1
|
Kim J, Seo M, Lim Y, Kim J. START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402029. [PMID: 39075726 DOI: 10.1002/advs.202402029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/31/2024] [Indexed: 07/31/2024]
Abstract
Recognition of signaling molecules for coordinated regulation of target genes is a fundamental process for biological systems. Cells often rely on transcription factors to accomplish these intricate tasks, yet the subtle conformational changes of protein structures, coupled with the complexity of intertwined protein interaction networks, pose challenges for repurposing these for bioengineering applications. This study introduces a novel platform for ligand-responsive gene regulation, termed START (Synthetic Trans-Acting Riboswitch with Triggering RNA). Inspired by the bacterial ligand sensing system, riboswitch, and the synthetic gene regulator, toehold switch, the START platform enables the implementation of synthetic biosensors for various ligands. Rational sequence design with targeted domain optimization yields high-performance STARTs with a dynamic range up to 67.29-fold and a tunable ligand sensitivity, providing a simple and intuitive strategy for sensor engineering. The START platform also exhibits modularity and composability to allow flexible genetic circuit construction, enabling seamless implementation of OR, AND, and NOT Boolean logic gates for multiple ligand inputs. The START design principle is capable of broadening the suite of synthetic biosensors for diverse chemical and protein ligands, providing a novel riboregulator chassis for synthetic biology and bioengineering applications.
Collapse
Affiliation(s)
- Jeongwon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Minchae Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Yelin Lim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| |
Collapse
|
2
|
Wolfe M, Cramer A, Webb S, Goorskey E, Chushak Y, Mirau P, Arroyo-Currás N, Chávez JL. Rational Approach to Optimizing Conformation-Switching Aptamers for Biosensing Applications. ACS Sens 2024; 9:717-725. [PMID: 38270529 PMCID: PMC10897929 DOI: 10.1021/acssensors.3c02004] [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: 09/22/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
The utilization of structure-switching aptamers (SSAs) has enabled the development of novel sensing platforms for the sensitive and continuous detection of molecules. De novo development of SSAs, however, is complex and laborious. Here we describe a rational approach to SSA optimization that simultaneously improves aptamer binding affinity and introduces target-dependent conformation-switching for compatibility with real-world biosensor applications. Key structural features identified from NMR and computational modeling were used to optimize conformational switching in the presence of target, while large-scale, microarray-based mutation analysis was used to map regions of the aptamer permissive to mutation and identify combinations of mutations with stronger binding affinity. Optimizations were carried out in a relevant biofluid to ensure a seamless transition of the aptamer to a biosensing platform. Initial proof-of-concept for this approach is demonstrated with a cortisol binding aptamer but can easily be translated to other relevant aptamers. Cortisol is a hormone correlated with the stress response that has been associated with various medical conditions and is present at quantifiable levels in accessible biofluids. The ability to continuously track levels of stress in real-time via cortisol monitoring, which can be enabled by the aptamers reported here, is crucial for assessing human health and performance.
Collapse
Affiliation(s)
- Monica Wolfe
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- UES,
Inc., Dayton, Ohio 45433, United States
| | - Alyssa Cramer
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- UES,
Inc., Dayton, Ohio 45433, United States
| | - Sean Webb
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- UES,
Inc., Dayton, Ohio 45433, United States
| | - Eva Goorskey
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
| | - Yaroslav Chushak
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- Henry
M. Jackson Foundation for the Advancement of Military Medicine, WPAFB, Ohio 45433, United States
| | - Peter Mirau
- Materials
and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
| | - Netzahualcóyotl Arroyo-Currás
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Jorge L. Chávez
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
| |
Collapse
|
3
|
Zhang T, Liu J, Zhang L, Irfan M, Su X. Recent advances in aptamer-based biosensors for potassium detection. Analyst 2023; 148:5340-5354. [PMID: 37750217 DOI: 10.1039/d3an01053h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Maintaining a stable level of potassium is crucial for proper bodily function because even a slight imbalance can result in serious disorders like hyperkalemia and hypokalemia. Therefore, detecting and monitoring potassium ion (K+) levels are of utmost importance. Various biosensors have been developed for rapid K+ detection, with aptamer-based biosensors garnering significant attention due to their high sensitivity and specificity. This review focuses on aptamer-based biosensors for K+ detection, providing an overview of their signal generation strategies, including electrochemical, field-effect transistor, nanopore, colorimetric, and fluorescent systems. The analytical performance of these biosensors is evaluated comprehensively. In addition, factors that affect their efficiency, such as their physicochemical properties, regeneration for reusability, and linkers/spacers, are listed. Lastly, this review examines the major challenges faced by aptamer-based biosensors in K+ detection and discusses potential future developments.
Collapse
Affiliation(s)
- Tengfang Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Jiajia Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Muhammad Irfan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
4
|
Johnson RE, Van Riesen AJ, Manderville RA. On-Strand Knoevenagel Insertion of a Hemicyanine Molecular Rotor Loop Residue for Turn-On Fluorescence Detection of Pb-Induced G-Quadruplex Rigidity. Bioconjug Chem 2021; 32:2224-2232. [PMID: 34543022 DOI: 10.1021/acs.bioconjchem.1c00386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We demonstrate the ability to distinguish Pb2+ from K+ within the central cavity of the antiparallel G-quadruplex (GQ) DNA produced by the thrombin binding aptamer (TBA) using an internal molecular rotor fluorescent probe. An indole-aldehyde containing an acyclic N-glycol group was first employed in the on-strand Knoevenagel condensation with five different heterocyclic quaternary cationic acceptors to assess the molecular rotor character of the resulting cyanine-styryl dyes within duplex DNA. An indole-pyridinium (4PI) nucleobase surrogate displayed the greatest turn-on emission response to duplex formation and was thus inserted into the loop residues of TBA to monitor GQ-folding in the presence of Pb2+ versus K+. TBA-4PI exhibits turn-on emission upon Pb2+-binding with a brightness (ε·Φfl) of 9000 cm-1 M-1 compared to K+-binding (ε·Φfl ∼ 2000 cm-1 M-1) due to Pb2+-induced GQ rigidity with 4PI-G-tetrad stacking interactions. The Pb2+-bound TBA-4PI GQ also provides energy-transfer (ET) fluorescence with a diagnostic excitation at 310 nm for distinguishing Pb2+ from K+ within the antiparallel GQ. The TBA-4PI GQ affords the desired turn-on fluorescence response for detecting Pb2+ ions with an apparent dissociation constant (Kd) of 63 nM and a limit of detection (LOD) of 19 nM in an aqueous buffer. It can also distinguish Pb2+ (230 nM) from K+ (1.5 mM, 6500-fold excess) in an antiparallel GQ recognition motif without topology twitching.
Collapse
Affiliation(s)
- Ryan E Johnson
- Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Abigail J Van Riesen
- Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Richard A Manderville
- Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
5
|
Development of Specific Inhibitors for Oncogenic Phosphatase PPM1D by Using Ion-Responsive DNA Aptamer Library. Catalysts 2020. [DOI: 10.3390/catal10101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
(1) Background: Ser/Thr protein phosphatase PPM1D is an oncogenic protein. In normal cells, however, PPM1D plays essential roles in spermatogenesis and immune response. Hence, it is necessary to develop novel PPM1D inhibitors without side effects on normal cells. Stimuli-responsive molecules are suitable for the spatiotemporal regulation of inhibitory activity. (2) Methods: In this study, we designed an ion-responsive DNA aptamer library based on G-quadruplex DNA that can change its conformation and function in response to monovalent cations. (3) Results: Using this library, we identified the PPM1D specific inhibitor M1D-Q5F aptamer. The M1D-Q5F aptamer showed anti-cancer activity against breast cancer MCF7 cells. Interestingly, the induction of the structural change resulting in the formation of G-quadruplex upon stimulation by monovalent cations led to the enhancement of the inhibitory activity and binding affinity of M1D-Q5F. (4) Conclusions: These data suggest that the M1D-Q5F aptamer may act as a novel stimuli-responsive anti-cancer agent.
Collapse
|
6
|
Fayazi R, Habibi-Rezaei M, Heiat M, Javadi-Zarnaghi F, Taheri RA. Glycated albumin precipitation using aptamer conjugated magnetic nanoparticles. Sci Rep 2020; 10:10716. [PMID: 32612182 PMCID: PMC7329883 DOI: 10.1038/s41598-020-67469-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 06/02/2020] [Indexed: 01/10/2023] Open
Abstract
To develop a strategy for the elimination of prefibrillar amyloid aggregates, a three-step non-modified DNA aptamer conjugation on silica-coated magnetic nanoparticles was carried out to achieve aptamer conjugated on MNP (Ap-SiMNP). Prefibrillar amyloid aggregates are generated under a diabetic condition which are prominently participated in developing diabetic complications. The binding properties of candidate DNA aptamer against serum albumin prefibrillar amyloid aggregates (AA20) were verified using electrophoretic mobility shift assay (EMSA) and surface plasmon resonance spectroscopy (SPR) analysis. The chloro-functionalized silica-coated MNPs were synthesized then a nano-targeting structure as aptamer conjugated on MNP (Ap-SiMNP) was constructed. Finally, Ap-SiMNP was verified for specific binding efficiency and AA20 removal using an external magnetic field. The candidate aptamer showed a high binding capacity at EMSA and SPR analysis (KD = 3.4 × 10─9 M) and successfully used to construct Ap-SiMNP. Here, we show a proof of concept for an efficient bio-scavenger as Ap-SiMNP to provide a promising opportunity to consider as a possible strategy to overcome some diabetic complications through specific binding/removal of toxic AA20 species.
Collapse
Affiliation(s)
- R Fayazi
- School of Biology, University of Tehran, P.O.Box 14155-6455, Tehran, Iran
| | - M Habibi-Rezaei
- School of Biology, University of Tehran, P.O.Box 14155-6455, Tehran, Iran.
- Center of Excellence in Nano-Biomedicine, University of Tehran, Tehran, Iran.
| | - M Heiat
- Research Center for Gastroenterology and Liver Disease, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - F Javadi-Zarnaghi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - R A Taheri
- Nanobiotechnolology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
7
|
YANG G, ZHAO Y, HAN SM, ZHU C, HUANG YY, QU F. Screening Aptamer of Apo-transferrin via Capillary Electrophoresis-Systematic Evolution of Ligands by Exponential Enrichment and Environmental Factors Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60019-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
8
|
Aptamers as a novel diagnostic and therapeutic tool and their potential use in parasitology. ACTA ACUST UNITED AC 2020; 40:148-165. [PMID: 32463617 PMCID: PMC7449109 DOI: 10.7705/biomedica.4765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 02/07/2023]
Abstract
Los aptámeros son secuencias de ADN o ARN de cadena sencilla que adoptan la forma de estructuras tridimensionales únicas, lo cual les permite reconocer un blanco específico con gran afinidad. Sus usos potenciales abarcan, entre otros, el diagnóstico de enfermedades, el desarrollo de nuevos agentes terapéuticos, la detección de riesgos alimentarios, la producción de biosensores, la detección de toxinas, el transporte de fármacos en el organismo y la señalización de nanopartículas. El pegaptanib es el único aptámero aprobado para uso comercial por la Food and Drug Administration (FDA). Otros aptámeros para el tratamiento de enfermedades están en la fase clínica de desarrollo. En parasitología, se destacan los estudios que se vienen realizando en Leishmania spp., con la obtención de aptámeros que reconocen la proteína de unión a poliA (LiPABP) y que pueden tener potencial utilidad en la investigación, el diagnóstico y el tratamiento de la leishmaniasis. En cuanto a la malaria, se han obtenido aptámeros que permiten identificar eritrocitos infectados e inhiben la formación de rosetas, y otros que prometen ser alternativas para el diagnóstico al detectar de forma específica la proteína lactato deshidrogenasa (PfLDH). Para Cryptosporidium parvuum se han seleccionado aptámeros que detectan ooquistes a partir de alimentos o aguas contaminadas. Para Entamoeba histolytica se han aislado dos aptámeros llamados C4 y C5, que inhiben la proliferación in vitro de los trofozoítos y tienen potencial terapéutico. Los aptámeros contra Trypanosoma cruzi inhiben la invasión de células LLC-MK2 (de riñón de mono) en un 50 a 70 % y aquellos contra T. brucei transportan moléculas tóxicas al lisosoma parasitario como una novedosa estrategia terapéutica. Los datos recopilados en esta revisión destacan los aptámeros como una alternativa para la investigación, el diagnóstico y el tratamiento contra parásitos de interés nacional.
Collapse
|
9
|
Slavkovic S, Eisen SR, Johnson PE. Designed Alteration of Binding Affinity in Structure-Switching Aptamers through the Use of Dangling Nucleotides. Biochemistry 2020; 59:663-670. [PMID: 31912723 DOI: 10.1021/acs.biochem.9b00630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to change binding affinity in a controlled fashion is a key step in the rational design of biomolecules in general and functional nucleic acids in particular. Here, we use dangling nucleotides to alter the binding affinity of structure-switching aptamers. Dangling nucleotides can stabilize or destabilize a nucleic acid structure with a known ΔG°37. When the dangling nucleotide stabilizes the structure, less free energy from ligand binding is needed to fold the molecule and hence the ligand is observed to bind tighter than in the absence of the unpaired nucleotide. For a destabilizing dangling nucleotide, the opposite occurs, and the observed binding is weaker. We demonstrate this concept using both the cocaine-binding aptamer and the ATP-binding aptamer systems. We find that for both aptamers there is a direct, but different, relationship between the predicted stabilization and the change in the observed binding free energy.
Collapse
Affiliation(s)
- Sladjana Slavkovic
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario , Canada M3J 1P3
| | - Sophie R Eisen
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario , Canada M3J 1P3
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario , Canada M3J 1P3
| |
Collapse
|
10
|
Citartan M, Tang TH. Recent developments of aptasensors expedient for point-of-care (POC) diagnostics. Talanta 2019; 199:556-566. [PMID: 30952298 DOI: 10.1016/j.talanta.2019.02.066] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 12/12/2022]
Abstract
Aptamers are nucleic acid-based molecular recognition elements that are specific and have high binding affinity against their respective targets. On account of their target recognition capacity, aptamers are widely utilized in a number of applications including diagnostics. This review aims to highlight the recent developments of aptasensors expedient for point-of-care (POC) diagnostics. Significant focus is given on the primary assay formats of aptamers such as fluorescence, electrochemical, surface plasmon resonance (SPR) and colorimetric assays. A potpourri of platforms such as paper-based device, lateral flow assay, portable electrodes, portable SPR and smart phones expedient for point-of-care (POC) diagnostics are discussed. Emphasis is also given on the technicalities and assay configurations associated with the sensors.
Collapse
Affiliation(s)
- Marimuthu Citartan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Penang 13200, Malaysia.
| | - Thean-Hock Tang
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Penang 13200, Malaysia
| |
Collapse
|
11
|
Cataldo R, Giotta L, Guascito MR, Alfinito E. Assessing the Quality of in Silico Produced Biomolecules: The Discovery of a New Conformer. J Phys Chem B 2019; 123:1265-1273. [PMID: 30642170 DOI: 10.1021/acs.jpcb.8b11456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The computational procedures for predicting the 3D structure of aptamers interacting with different biological molecules have gained increasing attention in recent years. The information acquired through these methods represents a crucial input for research, especially when relevant crystallographic data are not available. A number of software programs able to perform macromolecular docking are currently accessible, leading to the prediction of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Nevertheless, the scoring protocols employed for ranking the candidate structures do not always produce satisfactory results, making difficult the identification of structures that are most likely to occur in nature. In this paper, we propose a novel procedure to improve the predictive performances of computational scoring protocols, using a maximum likelihood estimate based on topological and electrical properties of interacting biomolecules. The reliability of the new computational approach, enabling the ranking of aptamer-protein configurations produced by an open source docking program, has been assessed by its successful application to a set of antiangiopoietin aptamers, for which experimental data highlighting the sequence-dependent affinity toward the target protein are available. The procedure led to the identification of two main types of aptamer conformers involved in angiopoietin binding. Interestingly, one of these reproduces the arrangement of angiopoietin with its natural target, tyrosine kinase, while the other one is completely unexpected. The possible scenarios related to these results have been discussed. The methodology here described can be used to refine the outcomes of different computational procedures and can be applied to a wide range of biological molecules, thus representing a new tool for guiding the design of bioinspired sensors with enhanced selectivity.
Collapse
Affiliation(s)
- R Cataldo
- Department of Mathematics and Physics, "Ennio De Giorgi" , University of Salento , Via Monteroni , I-73100 Lecce , Italy
| | - L Giotta
- Department of Biological and Environmental Sciences and Technologies , University of Salento , Via Monteroni , I-73100 Lecce , Italy
| | - M R Guascito
- Department of Biological and Environmental Sciences and Technologies , University of Salento , Via Monteroni , I-73100 Lecce , Italy
| | - E Alfinito
- Department of Innovation Engineering , University of Salento , Via Monteroni , I-73100 Lecce , Italy
| |
Collapse
|
12
|
Nakatsuka N, Cao HH, Deshayes S, Melkonian AL, Kasko AM, Weiss PS, Andrews AM. Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23490-23500. [PMID: 29851335 PMCID: PMC6087467 DOI: 10.1021/acsami.8b02837] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are chemically synthesized oligonucleotides or peptides with molecular recognition capabilities. We investigated recognition of substrate-tethered small-molecule targets, using neurotransmitters as examples, and fluorescently labeled DNA aptamers. Substrate regions patterned via microfluidic channels with dopamine or l-tryptophan were selectively recognized by previously identified dopamine or l-tryptophan aptamers, respectively. The on-substrate dissociation constant determined for the dopamine aptamer was comparable to, though, slightly greater than the previously determined solution dissociation constant. Using prefunctionalized neurotransmitter-conjugated oligo(ethylene glycol) alkanethiols and microfluidics patterning, we produced multiplexed substrates to capture and to sort aptamers. Substrates patterned with l-3,4-dihydroxyphenylalanine, l- threo-dihydroxyphenylserine, and l-5-hydroxytryptophan enabled comparison of the selectivity of the dopamine aptamer for different targets via simultaneous determination of in situ binding constants. Thus, beyond our previous demonstrations of recognition by protein binding partners (i.e., antibodies and G-protein-coupled receptors), strategically optimized small-molecule-functionalized substrates show selective recognition of nucleic acid binding partners. These substrates are useful for side-by-side target comparisons and future identification and characterization of novel aptamers targeting neurotransmitters or other important small molecules.
Collapse
Affiliation(s)
- Nako Nakatsuka
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Huan H. Cao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Stephanie Deshayes
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Arin L. Melkonian
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Andrea M. Kasko
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Paul S. Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Anne M. Andrews
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, CA 90095, United States
| |
Collapse
|
13
|
Wang CH, Chang CP, Lee GB. Integrated microfluidic device using a single universal aptamer to detect multiple types of influenza viruses. Biosens Bioelectron 2016; 86:247-254. [PMID: 27376195 DOI: 10.1016/j.bios.2016.06.071] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
DNA aptamers that can bind specific molecular targets have great potential as probes for microbial diagnostic applications. However, aptamers may change their conformation under different operating conditions, thus affecting their affinity and specificity towards the target molecules. In this study, a new integrated microfluidic system was developed that exploited the predictable change in conformation of a single universal influenza aptamer exposed to differing ion concentrations in order to detect multiple types of the influenza virus. Furthermore, the fluorescent-labeled universal aptamer used in this system could distinguish and detect three different influenza viruses (influenza A H1N1, H3N2, and influenza B) at the same time in 20min and therefore has great potential for point-of-care applications requiring rapid diagnosis of influenza viruses.
Collapse
Affiliation(s)
- Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Peng Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan; Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, Taiwan; Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan.
| |
Collapse
|
14
|
Schoukroun-Barnes LR, Macazo FC, Gutierrez B, Lottermoser J, Liu J, White RJ. Reagentless, Structure-Switching, Electrochemical Aptamer-Based Sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:163-81. [PMID: 27070185 PMCID: PMC5627773 DOI: 10.1146/annurev-anchem-071015-041446] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The development of structure-switching, electrochemical, aptamer-based sensors over the past ∼10 years has led to a variety of reagentless sensors capable of analytical detection in a range of sample matrices. The crux of this methodology is the coupling of target-induced conformation changes of a redox-labeled aptamer with electrochemical detection of the resulting altered charge transfer rate between the redox molecule and electrode surface. Using aptamer recognition expands the highly sensitive detection ability of electrochemistry to a range of previously inaccessible analytes. In this review, we focus on the methods of sensor fabrication and how sensor signaling is affected by fabrication parameters. We then discuss recent studies addressing the fundamentals of sensor signaling as well as quantitative characterization of the analytical performance of electrochemical aptamer-based sensors. Although the limits of detection of reported electrochemical aptamer-based sensors do not often reach that of gold-standard methods such as enzyme-linked immunosorbent assays, the operational convenience of the sensor platform enables exciting analytical applications that we address. Using illustrative examples, we highlight recent advances in the field that impact important areas of analytical chemistry. Finally, we discuss the challenges and prospects for this class of sensors.
Collapse
Affiliation(s)
- Lauren R Schoukroun-Barnes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Florika C Macazo
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Brenda Gutierrez
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Justine Lottermoser
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Juan Liu
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Ryan J White
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| |
Collapse
|
15
|
McKeague M, McConnell EM, Cruz-Toledo J, Bernard ED, Pach A, Mastronardi E, Zhang X, Beking M, Francis T, Giamberardino A, Cabecinha A, Ruscito A, Aranda-Rodriguez R, Dumontier M, DeRosa MC. Analysis of In Vitro Aptamer Selection Parameters. J Mol Evol 2015; 81:150-61. [PMID: 26530075 DOI: 10.1007/s00239-015-9708-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics and therapeutics. Here, we extracted detailed information about aptamer selection experiments housed in the Aptamer Base, spanning over two decades, to perform the first parameter analysis of conditions used to identify and isolate aptamers de novo. We used information from 492 published SELEX experiments and studied the relationships between the nucleic acid library, target choice, selection methods, experimental conditions, and the affinity of the resulting aptamer candidates. Our findings highlight that the choice of target and selection template made the largest and most significant impact on the success of a de novo aptamer selection. Our results further emphasize the need for improved documentation and more thorough experimentation of SELEX criteria to determine their correlation with SELEX success.
Collapse
Affiliation(s)
- Maureen McKeague
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Erin M McConnell
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Jose Cruz-Toledo
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Elyse D Bernard
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Amanda Pach
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Emily Mastronardi
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Xueru Zhang
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Michael Beking
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Tariq Francis
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Amanda Giamberardino
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ashley Cabecinha
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Annamaria Ruscito
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Rocio Aranda-Rodriguez
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Michel Dumontier
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. .,Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
| | - Maria C DeRosa
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
| |
Collapse
|
16
|
Hou L, Wu X, Chen G, Yang H, Lu M, Tang D. HCR-stimulated formation of DNAzyme concatamers on gold nanoparticle for ultrasensitive impedimetric immunoassay. Biosens Bioelectron 2015; 68:487-493. [DOI: 10.1016/j.bios.2015.01.043] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 01/13/2015] [Accepted: 01/19/2015] [Indexed: 12/16/2022]
|
17
|
Unusual Chair-Like G-Quadruplex Structures: Heterochiral TBA Analogues Containing Inversion of Polarity Sites. J CHEM-NY 2015. [DOI: 10.1155/2015/473051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterochiral oligodeoxynucleotides based on the thrombin binding aptamer sequence, namely, 5′gg3′-3′TT5′-5′ggtgtgg3′-3′TT5′-5′gg3′ (H1), 5′gg3′-3′TT5′-5′gg3′-3′TGT5′-5′gg3′-3′TT5′-5′gg3′ (H2), and 5′gGTTGgtgtgGTTGg3′ (H3), where lower case letters indicate L-residues, have been investigated in their ability to fold in G-quadruplex structures through a combination of gel electrophoresis, circular dichroism, and UV spectroscopy techniques. InH1andH2inversions of polarity sites have been introduced to control the strand direction in the loop regions. Collected data suggest that all modified sequences are able to fold in chair-like G-quadruplexes mimicking the originalTBAstructure.
Collapse
|