1
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Peng JM, Liu H, Ying ZM. Rapid one-pot isothermal amplification reassembled of fluorescent RNA aptamer for SARS-CoV-2 detection. Talanta 2024; 276:126264. [PMID: 38761661 DOI: 10.1016/j.talanta.2024.126264] [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: 01/17/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
The outbreak of SARS-CoV-2 poses a serious threat to human life and health. A rapid nucleic acid tests can effectively curb the spread of the disease. With the advantages of fluorescent RNA aptamers, low background and high sensitivity. A variety of fluorescent RNA aptamer sensors have been developed for the detection of nucleic acid. Here, we report a hypersensitive detection platform in which SARS-CoV-2 initiates RTF-EXPAR to amplify trigger fragments. This activation leads to the reassembled of the SRB2 fluorescent RNA aptamer, restoring its secondary structure for SR-DN binding and turn-on fluorescence. The platform completes the assay in 30 min and all reactions occur in one tube. The detection limit is as low as 116 aM. Significantly, the platform's quantitative analyses were almost identical to qPCR results in simulated tests of positive samples. In conclusion, the platform is sensitive, accurate and provides a new protocol for point-of-care testing of viruses.
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Affiliation(s)
- Jia-Min Peng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Hao Liu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Zhan-Ming Ying
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
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2
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Tang AA, Afasizheva A, Cano CT, Plath K, Black D, Franco E. Optimization of RNA Pepper Sensors for the Detection of Arbitrary RNA Targets. ACS Synth Biol 2024; 13:498-508. [PMID: 38295291 DOI: 10.1021/acssynbio.3c00426] [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] [Indexed: 02/02/2024]
Abstract
The development of fluorescent light-up RNA aptamers (FLAPs) has paved the way for the creation of sensors to track RNA in live cells. A major challenge with FLAP sensors is their brightness and limited signal-to-background ratio both in vivo and in vitro. To address this, we develop sensors using the Pepper aptamer, which exhibits superior brightness and photostability when compared to other FLAPs. The sensors are designed to fold into a low fluorescence conformation and to switch to a high fluorescence conformation through toehold or loop-mediated interactions with their RNA target. Our sensors detect RNA targets as short as 20 nucleotides in length with a wide dynamic range over 300-fold in vitro, and we describe strategies for optimizing the sensor's performance for any given RNA target. To demonstrate the versatility of our design approach, we generated Pepper sensors for a range of specific, biologically relevant RNA sequences. Our design and optimization strategies are portable to other FLAPs and offer a promising foundation for future development of RNA sensors with high specificity and sensitivity for detecting RNA biomarkers with multiple applications.
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Affiliation(s)
- Anli A Tang
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Kathrin Plath
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Douglas Black
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
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3
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Electrochemical aptasensor based on carboxylated graphene oxide modified carbon paste electrode for strontium ultrasensitive detection. Anal Biochem 2023; 666:115081. [PMID: 36773630 DOI: 10.1016/j.ab.2023.115081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023]
Abstract
Determination of strontium ions (Sr2+) is crucial with regard to human health and environmental protection. In this work, an electrochemical aptasensor was designed using carboxylated graphene oxide (CGO)-modified carbon paste electrode (CGO/CPE) for ultrasensitive determination of Sr2+ ions. The electrochemical determination was accomplished with employing the constructed G-quadruplex (G4) aptamer at the surface of aptasensor in presence of carmoisine (CA) as an electrochemical label. Moreover, NH2-functionalized aptamer was immobilized onto CGO/CPE via carboxylic group. Hence, differential pulse voltammetry was applied for detection of any possible signal changes of CA on the aptasensor surface. The reduction peak currents of CA in the absence and presence of Sr2+ in solution were different and this difference was linearly dependent to the concentration of Sr2+ in solution. The analytical results revealed that our novel aptasensor showed two appropriate linear ranges (0.1-8.0 pM and 3.0-20.0 nM) versus to Sr2+ ion concentrations with the limit of detection of 0.06 pM (S/N = 3). Excellent stability, selectivity and reproducibility were achieved with this new electrochemical aptasensor. Additionally, the aptasensor showed good achievements in analysis of Sr2+ in aqueous and urine real samples, which making this proposed method a promising candidate for electrochemical detection of Sr2+ in real samples.
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4
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023; 54:2467-2484. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [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] [Indexed: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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5
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R O'Steen M, M Kolpashchikov D. A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer. SENSORS AND ACTUATORS REPORTS 2022; 4:100125. [PMID: 36373144 PMCID: PMC9635949 DOI: 10.1016/j.snr.2022.100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Multiplex assays often rely on expensive sensors incorporating covalently linked fluorescent dyes. Herein, we developed a self-assembling aptamer-based multiplex assay. This multiplex approach utilizes a previously established split aptamer sensor in conjugation with a novel split aptamer sensor based upon a malachite green DNA aptamer. This system was capable of simultaneous fluorescent detection of two SARS COVID-19-related sequences in one sample with individual sensors that possesses a limit of detection (LOD) in the low nM range. Optimization of the Split Malachite Green (SMG) sensor yielded a minimized aptamer construct, Mini-MG, capable of inducing fluorescence of malachite green in both a DNA hairpin and sensor format.
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Affiliation(s)
- Martin R O'Steen
- Chemistry Department, University of Central Florida, Orlando, FL, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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6
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Wang L, Hast K, Aggarwal T, Baci M, Hong J, Izgu EC. MicroRNA detection in biologically relevant media using a split aptamer platform. Bioorg Med Chem 2022; 69:116909. [PMID: 35779513 DOI: 10.1016/j.bmc.2022.116909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
Abstract
MicroRNA (miRNA)-based intercellular communication has been implicated in many functional and dysfunctional biological processes. This has raised interest in the potential use of miRNAs as biomarkers for diagnosis and prognosis. Though the list of clinically significant miRNA biomarkers is expanding, it remains challenging to adapt current chemical tools to investigate miRNAs in complex environments native to cells and tissues. We describe here a methodology for rapidly developing aptamer-based fluorescent biosensors that can specifically detect miRNAs in biologically relevant media (10-30% v/v), including medium collected from cultured HeLa cells, human serum, and human plasma. This methodology involves the semi-rational design of the hybridization between DNA oligonucleotides and the miRNA target to build a pool of potential aptamers, and the screening of this pool for high signal-to-background ratio and target specificity. The DNA oligonucleotides are readily available and require no chemical modification, rendering these chemical tools highly adaptable to any novel and niche miRNA target. Following this approach, we developed sensors that detect distinct oncogenic miRNA targets (miR-19b, miR-21, and miR-92a) at concentrations as low as 5 nM without amplification and are selective against single-nucleotide mutants. This work provides a systematic approach toward the development of miRNA biosensors that are easily accessible and can perform in biological environments with minimal sample handling.
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Affiliation(s)
- Liming Wang
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Kern Hast
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Melih Baci
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Jonathan Hong
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
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7
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Citartan M. The dynamicity of light-up aptamers in one-pot in vitro diagnostic assays. Analyst 2021; 147:10-21. [PMID: 34860215 DOI: 10.1039/d1an01690c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Light-up aptamers are aptamers that ignite the fluorescence emission of certain dyes upon binding. Widely harnessed in in vivo imaging, the binding capacity of the light-up aptamers can also be deployed in in vitro diagnostic assays, engendering a mix-and-read format. Intrigued by this, I intend to provide an overview of the various formats of diagnostic assays developed using light-up aptamers from the direct modulation of the light-up aptamers, split aptamer-based configuration, strand displacement, in vitro transcription-based one-pot diagnostic assay, CRISPR-Cas system to the measurement of the ion reliance. The incorporation of the light-up aptamers into each configuration is expounded and further supported by describing the exemplary assays developed thus far. It is anticipated that the present study can be enlightening to any researchers who aspire to embark on the development of one-pot in vitro diagnostic assays based on light-up aptamers.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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8
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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9
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Chandler M, Johnson B, Khisamutdinov E, Dobrovolskaia MA, Sztuba-Solinska J, Salem AK, Breyne K, Chammas R, Walter NG, Contreras LM, Guo P, Afonin KA. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field. ACS NANO 2021; 15:16957-16973. [PMID: 34677049 PMCID: PMC9023608 DOI: 10.1021/acsnano.0c10240] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) hosts an annual meeting series focused on presenting the latest research achievements involving RNA-based therapeutics and strategies, aiming to expand their current biomedical applications while overcoming the remaining challenges of the burgeoning field of RNA nanotechnology. The most recent online meeting hosted a series of engaging talks and discussions from an international cohort of leading nanotechnologists that focused on RNA modifications and modulation, dynamic RNA structures, overcoming delivery limitations using a variety of innovative platforms and approaches, and addressing the newly explored potential for immunomodulation with programmable nucleic acid nanoparticles. In this Nano Focus, we summarize the main discussion points, conclusions, and future directions identified during this two-day webinar as well as more recent advances to highlight and to accelerate this exciting field.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47304, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Rouse Life Sciences Building, Auburn, Alabama 36849, United States
| | - Aliasger K Salem
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa 52242, United States
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachussets 02114, United States
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Centro de Investigação Translacional em Oncologia, Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de São Paulo - ICESP, Faculdade de Medicina da Universidade de São Paulo - FMUSP, Avenida Dr. Arnaldo 251, Cerqueira César, São Paulo 01246-000, São Paulo, Brazil
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering and Department of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78714, United States
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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10
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Gerasimova YV, Nedorezova DD, Kolpashchikov DM. Split light up aptamers as a probing tool for nucleic acids. Methods 2021; 197:82-88. [PMID: 33992774 DOI: 10.1016/j.ymeth.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
Aptamers that bind non-fluorescent dyes and increase their fluorescence can be converted to fluorescent sensors. Here, we discuss and provide guidance for the design of split (binary) light up aptameric sensors (SLAS) for nucleic acid analysis. SLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. The two strands hybridize to the analyzed DNA or RNA sequence and form a dye-binding pocket, followed by dye binding, and increase in its fluorescence. SLAS can detect nucleic acids in a cost-efficient label-free format since it does not require conjugation of organic dyes with nucleic acids. SLAS design is preferable over monolith fluorescent sensors due to simpler assay optimization and improved selectivity. RNA-based SLAS can be expressed in cells and used for intracellular monitoring and imaging biological molecules.
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Affiliation(s)
- Yulia V Gerasimova
- University of Central Florida, Chemistry Department, 4111 Libra Drive, Physical Sciences 255, Orlando, FL 32816-2366, United States.
| | - Daria D Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, ChemBio Cluster, SCAMT Institute, ITMO University, 9 Lomonosova Str., Saint Petersburg 191002, Russian Federation
| | - Dmitry M Kolpashchikov
- University of Central Florida, Chemistry Department, 4111 Libra Drive, Physical Sciences 255, Orlando, FL 32816-2366, United States; Laboratory of Molecular Robotics and Biosensor Materials, ChemBio Cluster, SCAMT Institute, ITMO University, 9 Lomonosova Str., Saint Petersburg 191002, Russian Federation.
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11
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Ryckelynck M. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More. Methods Mol Biol 2021; 2166:73-102. [PMID: 32710404 DOI: 10.1007/978-1-0716-0712-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.
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Affiliation(s)
- Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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12
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Connelly RP, Madalozzo PF, Mordeson JE, Pratt AD, Gerasimova YV. Promiscuous dye binding by a light-up aptamer: application for label-free multi-wavelength biosensing. Chem Commun (Camb) 2021; 57:3672-3675. [PMID: 33725073 DOI: 10.1039/d1cc00594d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Light-up DNA aptamers are promising label-free signal-transducers for biosensing applications due to their high chemical stability and low synthetic cost. Herein, we demonstrate that a dapoxyl DNA aptamer DAP-10-42 can be converted into a sensor generating a fluorescence signal at different wavelengths in the range of 500-660 nm depending on the dye that is present. This results from the discovered promiscuity of DAP-10-42 in binding fluorogenic dyes including arylmethane dyes. We have designed a split DAP-10-42 aptasensor for the detection of a katG gene fragment from Mycobacterium tuberculosis with a point mutation causing isoniazid resistance. Efficient interrogation of the gene fragment after nucleic acid sequence-based amplification (NASBA) is achieved directly in a protein-containing NASBA sample. This report lays a foundation for the application of the DAP-10-42 aptamer as a versatile sensing platform.
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Affiliation(s)
- Ryan P Connelly
- Department of Chemistry, University of Central Florida, 4111 Libra Dr, PSB 255, Orlando, Fl 32816, USA.
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13
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light‐up Aptameric Sensors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201914919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department University of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando FL 32816 USA
| | - Alexander A. Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
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14
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Bezerra AB, Kurian ASN, Easley CJ. Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques. Anal Chem 2021; 93:198-214. [PMID: 33147015 PMCID: PMC7855502 DOI: 10.1021/acs.analchem.0c04364] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light-up Aptameric Sensors. Angew Chem Int Ed Engl 2020; 60:4988-4999. [PMID: 32208549 DOI: 10.1002/anie.201914919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 12/12/2022]
Abstract
This Minireview discusses the design and applications of binary (also known as split) light-up aptameric sensors (BLAS). BLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. When associated, the two strands form a dye-binding site, followed by an increase in fluorescence of the aptamer-bound dye. The design is cost-efficient because it uses short oligonucleotides and does not require conjugation of organic dyes with nucleic acids. In some applications, BLAS design is preferable over monolithic sensors because of simpler assay optimization and improved selectivity. RNA-based BLAS can be expressed in cells and used for the intracellular monitoring of biological molecules. BLAS have been used as reporters of nucleic acid association events in RNA nanotechnology and nucleic-acid-based molecular computation. Other applications of BLAS include the detection of nucleic acids, proteins, and cancer cells, and potentially they can be tailored to report a broad range of biological analytes.
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Affiliation(s)
- Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Alexander A Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
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16
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Debiais M, Lelievre A, Smietana M, Müller S. Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors. Nucleic Acids Res 2020; 48:3400-3422. [PMID: 32112111 PMCID: PMC7144939 DOI: 10.1093/nar/gkaa132] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Amandine Lelievre
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
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17
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Zaitseva SO, Baleeva NS, Zatsepin TS, Myasnyanko IN, Turaev AV, Pozmogova GE, Khrulev AA, Varizhuk AM, Baranov MS, Aralov AV. Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues. SENSORS 2020; 20:s20030915. [PMID: 32050425 PMCID: PMC7038953 DOI: 10.3390/s20030915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
Aptasensors became popular instruments in bioanalytical chemistry and molecular biology. To increase specificity, perspective signaling elements in aptasensors can be separated into a G-quadruplex (G4) part and a free fluorescent dye that lights up upon binding to the G4 part. However, current systems are limited by relatively low enhancement of fluorescence upon dye binding. Here, we added duplex modules to G4 structures, which supposedly cause the formation of a dye-binding cavity between two modules. Screening of multiple synthetic GFP chromophore analogues and variation of the duplex module resulted in the selection of dyes that light up after complex formation with two-module structures and their RNA analogues by up to 20 times compared to parent G4s. We demonstrated that the short duplex part in TBA25 is preferable for fluorescence light up in comparison to parent TBA15 molecule as well as TBA31 and TBA63 stabilized by longer duplexes. Duplex part of TBA25 may be partially unfolded and has reduced rigidity, which might facilitate optimal dye positioning in the joint between G4 and the duplex. We demonstrated dye enhancement after binding to modified TBA, LTR-III, and Tel23a G4 structures and propose that such architecture of short duplex-G4 signaling elements will enforce the development of improved aptasensors.
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Affiliation(s)
- Snizhana O. Zaitseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (S.O.Z.); (N.S.B.); (I.N.M.); (A.A.K.)
| | - Nadezhda S. Baleeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (S.O.Z.); (N.S.B.); (I.N.M.); (A.A.K.)
| | - Timofei S. Zatsepin
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia;
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ivan N. Myasnyanko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (S.O.Z.); (N.S.B.); (I.N.M.); (A.A.K.)
| | - Anton V. Turaev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia; (A.V.T.); (G.E.P.); (A.M.V.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Galina E. Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia; (A.V.T.); (G.E.P.); (A.M.V.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Alexei A. Khrulev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (S.O.Z.); (N.S.B.); (I.N.M.); (A.A.K.)
| | - Anna M. Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia; (A.V.T.); (G.E.P.); (A.M.V.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Mikhail S. Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (S.O.Z.); (N.S.B.); (I.N.M.); (A.A.K.)
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Correspondence: (M.S.B.); (A.V.A.)
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (S.O.Z.); (N.S.B.); (I.N.M.); (A.A.K.)
- Correspondence: (M.S.B.); (A.V.A.)
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18
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Panigaj M, Johnson MB, Ke W, McMillan J, Goncharova EA, Chandler M, Afonin KA. Aptamers as Modular Components of Therapeutic Nucleic Acid Nanotechnology. ACS NANO 2019; 13:12301-12321. [PMID: 31664817 PMCID: PMC7382785 DOI: 10.1021/acsnano.9b06522] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nucleic acids play a central role in all domains of life, either as genetic blueprints or as regulators of various biochemical pathways. The chemical makeup of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), generally represented by a sequence of four monomers, also provides precise instructions for folding and higher-order assembly of these biopolymers that, in turn, dictate biological functions. The sequence-based specific 3D structures of nucleic acids led to the development of the directed evolution of oligonucleotides, SELEX (systematic evolution of ligands by exponential enrichment), against a chosen target molecule. Among the variety of functions, selected oligonucleotides named aptamers also allow targeting of cell-specific receptors with antibody-like precision and can deliver functional RNAs without a transfection agent. The advancements in the field of customizable nucleic acid nanoparticles (NANPs) opened avenues for the design of nanoassemblies utilizing aptamers for triggering or blocking cell signaling pathways or using aptamer-receptor combinations to activate therapeutic functionalities. A recent selection of fluorescent aptamers enables real-time tracking of NANP formation and interactions. The aptamers are anticipated to contribute to the future development of technologies, enabling an efficient assembly of functional NANPs in mammalian cells or in vivo. These research topics are of top importance for the field of therapeutic nucleic acid nanotechnology with the promises to scale up mass production of NANPs suitable for biomedical applications, to control the intracellular organization of biological materials to enhance the efficiency of biochemical pathways, and to enhance the therapeutic potential of NANP-based therapeutics while minimizing undesired side effects and toxicities.
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Affiliation(s)
- Martin Panigaj
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice 04154, Slovak Republic
| | - M. Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jessica McMillan
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Ekaterina A. Goncharova
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, St. Petersburg 191002, Russian Federation
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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19
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Sheng L, Lu Y, Deng S, Liao X, Zhang K, Ding T, Gao H, Liu D, Deng R, Li J. A transcription aptasensor: amplified, label-free and culture-independent detection of foodborne pathogens via light-up RNA aptamers. Chem Commun (Camb) 2019; 55:10096-10099. [PMID: 31380872 DOI: 10.1039/c9cc05036a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report a transcription aptasensor by using a light-up RNA aptamer. It allows for sensitive, label-free and culture-free detection of intact foodborne pathogens, and no separation, purification or enrichment processes are involved.
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Affiliation(s)
- Lele Sheng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China.
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20
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Soni R, Sharma D, Krishna AM, Sathiri J, Sharma A. A highly efficient Baby Spinach-based minimal modified sensor (BSMS) for nucleic acid analysis. Org Biomol Chem 2019; 17:7222-7227. [PMID: 31329202 DOI: 10.1039/c9ob01414d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Molecular recognition between nucleic acids has proven to be a powerful tool for designing hybridization probes for the detection of DNA and RNA sequences. Most detection probes rely on the conjugation of small molecule dyes to nucleic acids for fluorescence output, which is not cost-effective and also limits their applications in vivo, as they are not genetically encodable. More affordable sensors devoid of any chemical labeling are needed that show high fluorescence output and are genetically encodable. Here, we have designed a label-free Baby Spinach-based minimal modified sensor (BSMS) for the analysis of nucleic acids. The minimal modification in the sensor design reduces the complexity of the design, and provides additional stabilization after binding the target nucleic acids, leading to a high fluorescence output. BSMS is able to detect both DNA and RNA of potentially any lengths and is based on a Baby Spinach aptamer that binds and enhances the fluorescence of a small molecule dye. BSMS shows specificity towards its analyte in the presence of other sequences and selectively differentiates between closely related sequences. BSMS comprises genetically encodable unmodified RNA and has been shown to function at ambient temperature, and thus is anticipated to provide nucleic acid monitoring in vivo.
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Affiliation(s)
- Rashi Soni
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
| | - Deepti Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
| | - A Murali Krishna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
| | - Jagadeesh Sathiri
- Department of Biology, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Ashwani Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India. and Department of Biology, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
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21
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Wang Z, Liu W, Fan C, Chen N. Visualizing mRNA in live mammalian cells. Methods 2019; 161:16-23. [DOI: 10.1016/j.ymeth.2019.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 01/06/2023] Open
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22
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O'Hara JM, Marashi D, Morton S, Jaeger L, Grabow WW. Optimization of the Split-Spinach Aptamer for Monitoring Nanoparticle Assembly Involving Multiple Contiguous RNAs. NANOMATERIALS 2019; 9:nano9030378. [PMID: 30845655 PMCID: PMC6474029 DOI: 10.3390/nano9030378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 12/16/2022]
Abstract
The fact that structural RNA motifs can direct RNAs to fold and self-assemble into predictable pre-defined structures is an attractive quality and driving force for RNA’s use in nanotechnology. RNA’s recognized diversity concerning cellular and synthetically selected functionalities, however, help explain why it continues to draw attention for new nano-applications. Herein, we report the modification of a bifurcated reporter system based on the previously documented Spinach aptamer/DFHBI fluorophore pair that affords the ability to confirm the assembly of contiguous RNA strands within the context of the previously reported multi-stranded RNA nanoring. Exploration of the sequence space associated with the base pairs flanking the aptamer core demonstrate that fluorescent feedback can be optimized to minimize the fluorescence associated with partially-assembled RNA nanorings. Finally, we demonstrate that the aptamer-integrated nanoring is capable of assembling directly from transcribed DNA in one pot.
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Affiliation(s)
- Jack M O'Hara
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
| | - Dylan Marashi
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
| | - Sean Morton
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
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23
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Rossetti M, Del Grosso E, Ranallo S, Mariottini D, Idili A, Bertucci A, Porchetta A. Programmable RNA-based systems for sensing and diagnostic applications. Anal Bioanal Chem 2019; 411:4293-4302. [PMID: 30734852 DOI: 10.1007/s00216-019-01622-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/08/2019] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
The emerging field of RNA nanotechnology harnesses the versatility of RNA molecules to generate nature-inspired systems with programmable structure and functionality. Such methodology has therefore gained appeal in the fields of biosensing and diagnostics, where specific molecular recognition and advanced input/output processing are demanded. The use of RNA modules and components allows for achieving diversity in structure and function, for processing information with molecular precision, and for programming dynamic operations on the grounds of predictable non-covalent interactions. When RNA nanotechnology meets bioanalytical chemistry, sensing of target molecules can be performed by harnessing programmable interactions of RNA modules, advanced field-ready biosensors can be manufactured by interfacing RNA-based devices with supporting portable platforms, and RNA sensors can be engineered to be genetically encoded allowing for real-time imaging of biomolecules in living cells. In this article, we report recent advances in RNA-based sensing technologies and discuss current trends in RNA nanotechnology-enabled biomedical diagnostics. In particular, we describe programmable sensors that leverage modular designs comprising dynamic aptamer-based units, synthetic RNA nanodevices able to perform target-responsive regulation of gene expression, and paper-based sensors incorporating artificial RNA networks. Graphical Abstract ᅟ.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Simona Ranallo
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Davide Mariottini
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Idili
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Alessandro Bertucci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy. .,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy.
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24
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Zhou Y, Shen S, Lau C, Lu J. A conformational switch-based fluorescent biosensor for homogeneous detection of telomerase activity. Talanta 2019; 199:21-26. [PMID: 30952248 DOI: 10.1016/j.talanta.2019.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/30/2019] [Accepted: 02/03/2019] [Indexed: 10/27/2022]
Abstract
As a universal tumor biomarker, research on the activity and inhibition of telomerase is of great importance for cancer diagnosis and therapy. Herein, we demonstrate the conformational switch-based fluorescence detection of telomerase activity using a redesigned RNA aptamer Spinach. Briefly, the original Spinach aptamer was extended at its 5' end and folded into an inactive conformation, where association with the small molecule fluorophore, 5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) was prevented. Only in the presence of telomerase, (TTAGGG)n repeats were added to the 3' end of the telomerase substrate primer, and the elongation products hybridized with inactive Spinach molecules, triggering its conformational switch and refolding it into the active, DFHBI-binding conformation. Moreover, the fluorescence signal was further amplified through a target recycling circuit, where Ribonuclease H (RNase H) specifically hydrolyzed the phosphodiester bonds of RNA in the DNA-RNA hybrid. The released telomere products could then hybridize to new inactive Spinach molecules and initiate multiple amplification cycles. The proposed fluorescent biosensor presented great performance for telomerase activity detection from 100 to 5 × 104 Hela cells with a detection limit of 100 cells. Besides, this new assay offers a good biosensing platform for differentiation of cancer cell lines from normal cell line and evaluation the inhibition efficiency of telomere-binding ligand, which is of great importance for telomerase-related cancer diagnosis and therapy.
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Affiliation(s)
- Ying Zhou
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Shujuan Shen
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Choiwan Lau
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jianzhong Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
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25
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Kikuchi N, Reed A, Gerasimova YV, Kolpashchikov DM. Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons. Anal Chem 2019; 91:2667-2671. [PMID: 30680988 DOI: 10.1021/acs.analchem.8b03964] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hybridization probes have been used for the detection of single nucleotide variations (SNV) in DNA and RNA sequences in the mix-and-read formats. Among the most conventional are Taqman probes, which require expensive quantitative polymerase chain reaction (qPCR) instruments with melting capabilities. More affordable isothermal amplification format requires hybridization probes that can selectively detect SNVs isothermally. Here we designed a split DNA aptamer (SDA) hybridization probe based on a recently reported DNA sequence that binds a dapoxyl dye and increases its fluorescence ( Kato, T.; Shimada, I.; Kimura, R.; Hyuga, M., Light-up fluorophore-DNA aptamer pair for label-free turn-on aptamer sensors. Chem. Commun. 2016 , 52 , 4041 - 4044 ). SDA uses two DNA strands that have low affinity to the dapoxyl dye unless hybridized to abutting positions at a specific analyte and form a dye-binding site, which is accompanied by up to a 120-fold increase in fluorescence. SDA differentiates SNV in the inhA gene of Mycobacterium tuberculosis at ambient temperatures and detects a conserved region of the Zika virus after isothermal nucleic acid sequence based amplification (NASBA) reaction. The approach reported here can be used for detection of isothermal amplification products in the mix-and-read format as an alternative to qPCR.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Adam Reed
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Yulia V Gerasimova
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Dmitry M Kolpashchikov
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States.,Burnett School of Biomedical Sciences , University of Central Florida , Orlando , 32816 , Florida United States
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26
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Yang S, Yang C, Huang D, Song L, Chen J, Yang Q. Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits. Chemistry 2019; 25:5389-5405. [PMID: 30328639 DOI: 10.1002/chem.201804420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Indexed: 01/06/2023]
Abstract
DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Chunrong Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Dan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Lingbo Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jianchi Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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27
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Yang C, Yang S, Song L, Yao Y, Lin X, Cai K, Yang Q, Tang Y. A resettable supramolecular platform for constructing scalable encoders. Chem Commun (Camb) 2019; 55:8005-8008. [PMID: 31225570 DOI: 10.1039/c9cc00577c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A supramolecular platform prototype for implementing resettable encoding functions was designed, which could be configured into a series of encoders, from 4-to-2 to 7-to-3, and even 14-to-4 ECs.
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Affiliation(s)
| | - Shu Yang
- West China School of Pharmacy
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Lingbo Song
- West China School of Pharmacy
- Sichuan University
- Chengdu 610064
- P. R. China
| | - Ye Yao
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Xiao Lin
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Kaicong Cai
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry
- Ningde Normal University
- Ningde
- China
| | - Qianfan Yang
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Yalin Tang
- Institute of Chemistry, Chinese Academy of Sciences
- Beijing
- China
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28
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Yang S, Zhang F, Liang Q, Wang Z. A three-dimensional graphene-based ratiometric signal amplification aptasensor for MUC1 detection. Biosens Bioelectron 2018; 120:85-92. [DOI: 10.1016/j.bios.2018.08.036] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 08/03/2018] [Accepted: 08/16/2018] [Indexed: 02/07/2023]
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29
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Ying ZM, Xiao HY, Tang H, Yu RQ, Jiang JH. Light-up RNA aptamer enabled label-free protein detection via a proximity induced transcription assay. Chem Commun (Camb) 2018; 54:8877-8880. [PMID: 30043035 DOI: 10.1039/c8cc04498h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A novel proximity induced transcription assay for highly sensitive protein detection based on protein mediated ligation of a DNA template with the transcription of a light-up RNA aptamer for signal amplification has been developed.
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Affiliation(s)
- Zhan-Ming Ying
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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30
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Yang S, Zhang F, Wang Z, Liang Q. A graphene oxide-based label-free electrochemical aptasensor for the detection of alpha-fetoprotein. Biosens Bioelectron 2018; 112:186-192. [PMID: 29705616 DOI: 10.1016/j.bios.2018.04.026] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/25/2018] [Accepted: 04/13/2018] [Indexed: 02/07/2023]
Abstract
A label-free method for the determination of alpha-fetoprotein (AFP) was successfully developed by graphene oxide (GO)-based electrochemical aptasensor. This aptasensor was constructed by covalently immobilizing NH2-functionalized AFP-specific aptamer on GO with plenty of carboxylic groups. Cyclic voltammetry (CV) and electrochemical impedance spectra (EIS) analysis were carried out to investigate the practicability of the fabrication procedures. Fourier transform infrared spectra (FTIR), Raman, atomic force microscopy (AFM) and scanning electron microscope (SEM) were performed to indicate the changes of the sensing interface. CV was used to detect the signal change of the aptasensor. Peak current of CVs changed before and after incubating the aptasensor with different concentration of AFP solution. The changes of peak current were proportional to the AFP concentration, with a wide linear range of 0.01-100 ng mL-1, a low detection limit of 3 pg mL-1 and good specificity. The proposed simple and cost-effective label-free strategy is promising for the determination of clinical biomarkers such as AFP.
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Affiliation(s)
- Shaohong Yang
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University, Qingdao, Shandong 266071, China; MOE Key Lab of Bioorganic Phosphorus & Chemical Biology, Beijing Key Lab of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Feifei Zhang
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University, Qingdao, Shandong 266071, China
| | - Zonghua Wang
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University, Qingdao, Shandong 266071, China.
| | - Qionglin Liang
- MOE Key Lab of Bioorganic Phosphorus & Chemical Biology, Beijing Key Lab of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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31
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Ying ZM, Tu B, Liu L, Tang H, Tang LJ, Jiang JH. Spinach-based fluorescent light-up biosensors for multiplexed and label-free detection of microRNAs. Chem Commun (Camb) 2018; 54:3010-3013. [PMID: 29511749 DOI: 10.1039/c8cc00123e] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel Spinach-based fluorescent light-up biosensor utilizing the T7 in vitro transcription process to generate unmodified Spinach sequences for multiplexed microRNA detection has been developed.
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Affiliation(s)
- Zhan-Ming Ying
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Bin Tu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Lan Liu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Hao Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Li-Juan Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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Bouhedda F, Autour A, Ryckelynck M. Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications. Int J Mol Sci 2017; 19:ijms19010044. [PMID: 29295531 PMCID: PMC5795994 DOI: 10.3390/ijms19010044] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 12/31/2022] Open
Abstract
An RNA-based fluorogenic module consists of a light-up RNA aptamer able to specifically interact with a fluorogen to form a fluorescent complex. Over the past decade, significant efforts have been devoted to the development of such modules, which now cover the whole visible spectrum, as well as to their engineering to serve in a wide range of applications. In this review, we summarize the different strategies used to develop each partner (the fluorogen and the light-up RNA aptamer) prior to giving an overview of their applications that range from live-cell RNA imaging to the set-up of high-throughput drug screening pipelines. We then conclude with a critical discussion on the current limitations of these modules and how combining in vitro selection with screening approaches may help develop even better molecules.
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Affiliation(s)
- Farah Bouhedda
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Alexis Autour
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
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Smith AL, Kolpashchikov DM. Divide and Control: Comparison of Split and Switch Hybridization Sensors. ChemistrySelect 2017; 2:5427-5431. [PMID: 29372178 PMCID: PMC5777618 DOI: 10.1002/slct.201701179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hybridization probes have been intensively used for nucleic acid analysis in medicine, forensics and fundamental research. Instantaneous hybridization probes (IHPs) enable signalling immediately after binding to a targeted DNA or RNA sequences without the need to isolate the probe-target complex (e. g. by gel electrophoresis). The two most common strategies for IHP design are conformational switches and split approach. A conformational switch changes its conformation and produces signal upon hybridization to a target. Split approach uses two (or more) strands that independently or semi independently bind the target and produce an output signal only if all components associate. Here, we compared the performance of split vs switch designs for deoxyribozyme (Dz) hybridization probes under optimal conditions for each of them. The split design was represented by binary Dz (BiDz) probes; while catalytic molecular beacon (CMB) probes represented the switch design. It was found that BiDz were significantly more selective than CMBs in recognition of single base substitution. CMBs produced high background signal when operated at 55°C. An important advantage of BiDz over CMB is more straightforward design and simplicity of assay optimization.
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Affiliation(s)
- Alexandra L Smith
- Chemistry Department, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
| | - Dmitry M Kolpashchikov
- Chemistry Department, Burnett School of Biomedical Sciences, National Center for Forensic Science, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
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