1
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Sorrentino D, Ranallo S, Nakamura E, Franco E, Ricci F. Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors. Angew Chem Int Ed Engl 2024; 63:e202319382. [PMID: 38457363 DOI: 10.1002/anie.202319382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
We present a strategy to control dynamically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be cotranscriptionally regulated (activated or inhibited) through specific RNA molecules produced by rationally designed synthetic genes. The kinetics of our DNA sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling.
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Affiliation(s)
- Daniela Sorrentino
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Simona Ranallo
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Eiji Nakamura
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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2
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Zhao Y, Poudel P, Wang S. Detection of MicroRNAs Using Synthetic Toehold Switch in Mammalian Cells. Methods Mol Biol 2024; 2774:243-258. [PMID: 38441769 DOI: 10.1007/978-1-0716-3718-0_16] [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: 03/07/2024]
Abstract
Engineering synthetic gene circuits to control cellular functions has a broad application in the field of synthetic biology. Synthetic RNA-based switches that can operate at the transcriptional and posttranscriptional level have also drawn significant interest for the application of next-generation therapeutics and diagnostics. Thus, RNA-based switchable platforms are needed to report dynamic cellular mechanisms which play an important role in cell development and diseases. Recently, several RNA-based switches have been designed and utilized for biosensing and molecular diagnostics. However, miRNA-based switches have not been well established or characterized, especially for eukaryotic translational control. Here, we designed a novel synthetic toehold switch for detection of exogenously and endogenously expressed miRNAs in CHO, HeLa, HEK 293, and MDA-MB-231 breast cancer cells. Multiplex detection of miR-155 and miR-21 was tested using two toehold switches to evaluate the orthogonality and programmability of this synthetic platform.
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Affiliation(s)
- Yuwen Zhao
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Pratima Poudel
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA
| | - Shue Wang
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA.
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3
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Brannetti S, Gentile S, Chamorro-Garcia A, Barbero L, Del Grosso E, Ricci F. Decorated DNA-Based Scaffolds as Lateral Flow Biosensors. Angew Chem Int Ed Engl 2023; 62:e202313243. [PMID: 37804080 DOI: 10.1002/anie.202313243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/08/2023]
Abstract
Here we develop Lateral Flow Assays (LFAs) that employ as functional elements DNA-based structures decorated with reporter tags and recognition elements. We have rationally re-engineered tile-based DNA tubular structures that can act as scaffolds and can be decorated with recognition elements of different nature (i.e. antigens, aptamers or proteins) and with orthogonal fluorescent dyes. As a proof-of-principle we have developed sandwich and competitive multiplex lateral flow platforms for the detection of several targets, ranging from small molecules (digoxigenin, Dig and dinitrophenol, DNP), to antibodies (Anti-Dig, Anti-DNP and Anti-MUC1/EGFR bispecific antibodies) and proteins (thrombin). Coupling the advantages of functional DNA-based scaffolds together with the simplicity of LFAs, our approach offers the opportunity to detect a wide range of targets with nanomolar sensitivity and high specificity.
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Affiliation(s)
- Simone Brannetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Serena Gentile
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alejandro Chamorro-Garcia
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Luca Barbero
- RBM-Merck an affiliate of Merck KGaA, Via Ribes 1, 10010, Turin, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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4
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Périllat VJ, Del Grosso E, Berton C, Ricci F, Pezzato C. Controlling DNA nanodevices with light-switchable buffers. Chem Commun (Camb) 2023; 59:2146-2149. [PMID: 36727426 PMCID: PMC9933455 DOI: 10.1039/d2cc06525h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Control over synthetic DNA-based nanodevices can be achieved with a variety of physical and chemical stimuli. Actuation with light, however, is as advantageous as difficult to implement without modifying DNA strands with photo-switchable groups. Herein, we show that DNA nanodevices can be controlled using visible light in photo-switchable aqueous buffer solutions in a reversible and highly programmable fashion. The strategy presented here is non-invasive and allows the remote control with visible light of complex operations of DNA-based nanodevices such as the reversible release/loading of cargo molecules.
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Affiliation(s)
- Valentin Jean Périllat
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata Via della Ricerca Scientifica, 00133 Rome, Italy.
| | - Cesare Berton
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata Via della Ricerca Scientifica, 00133 Rome, Italy.
| | - Cristian Pezzato
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,Department of Chemical Sciences, University of Padua Via Marzolo 1, 35131 Padua, Italy.
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5
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Giakountis A, Stylianidou Z, Zaka A, Pappa S, Papa A, Hadjichristodoulou C, Mathiopoulos KD. Development of Toehold Switches as a Novel Ribodiagnostic Method for West Nile Virus. Genes (Basel) 2023; 14:237. [PMID: 36672977 PMCID: PMC9859090 DOI: 10.3390/genes14010237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
West Nile virus (WNV) is an emerging neurotropic RNA virus and a member of the genus Flavivirus. Naturally, the virus is maintained in an enzootic cycle involving mosquitoes as vectors and birds that are the principal amplifying virus hosts. In humans, the incubation period for WNV disease ranges from 3 to 14 days, with an estimated 80% of infected persons being asymptomatic, around 19% developing a mild febrile infection and less than 1% developing neuroinvasive disease. Laboratory diagnosis of WNV infection is generally accomplished by cross-reacting serological methods or highly sensitive yet expensive molecular approaches. Therefore, current diagnostic tools hinder widespread surveillance of WNV in birds and mosquitoes that serve as viral reservoirs for infecting secondary hosts, such as humans and equines. We have developed a synthetic biology-based method for sensitive and low-cost detection of WNV. This method relies on toehold riboswitches designed to detect WNV genomic RNA as transcriptional input and process it to GFP fluorescence as translational output. Our methodology offers a non-invasive tool with reduced operating cost and high diagnostic value that can be used for field surveillance of WNV in humans as well as in bird and mosquito populations.
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Affiliation(s)
- Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
| | - Zoe Stylianidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
| | - Anxhela Zaka
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
| | - Styliani Pappa
- Department of Microbiology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anna Papa
- Department of Microbiology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | | | - Kostas D. Mathiopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
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6
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Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
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7
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Krämer J, Kang R, Grimm LM, De Cola L, Picchetti P, Biedermann F. Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids. Chem Rev 2022; 122:3459-3636. [PMID: 34995461 PMCID: PMC8832467 DOI: 10.1021/acs.chemrev.1c00746] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 02/08/2023]
Abstract
Synthetic molecular probes, chemosensors, and nanosensors used in combination with innovative assay protocols hold great potential for the development of robust, low-cost, and fast-responding sensors that are applicable in biofluids (urine, blood, and saliva). Particularly, the development of sensors for metabolites, neurotransmitters, drugs, and inorganic ions is highly desirable due to a lack of suitable biosensors. In addition, the monitoring and analysis of metabolic and signaling networks in cells and organisms by optical probes and chemosensors is becoming increasingly important in molecular biology and medicine. Thus, new perspectives for personalized diagnostics, theranostics, and biochemical/medical research will be unlocked when standing limitations of artificial binders and receptors are overcome. In this review, we survey synthetic sensing systems that have promising (future) application potential for the detection of small molecules, cations, and anions in aqueous media and biofluids. Special attention was given to sensing systems that provide a readily measurable optical signal through dynamic covalent chemistry, supramolecular host-guest interactions, or nanoparticles featuring plasmonic effects. This review shall also enable the reader to evaluate the current performance of molecular probes, chemosensors, and nanosensors in terms of sensitivity and selectivity with respect to practical requirement, and thereby inspiring new ideas for the development of further advanced systems.
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Affiliation(s)
- Joana Krämer
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rui Kang
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Laura M. Grimm
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Luisa De Cola
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Dipartimento
DISFARM, University of Milano, via Camillo Golgi 19, 20133 Milano, Italy
- Department
of Molecular Biochemistry and Pharmacology, Instituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156 Milano, Italy
| | - Pierre Picchetti
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Frank Biedermann
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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8
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Arshad R, Fatima I, Sargazi S, Rahdar A, Karamzadeh-Jahromi M, Pandey S, Díez-Pascual AM, Bilal M. Novel Perspectives towards RNA-Based Nano-Theranostic Approaches for Cancer Management. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:3330. [PMID: 34947679 PMCID: PMC8708502 DOI: 10.3390/nano11123330] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/24/2021] [Accepted: 12/05/2021] [Indexed: 12/19/2022]
Abstract
In the fight against cancer, early diagnosis is critical for effective treatment. Traditional cancer diagnostic technologies, on the other hand, have limitations that make early detection difficult. Therefore, multi-functionalized nanoparticles (NPs) and nano-biosensors have revolutionized the era of cancer diagnosis and treatment for targeted action via attaching specified and biocompatible ligands to target the tissues, which are highly over-expressed in certain types of cancers. Advancements in multi-functionalized NPs can be achieved via modifying molecular genetics to develop personalized and targeted treatments based on RNA interference. Modification in RNA therapies utilized small RNA subunits in the form of small interfering RNAs (siRNA) for overexpressing the specific genes of, most commonly, breast, colon, gastric, cervical, and hepatocellular cancer. RNA-conjugated nanomaterials appear to be the gold standard for preventing various malignant tumors through focused diagnosis and delivering to a specific tissue, resulting in cancer cells going into programmed death. The latest advances in RNA nanotechnology applications for cancer diagnosis and treatment are summarized in this review.
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Affiliation(s)
- Rabia Arshad
- Faculty of Pharmacy, University of Lahore, Lahore 45320, Pakistan;
| | - Iqra Fatima
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan 98167-43463, Iran;
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol 98613-35856, Iran
| | | | - Sadanand Pandey
- Department of Chemistry, College of Natural Science, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Korea;
| | - Ana M. Díez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona, Km. 33.6, 28805 Alcalá de Henares, Madrid, Spain
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China;
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9
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Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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10
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Shanaa OA, Rumyantsev A, Sambuk E, Padkina M. In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects. Molecules 2021; 26:molecules26051422. [PMID: 33800717 PMCID: PMC7961669 DOI: 10.3390/molecules26051422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.
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Affiliation(s)
- Ousama Al Shanaa
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Atomic Energy Commission of Syria, Damascus P.O.B 6091, Syria
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
| | - Andrey Rumyantsev
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Elena Sambuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Marina Padkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
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11
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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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12
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Vasilev RA, Chernikovich VY, Evteeva MA, Sakharov DA, Patrushev MV. Synthetic Biology: Current State and Applications. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2021. [DOI: 10.3103/s0891416821010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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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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