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Yuan Y, Arroyo-Currás N. Continuous Molecular Monitoring in the Body via Nucleic Acid-based Electrochemical Sensors: The Need for Statistically-powered Validation. CURRENT OPINION IN ELECTROCHEMISTRY 2023; 39:101305. [PMID: 37274549 PMCID: PMC10237360 DOI: 10.1016/j.coelec.2023.101305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nucleic acid-based electrochemical (NBE) sensors offer real-time and reagent-free sensing capabilities that overcome limitations of target-specific reactivity via affinity-based molecular detection. By leveraging affinity probes, NBE sensors become modular and versatile, allowing the monitoring of a variety of molecular targets by simply swapping the recognition probe without the need to change their sensor architecture. However, NBE sensors have not been rigorously validated in vivo in terms of analytical performance and clinical agreement relative to benchmark methods. In this article, we highlight reports from the past three years that evaluate NBE sensors performance in vivo. We hope this discussion will inspire future translational efforts with statistically robust experimental design, thus enabling real-world clinical applications and commercial development of NBE sensors.
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Affiliation(s)
- Yuchan Yuan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21202
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21202
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218
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2
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Shaver A, Arroyo-Currás N. The challenge of long-term stability for nucleic acid-based electrochemical sensors. CURRENT OPINION IN ELECTROCHEMISTRY 2022; 32:100902. [PMID: 36092288 PMCID: PMC9455832 DOI: 10.1016/j.coelec.2021.100902] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nucleic acid-based electrochemical sensors are a versatile technology enabling affinity-based detection of a great variety of molecular targets, regardless of inherent electrochemical activity or enzymatic reactivity. Additionally, their modular interface and ease of fabrication enable rapid prototyping and sensor development. However, the technology has inhibiting limitations in terms of long-term stability that have precluded translation into clinically valuable platforms like continuous molecular monitors. In this opinion, we discuss published methods to address various aspects of sensor stability, including thiol-based monolayers and anti-biofouling capabilities. We hope the highlighted works will motivate the field to develop innovative strategies for extending the long-term operational life of nucleic acid-based electrochemical sensors.
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Affiliation(s)
- Alexander Shaver
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
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Dantsu Y, Zhang Y, Zhang W. Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness. Genes (Basel) 2021; 13:46. [PMID: 35052385 PMCID: PMC8774879 DOI: 10.3390/genes13010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/19/2022] Open
Abstract
Nucleic-acid-based small molecule and oligonucleotide therapies are attractive topics due to their potential for effective target of disease-related modules and specific control of disease gene expression. As the non-naturally occurring biomolecules, modified DNA/RNA nucleoside and oligonucleotide analogues composed of L-(deoxy)riboses, have been designed and applied as innovative therapeutics with superior plasma stability, weakened cytotoxicity, and inexistent immunogenicity. Although all the chiral centers in the backbone are mirror converted from the natural D-nucleic acids, L-nucleic acids are equipped with the same nucleobases (A, G, C and U or T), which are critical to maintain the programmability and form adaptable tertiary structures for target binding. The types of L-nucleic acid drugs are increasingly varied, from chemically modified nucleoside analogues that interact with pathogenic polymerases to nanoparticles containing hundreds of repeating L-nucleotides that circulate durably in vivo. This article mainly reviews three different aspects of L-nucleic acid therapies, including pharmacological L-nucleosides, Spiegelmers as specific target-binding aptamers, and L-nanostructures as effective drug-delivery devices.
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Affiliation(s)
- Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
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Shaver A, Kundu N, Young BE, Vieira PA, Sczepanski JT, Arroyo-Currás N. Nuclease Hydrolysis Does Not Drive the Rapid Signaling Decay of DNA Aptamer-Based Electrochemical Sensors in Biological Fluids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5213-5221. [PMID: 33876937 PMCID: PMC8176561 DOI: 10.1021/acs.langmuir.1c00166] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Electrochemical aptamer-based (E-AB) sensors are a technology capable of real-time monitoring of drug concentrations directly in the body. These sensors achieve their selectivity from surface-attached aptamers, which alter their conformation upon target binding, thereby causing a change in electron transfer kinetics between aptamer-bound redox reporters and the electrode surface. Because, in theory, aptamers can be selected for nearly any target of interest, E-AB sensors have far-reaching potential for diagnostic and biomedical applications. However, a remaining critical weakness in the platform lies in the time-dependent, spontaneous degradation of the bioelectronic interface. This progressive degradation-seen in part as a continuous drop in faradaic current from aptamer-attached redox reporters-limits the in vivo operational life of E-AB sensors to less than 12 h, prohibiting their long-term application for continuous molecular monitoring in humans. In this work, we study the effects of nuclease action on the signaling lifetime of E-AB sensors, to determine whether the progressive signal loss is caused by hydrolysis of DNA aptamers and thus the loss of signaling moieties from the sensor surface. We continuously interrogate sensors deployed in several undiluted biological fluids at 37 °C and inject nuclease to reach physiologically relevant concentrations. By employing both naturally occurring d-DNA and the nuclease-resistant enantiomer l-DNA, we determine that within the current lifespan of state-of-the-art E-AB sensors, nuclease hydrolysis is not the dominant cause of sensor signal loss under the conditions we tested. Instead, signal loss is driven primarily by the loss of monolayer elements-both blocking alkanethiol and aptamer monolayers-from the electrode surface. While use of l-DNA aptamers may extend the E-AB operational life in the long term, the critical issue of passive monolayer loss must be addressed before those effects can be seen.
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Affiliation(s)
- Alexander Shaver
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Brian E Young
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Philip A Vieira
- Department of Psychology, California State University Dominguez Hills, Carson, California 90747, United States
| | - Jonathan T Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
- Department of Chemical and Biomolecular Engineering and Institute for NanoBioTechnology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Feng XN, Cui YX, Zhang J, Tang AN, Mao HB, Kong DM. Chiral Interaction Is a Decisive Factor To Replace d-DNA with l-DNA Aptamers. Anal Chem 2020; 92:6470-6477. [PMID: 32249564 DOI: 10.1021/acs.analchem.9b05676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleic acid aptamers have been widely used in various fields such as biosensing, DNA chip, and medical diagnosis. However, the high susceptibility of nucleic acids to ubiquitous nucleases reduces the biostability of aptamers and limits their applications in biological contexts. Therefore, improving the biostability of aptamers becomes an urgent need. Herein, we present a simple strategy to resolve this problem by directly replacing the d-DNA-based aptamers with left-handed l-DNA. By testing several reported aptamers against respective targets, we found that our proposed strategy stood up well for nonchiral small molecule targets (e.g., Hemin and cationic porphyrin) and chiral targets whose interactions with aptamers are chirality-independent (e.g., ATP). We also found that the l-DNA aptamers were indeed endowed with greatly improved biostability due to the extraordinary resistance of l-DNA to nuclease digestion. With respect to other small-molecule targets whose interactions with aptamers are chirality-dependent (e.g., kanamycin) and biomacromolecules (e.g., tyrosine kinase-7), however, the proposed strategy was not entirely effective likely due to the participation of the DNA backbone chirality into the target recognition. In spite of this limitation, this strategy indeed paves an easy way to screen highly biostable aptamers important for the applications in many fields.
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Affiliation(s)
- Xue-Nan Feng
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jing Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Han-Bin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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Development of a histamine aptasensor for food safety monitoring. Sci Rep 2019; 9:16659. [PMID: 31723193 PMCID: PMC6853955 DOI: 10.1038/s41598-019-52876-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
Histamine produced by bacteria through decarboxylation of histidine in spoiled foods such as fish is known to cause food poisoning. Therefore, accurate and facile measurement of histamine is of practical importance. Using the recently discovered RNA aptamer that specifically recognizes histamine (A1-949 aptamer), we developed an aptasensor based on the structure-switching mechanism. Specifically, the aptamer A1-949 was fluorescently labeled at the 5′ end and hybridized with a short quencher DNA strand that is partially complementary to the aptamer. The quencher strand was modified with a fluorescence quencher at its 3′ terminus. Displacement of the quencher strand upon histamine binding results in an increased fluorescence. After optimizing the assay condition, the enantiomeric version of the aptasensor (L-RNA and L-DNA) was synthesized which could detect the achiral analyte with identical sensitivity and improved biochemical stability. The aptasensor performance was validated by measuring fish samples spiked with known concentrations of histamine. Finally, histamine content in spoiled fish samples was measured, and the results were compared with the measurements using a commercial enzymatic assay kit.
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Luo X, Chen Z, Li H, Li W, Cui L, Huang J. Exploiting the application of l-aptamer with excellent stability: an efficient sensing platform for malachite green in fish samples. Analyst 2019; 144:4204-4209. [PMID: 31187804 DOI: 10.1039/c9an00332k] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Effective monitoring of the content of malachite green (MG) in aquaculture is of great importance for food safety. Traditional methods for MG assay, such as chromatography and spectroscopy, have been criticized for expensive instrumentation and complicated pretreatments. An MG RNA aptamer (MGA) is a powerful tool for immediate and rapid detection of MG. However, RNA is easily degraded by nucleases and is unstable in the environment, making accurate and reliable detection of MG difficult. In order to address the problems, an innovative levo (l)-MGA with excellent stability is designed to perform the specific recognition function. Interestingly, the gel electrophoresis and fluorescence measurement results indicate that this unnaturally occurring l-aptamer is resistant to nuclease degradation and it can be kept intact in the standard buffer solution under room temperature for quite a long time. A label-free, simple, and efficient method has been developed for sensitive detection of MG in fish tissue, which holds promising potential in food analysis and environmental monitoring.
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Affiliation(s)
- Xiaowei Luo
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China. and Department of Chemistry, University of Washington, Washington 98195, USA
| | - Zhifeng Chen
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Hongfeng Li
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Wenqin Li
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Liang Cui
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310008, China.
| | - Jiahao Huang
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. Mirror-image aptamer kissing complex for arginine-vasopressin sensing. Anal Chim Acta 2017; 1001:143-150. [PMID: 29291797 DOI: 10.1016/j.aca.2017.11.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/03/2017] [Accepted: 11/13/2017] [Indexed: 12/31/2022]
Abstract
The recently reported aptamer kissing complex (AKC) strategy has allowed for the development of a new kind of sandwich-like sensing tools. Currently AKC assays have been only applied to low molecular weight molecules and their functionality in complex matrices remains challenging. The objective of the present study broken down into two sub-aims; exploring the propensity to broaden the scope of detectable analytes and designing a more robust system for potential applications to realistic samples. An all L-configuration aptaswitch module derived from a hairpin spiegelmer specific to a larger target, i.e. the arginine-vasopressin (AVP) hormone, was elaborated. The target-induced AKC formation in presence of a specific mirror-image RNA hairpin (L-aptakiss) probe were analyzed by using fluorescence anisotropy. The mirror-image kissing complex was successfully formed when the L-AVP target bound to the engineered L-aptaswitch element. It was also established that the use of methanol as cosolvent significantly improved the assay sensitivity through the stabilization of the ternary complex. Finally, the capability of the mirror-image method to operate in 10-fold diluted, untreated human serum was illustrated. The current work revealed that the AKC concept can be expanded to a wider range of targets and converted to a L-configuration sensing platform especially suitable for bioanalysis purposes.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France; University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
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Aptamers as the Agent in Decontamination Assays (Apta-Decontamination Assays): From the Environment to the Potential Application In Vivo. J Nucleic Acids 2017; 2017:3712070. [PMID: 29225967 PMCID: PMC5684557 DOI: 10.1155/2017/3712070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/10/2017] [Indexed: 12/21/2022] Open
Abstract
The binding specificity and affinity of aptamers have long been harnessed as the key elements in the development of aptamer-based assays, particularly aptasensing application. One promising avenue that is currently explored based on the specificity and affinity of aptamers is the application of aptamers in the decontamination assays. Aptamers have been successfully harnessed as the decontamination agents to remove contaminants from the environment and to decontaminate infectious elements. The reversible denaturation property inherent in aptamers enables the repeated usage of aptamers, which can immensely save the cost of decontamination. Analogous to the point-of-care diagnostics, there is no doubt that aptamers can also be deployed in the point-of-care aptamer-based decontamination assay, whereby decontamination can be performed anywhere and anytime for instantaneous decision-making. It is also prophesied that aptamers can also serve more than as a decontaminant, probably as a tool to capture and kill hazardous elements, particularly pathogenic agents.
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