
- Pascale Mathonet
- Laboratoire de Biochimie Physique et des Biopolymères, Institut des Sciences de la Vie, place Louis Pasteur 1, B1348 Louvain-la-Neuve, Belgium
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