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Carota AG, Bonini A, Urban M, Poma N, Vivaldi FM, Tavanti A, Rossetti M, Rosati G, Merkoçi A, Di Francesco F. Low-cost inkjet-printed nanostructured biosensor based on CRISPR/Cas12a system for pathogen detection. Biosens Bioelectron 2024; 258:116340. [PMID: 38718633 DOI: 10.1016/j.bios.2024.116340] [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: 02/08/2024] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
The escalating global incidence of infectious diseases caused by pathogenic bacteria, especially in developing countries, emphasises the urgent need for rapid and portable pathogen detection devices. This study introduces a sensitive and specific electrochemical biosensing platform utilising cost-effective electrodes fabricated by inkjet-printing gold and silver nanoparticles on a plastic substrate. The biosensor exploits the CRISPR/Cas12a system for detecting a specific DNA sequence selected from the genome of the target pathogen. Upon detection, the trans-activity of Cas12a/gRNA is triggered, leading to the cleavage of rationally designed single-strand DNA reporters (linear and hairpin) labelled with methylene blue (ssDNA-MB) and bound to the electrode surface. In principle, this sensing mechanism can be adapted to any bacterium by choosing a proper guide RNA to target a specific sequence of its DNA. The biosensor's performance was assessed for two representative pathogens (a Gram-negative, Escherichia coli, and a Gram-positive, Staphylococcus aureus), and results obtained with inkjet-printed gold electrodes were compared with those obtained by commercial screen-printed gold electrodes. Our results show that the use of inkjet-printed nanostructured gold electrodes, which provide a large surface area, in combination with the use of hairpin reporters containing a poly-T loop can increase the sensitivity of the assay corresponding to a signal variation of 86%. DNA targets amplified from various clinically isolated bacteria, have been tested and demonstrate the potential of the proposed platform for point-of-need applications.
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Affiliation(s)
- Angela Gilda Carota
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Andrea Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy; Department of Biology, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy.
| | - Massimo Urban
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Noemi Poma
- Department of Biology, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy
| | - Federico Maria Vivaldi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Arianna Tavanti
- Department of Biology, University of Pisa, Via San Zeno 37, 56127 Pisa, Italy
| | - Marianna Rossetti
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Giulio Rosati
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Arben Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain
| | - Fabio Di Francesco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy.
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Johansson TB, Davtyan R, Valderas-Gutiérrez J, Gonzalez Rodriguez A, Agnarsson B, Munita R, Fioretos T, Lilljebjörn H, Linke H, Höök F, Prinz CN. Sub-Nanomolar Detection of Oligonucleotides Using Molecular Beacons Immobilized on Lightguiding Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:453. [PMID: 38470783 DOI: 10.3390/nano14050453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024]
Abstract
The detection of oligonucleotides is a central step in many biomedical investigations. The most commonly used methods for detecting oligonucleotides often require concentration and amplification before detection. Therefore, developing detection methods with a direct read-out would be beneficial. Although commonly used for the detection of amplified oligonucleotides, fluorescent molecular beacons have been proposed for such direct detection. However, the reported limits of detection using molecular beacons are relatively high, ranging from 100 nM to a few µM, primarily limited by the beacon fluorescence background. In this study, we enhanced the relative signal contrast between hybridized and non-hybridized states of the beacons by immobilizing them on lightguiding nanowires. Upon hybridization to a complementary oligonucleotide, the fluorescence from the surface-bound beacon becomes coupled in the lightguiding nanowire core and is re-emitted at the nanowire tip in a narrower cone of light compared with the standard 4π emission. Prior knowledge of the nanowire positions allows for the continuous monitoring of fluorescence signals from each nanowire, which effectively facilitates the discrimination of signals arising from hybridization events against background signals. This resulted in improved signal-to-background and signal-to-noise ratios, which allowed for the direct detection of oligonucleotides at a concentration as low as 0.1 nM.
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Affiliation(s)
- Therese B Johansson
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Rubina Davtyan
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Julia Valderas-Gutiérrez
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | | | - Björn Agnarsson
- Division of Nano and Biophysics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Heiner Linke
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Fredrik Höök
- NanoLund, Lund University, 221 00 Lund, Sweden
- Division of Nano and Biophysics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Christelle N Prinz
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
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Erdem A, Eksin E. Zip Nucleic Acid-Based Genomagnetic Assay for Electrochemical Detection of microRNA-34a. BIOSENSORS 2023; 13:bios13010144. [PMID: 36671979 PMCID: PMC9856502 DOI: 10.3390/bios13010144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 05/17/2023]
Abstract
Zip nucleic acid (ZNA)-based genomagnetic assay was developed herein for the electrochemical detection of microRNA-34a (miR-34a), which is related to neurological disorders and cancer. The hybridization between the ZNA probe and miR-34a target was performed in the solution phase; then, the resultant hybrids were immobilized onto the surface of magnetic beads (MBs). After magnetic separation, the hybrids were separated from the surface of MBs and then immobilized on the surface of pencil graphite electrodes (PGEs). In the case of a full-match hybridization, the guanine oxidation signal was measured via the differential pulse voltammetry (DPV) technique. All the experimental parameters that influenced the hybridization efficiency (i.e., hybridization strategy, probe concentration, hybridization temperature, etc.) were optimized. The cross-selectivity of the genomagnetic assay was tested against two different miRNAs, miR-155 and miR-181b, individually as well as in mixture samples. To show the applicability of the ZNA-based genomagnetic assay for miR-34a detection in real samples, a batch of experiments was carried out in this study by using the total RNA samples isolated from the human hepatocellular carcinoma cell line (HUH-7).
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Affiliation(s)
- Arzum Erdem
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Izmir 35100, Turkey
- Correspondence: ; Tel.: +90-232-311-5131
| | - Ece Eksin
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Izmir 35100, Turkey
- Biomedical Device Technology Program, Vocational School of Health Services, Izmir Democracy University, Izmir 35290, Turkey
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4
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Chen X, Zhu J, Sun B, Zhang X, Hu Y, Chen Y. A mass-tagged MOF nanoprobe approach for ultra-sensitive protein quantification in tumor-educated platelets. Chem Commun (Camb) 2022; 58:7160-7163. [PMID: 35667628 DOI: 10.1039/d2cc01815b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mass-tagged metal-organic framework (MOF) nanoprobe approach was developed for ultra-sensitive quantification of platelet protein CD44 by integrating activable aptamer recognition and MOF nanoprobe signal amplification with mass spectrometric detection. This approach offered high sensitivity and quantitative capability for low abundant protein analysis in tumor-educated platelets (TEPs), exhibiting great potential in cancer diagnosis and management.
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Affiliation(s)
- Xiuyu Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Jianhua Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Bo Sun
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Xian Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Yechen Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China. .,State Key Laboratory of Reproductive Medicine, 210029, China.,Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Nanjing, 211166, China
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Zhang Q, Yin B, Hao J, Ma L, Huang Y, Shao X, Li C, Chu Z, Yi C, Wong SHD, Yang M. An AIEgen/graphene oxide nanocomposite (AIEgen@GO)-based two-stage "turn-on" nucleic acid biosensor for rapid detection of SARS-CoV-2 viral sequence. AGGREGATE (HOBOKEN, N.J.) 2022; 4:e195. [PMID: 35539693 PMCID: PMC9073974 DOI: 10.1002/agt2.195] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 03/08/2022] [Indexed: 05/24/2023]
Abstract
The ongoing outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has posed significant challenges in early viral diagnosis. Hence, it is urgently desirable to develop a rapid, inexpensive, and sensitive method to aid point-of-care SARS-CoV-2 detection. In this work, we report a highly sequence-specific biosensor based on nanocomposites with aggregation-induced emission luminogens (AIEgen)-labeled oligonucleotide probes on graphene oxide nanosheets (AIEgen@GO) for one step-detection of SARS-CoV-2-specific nucleic acid sequences (Orf1ab or N genes). A dual "turn-on" mechanism based on AIEgen@GO was established for viral nucleic acids detection. Here, the first-stage fluorescence recovery was due to dissociation of the AIEgen from GO surface in the presence of target viral nucleic acid, and the second-stage enhancement of AIE-based fluorescent signal was due to the formation of a nucleic acid duplex to restrict the intramolecular rotation of the AIEgen. Furthermore, the feasibility of our platform for diagnostic application was demonstrated by detecting SARS-CoV-2 virus plasmids containing both Orf1ab and N genes with rapid detection around 1 h and good sensitivity at pM level without amplification. Our platform shows great promise in assisting the initial rapid detection of the SARS-CoV-2 nucleic acid sequence before utilizing quantitative reverse transcription-polymerase chain reaction for second confirmation.
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Affiliation(s)
- Qin Zhang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Bohan Yin
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Jianhua Hao
- Department of Applied PhysicsThe Hong Kong Polytechnic UniversityHong KongChina
| | - Linjie Ma
- Department of Electrical and Electronic EngineeringJoint Appointment with School of Biomedical SciencesThe University of Hong KongHong KongChina
| | - Yingying Huang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Xueying Shao
- Department of Electrical and Electronic EngineeringJoint Appointment with School of Biomedical SciencesThe University of Hong KongHong KongChina
| | - Chuanqi Li
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Zhiqin Chu
- Department of Electrical and Electronic EngineeringJoint Appointment with School of Biomedical SciencesThe University of Hong KongHong KongChina
| | - Changqing Yi
- Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province)School of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhouPR China
| | - Siu Hong Dexter Wong
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Mo Yang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
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Li J, Fan YY, Wen J, Zhang J, Zhang ZQ. Metal-Enhanced Aggregation-Induced Emission Strategy for the HIV-I RNA-Binding Ligand Assay. Anal Chem 2022; 94:4695-4702. [PMID: 35258935 DOI: 10.1021/acs.analchem.1c04889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The HIV-Ι trans-activation responsive (TAR) RNA-trans-activator of transcription (Tat) protein complex is crucial for the efficient transcription of the integrated human immunodeficiency virus-I genome and is an established therapeutic target for AIDS diagnosis and treatment. Developing a sensitive strategy for the TAR RNA-binding ligand assay could provide antiviral leads with a radically new mechanism for the treatment of AIDS. Herein, a new TAR RNA-binding ligand assay platform was established using a signal amplification strategy that combines aggregation-induced emission (AIE) with a metal-enhanced fluorescence (MEF) concept. The tetraphenylethylene (TPE) derivative was labeled on the Tat peptide as a fluorescent molecule, while the TAR RNA was immobilized on the surface of the Fe3O4@Au@Ag@SiO2 nanoparticles (NPs) to specifically bind the TPE-Tat peptide. The TPE-Tat peptide was weakly emissive itself while emitting strongly in the NP-TAR-TPE-Tat complex by the AIE and MEF signal amplification effect. It was confirmed by known Tat peptide competitors that this system could be applied to the screening and detection of TAR RNA-binding ligands because they could replace the TPE-Tat peptide from the complex and make the system fluorescence decrease. When this system was adopted to test four candidate ligands, it was found that bisantrene had a favorable TAR RNA-binding ability. The proposed AIE-MEF strategy not only provides a sensitive and reliable method for the TAR RNA-binding ligand assay but also can avoid the influence of ligands on fluorescent detection in the conventional displacement assay.
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Affiliation(s)
- Jun Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yao-Yao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jie Wen
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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7
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Corchuelo S, Gómez CY, Rosales AA, Santamaria G, Rivera JA, Saad EP, Torres-Fernández O, Rengifo AC. CISH and IHC for the Simultaneous Detection of ZIKV RNA and Antigens in Formalin-Fixed Paraffin-Embedded Cell Blocks and Tissues. Curr Protoc 2021; 1:e319. [PMID: 34936226 DOI: 10.1002/cpz1.319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Zika virus is an arthropod-borne virus that has recently emerged as a significant public health emergency due to its association with congenital malformations. Serological and molecular tests are typically used to confirm Zika virus infection. These methods, however, have limitations when the interest is in localizing the virus within the tissue and identifying the specific cell types involved in viral dissemination. Chromogenic in situ hybridization (CISH) and immunohistochemistry (IHC) are common histological techniques used for intracellular localization of RNA and protein expression, respectively. The combined use of CISH and IHC is important to obtain information about RNA replication and the location of infected target cells involved in Zika virus neuropathogenesis. There are no reports, however, of detailed procedures for the simultaneous detection of Zika virus RNA and proteins in formalin-fixed paraffin-embedded (FFPE) samples. Furthermore, the chromogenic detection methods for Zika virus RNA published thus far use expensive commercial kits, limiting their widespread use. As an alternative, we describe here a detailed and cost-effective step-by-step procedure for the simultaneous detection of Zika virus RNA and proteins in FFPE samples. First, we describe how to synthesize and purify homemade RNA probes conjugated with digoxygenin. Then, we outline the steps to perform the chromogenic detection of Zika virus RNA using these probes, and how to combine this technique with the immunodetection of viral antigens. To illustrate the entire workflow, we use FFPE samples derived from infected Vero cells as well as from human and mouse brain tissues. These methods are highly adaptable and can be used to study Zika virus or even other viruses of public health relevance, providing an optimal and economical alternative for laboratories with limited resources. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of RNA probes conjugated with digoxigenin (DIG) Basic Protocol 2: Simultaneous detection of ZIKV RNA and proteins in FFPE cell blocks and tissues.
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Affiliation(s)
- Sheryll Corchuelo
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
| | - Claudia Y Gómez
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
| | - Alicia A Rosales
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
| | - Gerardo Santamaria
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
| | - Jorge Alonso Rivera
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
| | - Edgar Parra Saad
- Grupo de Patología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
| | - Orlando Torres-Fernández
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
| | - Aura Caterine Rengifo
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, DC, Colombia
- Doctorado en Ciencias Biomédicas, Universidad Nacional de Colombia, Bogotá, DC, Colombia
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8
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Zhang Z, Liu N, Zhang Z, Xu D, Ma S, Wang X, Zhou T, Zhang G, Wang F. Construction of Aptamer-Based Molecular Beacons with Varied Blocked Structures and Targeted Detection of Thrombin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8738-8745. [PMID: 34270267 DOI: 10.1021/acs.langmuir.1c00994] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A kind of blocked aptamer-functionalized molecular beacon (MB) was designed as fluorescence sensors to detect thrombins by binding-induced "turn on" structural transformation. Three MBs named MB(8 + 8), MB(15 + 8), and MB(15 + 6) consisted of two single-stranded oligonucleotides. One long single-stranded oligonucleotide (abbreviated as SS) contained a thrombin aptamer sequence and was modified with a fluorescence group and quenching group on each end side. Another short single-stranded oligonucleotide (written as cDNA) was partially complementary to the long SS. It was interesting to find that the complementary sequence length of cDNA greatly influenced the structure of the MBs. The construction of MB experiments proved that MB(8 + 8) and MB(15 + 8) could form the quenching MBs but MB(15 + 6) could not. MB(8 + 8) was composed of a SS strand paired with a complementary cDNA(8 + 8), which was called one-to-one combination, while MB(15 + 8) was two-to-two combination and MB(15 + 6) was one-to-two combination. When the ratio of SS and cDNA (15 + 8) was 1:1, the quenching efficiency reached maximum. But with the molar ratio of SS and cDNA(8 + 8) increasing, the quenching efficiency increased continuously. Under the optimal conditions that we studied, the detection limit of thrombin by MB(8 + 8) and MB(15 + 8) was 0.19 and 1.2 nM, respectively. In addition, the assay proved to be selective, and the average recovery of thrombin detected by MB(8 + 8) and MB(15 + 8) in diluted serum was 95.4 and 94.5%, respectively.
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Affiliation(s)
- Zhiqing Zhang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Nana Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Zichen Zhang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Dongyan Xu
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Shuai Ma
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiufeng Wang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Ting Zhou
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Guodong Zhang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Wang
- College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
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9
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Toward a Quantitative Relationship between Nanoscale Spatial Organization and Hybridization Kinetics of Surface Immobilized Hairpin DNA Probes. ACS Sens 2021; 6:371-379. [PMID: 32945167 DOI: 10.1021/acssensors.0c01278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hybridization of DNA probes immobilized on a solid support is a key process for DNA biosensors and microarrays. Although the surface environment is known to influence the kinetics of DNA hybridization, so far it has not been possible to quantitatively predict how hybridization kinetics is influenced by the complex interactions of the surface environment. Using spatial statistical analysis of probes and hybridized target molecules on a few electrochemical DNA (E-DNA) sensors, functioning through hybridization-induced conformational change of redox-tagged hairpin probes, we developed a phenomenological model that describes how the hybridization rates for single probe molecules are determined by the local environment. The predicted single-molecule rate constants, upon incorporation into numerical simulation, reproduced the overall kinetics of E-DNA sensor surfaces at different probe densities and different degrees of probe clustering. Our study showed that the nanoscale spatial organization is a major factor behind the counterintuitive trends in hybridization kinetics. It also highlights the importance of models that can account for heterogeneity in surface hybridization. The molecular level understanding of hybridization at surfaces and accurate prediction of hybridization kinetics may lead to new opportunities in development of more sensitive and reproducible DNA biosensors and microarrays.
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10
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Chen X, Lisi F, Bakthavathsalam P, Longatte G, Hoque S, Tilley RD, Gooding JJ. Impact of the Coverage of Aptamers on a Nanoparticle on the Binding Equilibrium and Kinetics between Aptamer and Protein. ACS Sens 2021; 6:538-545. [PMID: 33296177 DOI: 10.1021/acssensors.0c02212] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Knowledge of the interaction between aptamer and protein is integral to the design and development of aptamer-based biosensors. Nanoparticles functionalized with aptamers are commonly used in these kinds of sensors. As such, studies into how the number of aptamers on the nanoparticle surface influence both kinetics and thermodynamics of the binding interaction are required. In this study, aptamers specific for interferon gamma (IFN-γ) were immobilized on the surface of gold nanoparticles (AuNPs), and the effect of surface coverage of aptamer on the binding interaction with its target was investigated using fluorescence spectroscopy. The number of aptamers were adjusted from an average of 9.6 to 258 per particle. The binding isotherm between AuNPs-aptamer conjugate and protein was modeled with the Hill-Langmuir equation, and the determined equilibrium dissociation constant (K'D) decreased 10-fold when increasing the coverage of aptamer. The kinetics of the reaction as a function of coverage of aptamer were also investigated, including the association rate constant (kon) and the dissociation rate constant (koff). The AuNPs-aptamer conjugate with 258 aptamers per particle had the highest kon, while the koff was similar for AuNPs-aptamer conjugates with different surface coverages. Therefore, the surface coverage of aptamers on AuNPs affects both the thermodynamics and the kinetics of the binding. The AuNPs-aptamer conjugate with the highest surface coverage is the most favorable in biosensors considering the limit of detection, sensitivity, and response time of the assay. These findings deepen our understanding of the interaction between aptamer and target protein on the particle surface, which is important to both improve the scientific design and increase the application of aptamer-nanoparticle based biosensor.
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Affiliation(s)
- Xueqian Chen
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Fabio Lisi
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Padmavathy Bakthavathsalam
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Guillaume Longatte
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Sharmin Hoque
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D. Tilley
- School of Chemistry and Electron Microscope Unit a Microscopy Australia Node, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J. Justin Gooding
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
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11
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Direct PCR-free electrochemical biosensing of plant-food derived nucleic acids in genomic DNA extracts. Application to the determination of the key allergen Sola l 7 in tomato seeds. Biosens Bioelectron 2019; 137:171-177. [DOI: 10.1016/j.bios.2019.05.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 12/14/2022]
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12
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Gu Q, Nanney W, Cao HH, Wang H, Ye T. Single Molecule Profiling of Molecular Recognition at a Model Electrochemical Biosensor. J Am Chem Soc 2018; 140:14134-14143. [PMID: 30293418 DOI: 10.1021/jacs.8b07325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The spatial arrangement of target and probe molecules on the biosensor is a key aspect of the biointerface structure that ultimately determines the properties of interfacial molecular recognition and the performance of the biosensor. However, the spatial patterns of single molecules on practical biosensors have been unknown, making it difficult to rationally engineer biosensors. Here, we have used high-resolution atomic force microscopy to map closely spaced individual probes as well as discrete hybridization events on a functioning electrochemical DNA sensor surface. We also applied spatial statistical methods to characterize the spatial patterns at the single molecule level. We observed the emergence of heterogeneous spatiotemporal patterns of surface hybridization of hairpin probes. The clustering of target capture suggests that hybridization may be enhanced by proximity of probes and targets that are about 10 nm away. The unexpected enhancement was rationalized by the complex interplay between the nanoscale spatial organization of probe molecules, the conformational changes of the probe molecules, and target binding. Such molecular level knowledge may allow one to tailor the spatial patterns of the biosensor surfaces to improve the sensitivity and reproducibility.
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13
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Povedano E, Valverde A, Montiel VR, Pedrero M, Yáñez‐Sedeño P, Barderas R, San Segundo‐Acosta P, Peláez‐García A, Mendiola M, Hardisson D, Campuzano S, Pingarrón JM. Rapid Electrochemical Assessment of Tumor Suppressor Gene Methylations in Raw Human Serum and Tumor Cells and Tissues Using Immunomagnetic Beads and Selective DNA Hybridization. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Eloy Povedano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Alejandro Valverde
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Víctor Ruiz‐Valdepeñas Montiel
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - María Pedrero
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Paloma Yáñez‐Sedeño
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Rodrigo Barderas
- CROSADISInstituto de Salud Carlos III 28220 Majadahonda Madrid Spain
| | | | - Alberto Peláez‐García
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Susana Campuzano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - José M. Pingarrón
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
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14
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Povedano E, Valverde A, Montiel VR, Pedrero M, Yáñez‐Sedeño P, Barderas R, San Segundo‐Acosta P, Peláez‐García A, Mendiola M, Hardisson D, Campuzano S, Pingarrón JM. Rapid Electrochemical Assessment of Tumor Suppressor Gene Methylations in Raw Human Serum and Tumor Cells and Tissues Using Immunomagnetic Beads and Selective DNA Hybridization. Angew Chem Int Ed Engl 2018; 57:8194-8198. [DOI: 10.1002/anie.201804339] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/05/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Eloy Povedano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Alejandro Valverde
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Víctor Ruiz‐Valdepeñas Montiel
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - María Pedrero
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Paloma Yáñez‐Sedeño
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Rodrigo Barderas
- CROSADISInstituto de Salud Carlos III 28220 Majadahonda Madrid Spain
| | | | - Alberto Peláez‐García
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Susana Campuzano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - José M. Pingarrón
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
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15
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Giust D, Lucío MI, El-Sagheer AH, Brown T, Williams LE, Muskens OL, Kanaras AG. Graphene Oxide-Upconversion Nanoparticle Based Portable Sensors for Assessing Nutritional Deficiencies in Crops. ACS NANO 2018; 12:6273-6279. [PMID: 29873479 DOI: 10.1021/acsnano.8b03261] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The development of innovative technologies to rapidly detect biomarkers associated with nutritional deficiencies in crops is highly relevant to agriculture and thus could impact the future of food security. Zinc (Zn) is an important micronutrient in plants, and deficiency leads to poor health, quality, and yield of crops. We have developed portable sensors, based on graphene oxide and upconversion nanoparticles, which could be used in the early detection of Zn deficiency in crops, sensing mRNAs encoding members of the ZIP-transporter family in crops. ZIPs are membrane transport proteins, some of which are up-regulated at the early stages of Zn deficiency, and they are part of the biological mechanism by which crops respond to nutritional deficiency. The principle of these sensors is based on the intensity of the optical output resulting from the interaction of oligonucleotide-coated upconversion nanoparticles and graphene oxide in the absence or presence of a specific oligonucleotide target. The sensors can reliably detect mRNAs in RNA extracts from plants using a smartphone camera. Our work introduces the development of accurate and highly sensitive sensors for use in the field to determine crop nutrient status and ultimately facilitate economically important nutrient management decisions.
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Affiliation(s)
| | | | - Afaf H El-Sagheer
- Department of Chemistry , University of Oxford, Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , U.K
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Department of Chemistry , University of Oxford, Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , U.K
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16
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Liu Y, Kannegulla A, Wu B, Cheng LJ. Quantum Dot Fullerene-Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection. ACS APPLIED MATERIALS & INTERFACES 2018; 10:18524-18531. [PMID: 29763288 DOI: 10.1021/acsami.8b03552] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Spherical fullerene (C60) can quench the fluorescence of a quantum dot (QD) through energy-transfer and charge-transfer processes, with the quenching efficiency regulated by the number of proximate C60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C60-labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C60-based MBs carried by magnetic nanoparticles. The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance three-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (<10 min) with a small sample volume (1-10 μL). The high signal-to-noise ratio produced by the QD-C60 pairs and magnetic concentration yielded a detection limit of 100 fM (∼106 target DNA copies for a 10 μL analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.
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Affiliation(s)
- Ye Liu
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Akash Kannegulla
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Bo Wu
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Li-Jing Cheng
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
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17
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Ma Y, Teng F, Libera M. Solid-Phase Nucleic Acid Sequence-Based Amplification and Length-Scale Effects during RNA Amplification. Anal Chem 2018; 90:6532-6539. [PMID: 29653055 DOI: 10.1021/acs.analchem.8b00058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-phase oligonucleotide amplification is of interest because of possible applications to next-generation sequencing, multiplexed microarray-based detection, and cell-free synthetic biology. Its efficiency is, however, less than that of traditional liquid-phase amplification involving unconstrained primers and enzymes, and understanding how to optimize the solid-phase amplification process remains challenging. Here, we demonstrate the concept of solid-phase nucleic acid sequence-based amplification (SP-NASBA) and use it to study the effect of tethering density on amplification efficiency. SP-NASBA involves two enzymes, avian myeloblastosis virus reverse transcriptase (AMV-RT) and RNase H, to convert tethered forward and reverse primers into tethered double-stranded DNA (ds-DNA) bridges from which RNA- amplicons can be generated by a third enzyme, T7 RNA polymerase. We create microgels on silicon surfaces using electron-beam patterning of thin-film blends of hydroxyl-terminated and biotin-terminated poly(ethylene glycol) (PEG-OH, PEG-B). The tethering density is linearly related to the PEG-B concentration, and biotinylated primers and molecular beacon detection probes are tethered to streptavidin-activated microgels. While SP-NASBA is very efficient at low tethering densities, the efficiency decreases dramatically with increasing tethering density due to three effects: (a) a reduced hybridization efficiency of tethered molecular beacon detection probes; (b) a decrease in T7 RNA polymerase efficiency;
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Affiliation(s)
- Youlong Ma
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
| | - Feiyue Teng
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
| | - Matthew Libera
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
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18
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Yu H, Canoura J, Guntupalli B, Alkhamis O, Xiao Y. Sensitive Detection of Small-Molecule Targets Using Cooperative Binding Split Aptamers and Enzyme-Assisted Target Recycling. Anal Chem 2018; 90:1748-1758. [PMID: 29294287 PMCID: PMC5803384 DOI: 10.1021/acs.analchem.7b03625] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Signal amplification via enzyme-assisted target recycling (EATR) offers a powerful means for improving the sensitivity of DNA detection assays, but it has proven challenging to employ EATR with aptamer-based assays for small-molecule detection due to insensitive target response of aptamers. Here, we describe a general approach for the development of rapid and sensitive EATR-amplified small-molecule sensors based on cooperative binding split aptamers (CBSAs). CBSAs contain two target-binding domains and exhibit enhanced target response compared with single-domain split aptamers. We introduced a duplexed C3 spacer abasic site between the two binding domains, enabling EATR signal amplification through exonuclease III's apurinic endonuclease activity. As a demonstration, we engineered a CBSA-based EATR-amplified fluorescence assay to detect dehydroisoandrosterone-3-sulfate. This assay achieved 100-fold enhanced target sensitivity relative to a non-EATR-based assay, with a detection limit of 1 μM in 50% urine. We further developed an instrument-free colorimetric assay employing EATR-mediated aggregation of CBSA-modified gold nanoparticles for the visual detection of low-micromolar concentrations of cocaine. On the basis of the generalizability of CBSA engineering and the robust performance of EATR in complex samples, we believe that such assays should prove valuable for detecting small-molecule targets in diverse fields.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Bhargav Guntupalli
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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19
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Ruiz-Valdepeñas Montiel V, Gutiérrez ML, Torrente-Rodríguez RM, Povedano E, Vargas E, Reviejo ÁJ, Linacero R, Gallego FJ, Campuzano S, Pingarrón JM. Disposable Amperometric Polymerase Chain Reaction-Free Biosensor for Direct Detection of Adulteration with Horsemeat in Raw Lysates Targeting Mitochondrial DNA. Anal Chem 2017; 89:9474-9482. [DOI: 10.1021/acs.analchem.7b02412] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - María L. Gutiérrez
- Departamento
de Genética, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Rebeca M. Torrente-Rodríguez
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Eloy Povedano
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Eva Vargas
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Á. Julio Reviejo
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Rosario Linacero
- Departamento
de Genética, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Francisco J. Gallego
- Departamento
de Genética, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Susana Campuzano
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - José M. Pingarrón
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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20
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Laser-fabricated gold nanoparticles for lateral flow immunoassays. Colloids Surf B Biointerfaces 2017; 149:351-357. [DOI: 10.1016/j.colsurfb.2016.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/14/2016] [Accepted: 10/17/2016] [Indexed: 11/21/2022]
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21
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Minero GAS, Fock J, McCaskill JS, Hansen MF. Optomagnetic detection of DNA triplex nanoswitches. Analyst 2017; 142:582-585. [DOI: 10.1039/c6an02419j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Triplex DNA formation is studied using rapid low-cost and dose-dependent optomagnetic method with an assay time of max 10 min and limit of detection of 100 pM.
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Affiliation(s)
- Gabriel Antonio S. Minero
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- DTU Nanotech
- DK-2800 Kongens Lyngby
- Denmark
| | - Jeppe Fock
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- DTU Nanotech
- DK-2800 Kongens Lyngby
- Denmark
| | - John S. McCaskill
- Ruhr-Universitaet Bochum
- Microsystems Chemistry and BioIT (BioMIP)
- NC3
- 44801 Bochum
- Germany
| | - Mikkel F. Hansen
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- DTU Nanotech
- DK-2800 Kongens Lyngby
- Denmark
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22
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Haag AL, Toader V, Lennox RB, Grutter P. Selective in situ potential-assisted SAM formation on multi electrode arrays. NANOTECHNOLOGY 2016; 27:455501. [PMID: 27694698 DOI: 10.1088/0957-4484/27/45/455501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The selective modification of individual components in a biosensor array is challenging. To address this challenge, we present a generalizable approach to selectively modify and characterize individual gold surfaces in an array, in an in situ manner. This is achieved by taking advantage of the potential dependent adsorption/desorption of surface-modified organic molecules. Control of the applied potential of the individual sensors in an array where each acts as a working electrode provides differential derivatization of the sensor surfaces. To demonstrate this concept, two different self-assembled monolayer (SAM)-forming electrochemically addressable ω-ferrocenyl alkanethiols (C11) are chemisorbed onto independent but spatially adjacent gold electrodes. The ferrocene alkanethiol does not chemisorb onto the surface when the applied potential is cathodic relative to the adsorption potential and the electrode remains underivatized. However, applying potentials that are modestly positive relative to the adsorption potential leads to extensive coverage within 10 min. The resulting SAM remains in a stable state while held at potentials <200 mV above the adsorption potential. In this state, the chemisorbed SAM does not significantly desorb nor do new ferrocenylalkythiols adsorb. Using three set applied potentials provides for controlled submonolayer alkylthiol marker coverage of each independent gold electrode. These three applied potentials are dependent upon the specifics of the respective adsorbate. Characterization of the ferrocene-modified electrodes via cyclic voltammetry demonstrates that each specific ferrocene marker is exclusively adsorbed to the desired target electrode.
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Affiliation(s)
- Ann-Lauriene Haag
- Ernest Rutherford Physics Building, Department of Physics, McGill University, 3600 Rue University, Montreal, H3A 2T8, QC, Canada
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23
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Wei G, Yu J, Wang J, Gu P, Birch DJS, Chen Y. Hairpin DNA-functionalized gold nanorods for mRNA detection in homogenous solution. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:97001. [PMID: 27604563 DOI: 10.1117/1.jbo.21.9.097001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
We report a fluorescent probe for mRNA detection. It consists of a gold nanorod (GNR) functionalized with fluorophore-labeled hairpin oligonucleotides (hpDNA) that are complementary to the mRNA of a target gene. This nanoprobe was found to be sensitive to a complementary oligonucleotide, as indicated by significant changes in both fluorescence intensity and lifetime. The influence of the surface density of hpDNA on the performance of this nanoprobe was investigated, suggesting that high hybridization efficiency could be achieved at a relatively low surface loading density of hpDNA. However, steady-state fluorescence spectroscopy revealed better overall performance, in terms of sensitivity and detection range, for nanoprobes with higher hairpin coverage. Time-resolved fluorescence lifetime spectroscopy revealed significant lifetime changes of the fluorophore upon hybridization of hpDNA with targets, providing further insight on the hybridization kinetics of the probe as well as the quenching efficiency of GNRs.
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Affiliation(s)
- Guoke Wei
- University of Strathclyde, Photophysics Group, Center for Molecular Nanometrology, Department of Physics, SUPA, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, United KingdombBeihang University, Department of Physics, 37 Xuequan Road, Haidan, Beijing 100191, China
| | - Jun Yu
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Royal College, 204 George Street, Glasgow G1 1XW, United Kingdom
| | - Jinliang Wang
- Beihang University, Department of Physics, 37 Xuequan Road, Haidan, Beijing 100191, China
| | - Peng Gu
- University of Strathclyde, Photophysics Group, Center for Molecular Nanometrology, Department of Physics, SUPA, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - David J S Birch
- University of Strathclyde, Photophysics Group, Center for Molecular Nanometrology, Department of Physics, SUPA, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - Yu Chen
- University of Strathclyde, Photophysics Group, Center for Molecular Nanometrology, Department of Physics, SUPA, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
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24
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Ma Y, Libera M. Molecular Crowding Effects on Microgel-Tethered Oligonucleotide Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6551-6558. [PMID: 27253904 DOI: 10.1021/acs.langmuir.6b01518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Microgel tethering is a nontraditional method with which to bind oligonucleotide hybridization probes to a solid surface. Microgel-tethering physically positions the probes away from the underlying hard substrate and maintains them in a highly waterlike environment. This paper addresses the question of whether molecular crowding affects the performance of microgel-tethered molecular beacon probes. The density of probe-tethering sites is controlled experimentally using thin-film blends of biotin-terminated [PEG-B] and hydroxyl-terminated [PEG-OH] poly(ethylene glycol) from which microgels are synthesized and patterned by electron beam lithography. Fluorescence measurements indicate that the number of streptavidins, linear DNA probes, hairpin probes, and molecular beacon probes bound to the microgels increases linearly with increasing PEG-B/PEG-OH ratio. For a given tethering-site concentration, more linear probes can bind than structured probes. Crowding effects emerge during the hybridization of microgel-tethered molecular beacons but not during the hybridization of linear probes, as the tethering density increases. Crowding during hybridization is associated with conformational constraints imposed by the close proximity of closed and hybridized structured probes. The signal-to-background ratio (SBR) of hybridized beacons is highest and roughly constant for low tethering densities and decreases at the highest tethering densities. Despite differences between microgel tethering and traditional oligonucleotide surface-immobilization approaches, these results show that crowding defines an optimum tethering density for molecular beacon probes that is less than the maximum possible, which is consistent with previous studies involving various linear and structured oligonucleotide probes.
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Affiliation(s)
- Youlong Ma
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology , Hoboken, New Jersey 07030, United States
| | - Matthew Libera
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology , Hoboken, New Jersey 07030, United States
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25
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Molecular beacon-decorated polymethylmethacrylate core-shell fluorescent nanoparticles for the detection of survivin mRNA in human cancer cells. Biosens Bioelectron 2016; 88:15-24. [PMID: 27321444 DOI: 10.1016/j.bios.2016.05.102] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/20/2016] [Accepted: 05/31/2016] [Indexed: 01/06/2023]
Abstract
One of the main goals of nanomedicine in cancer is the development of effective drug delivery systems, primarily nanoparticles. Survivin, an overexpressed anti-apoptotic protein in cancer, represents a pharmacological target for therapy and a Molecular Beacon (MB) specific for survivin mRNA is available. In this study, the ability of polymethylmethacrylate nanoparticles (PMMA-NPs) to promote survivin MB uptake in human A549 cells was investigated. Fluorescent and positively charged core PMMA-NPs of nearly 60nm, obtained through an emulsion co-polymerization reaction, and the MB alone were evaluated in solution, for their analytical characterization; then, the MB specificity and functionality were verified after adsorption onto the PMMA-NPs. The carrier ability of PMMA-NPs in A549 was examined by confocal microscopy. With the optimized protocol, a hardly detectable fluorescent signal was obtained after incubation of the cells with the MB alone (fluorescent spots per cell of 1.90±0.40 with a mean area of 1.04±0.20µm2), while bright fluorescent spots inside the cells were evident by using the MB loaded onto the PMMA-NPs. (27.50±2.30 fluorescent spots per cell with a mean area of 2.35±0.16µm2). These results demonstrate the ability of the PMMA-NPs to promote the survivin-MB internalization, suggesting that this complex might represent a promising strategy for intracellular sensing and for the reduction of cancer cell proliferation.
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26
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Cao HH, Nakatsuka N, Serino AC, Liao WS, Cheunkar S, Yang H, Weiss PS, Andrews AM. Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters. ACS NANO 2015; 9:11439-54. [PMID: 26426585 DOI: 10.1021/acsnano.5b05546] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nucleotide arrays require controlled surface densities and minimal nucleotide-substrate interactions to enable highly specific and efficient recognition by corresponding targets. We investigated chemical lift-off lithography with hydroxyl- and oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers as a means to produce substrates optimized for tethered DNA insertion into post-lift-off regions. Residual alkanethiols in the patterned regions after lift-off lithography enabled the formation of patterned DNA monolayers that favored hybridization with target DNA. Nucleotide densities were tunable by altering surface chemistries and alkanethiol ratios prior to lift-off. Lithography-induced conformational changes in oligo(ethylene glycol)-terminated monolayers hindered nucleotide insertion but could be used to advantage via mixed monolayers or double-lift-off lithography. Compared to thiolated DNA self-assembly alone or with alkanethiol backfilling, preparation of functional nucleotide arrays by chemical lift-off lithography enables superior hybridization efficiency and tunability.
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Affiliation(s)
- Huan H Cao
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Nako Nakatsuka
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Andrew C Serino
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Wei-Ssu Liao
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Sarawut Cheunkar
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Hongyan Yang
- Department of Psychiatry and Biobehavioral Health, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Paul S Weiss
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Anne M Andrews
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Psychiatry and Biobehavioral Health, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles , Los Angeles, California 90095, United States
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27
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Minero GAS, Wagler PF, Oughli AA, McCaskill JS. Electronic pH switching of DNA triplex reactions. RSC Adv 2015. [DOI: 10.1039/c5ra02628h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remote electronic control of fast DNA processing reactions such as S–S-ligation is achievedviapH switching of triplex structures.
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Affiliation(s)
- Gabriel Antonio S. Minero
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - Patrick F. Wagler
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - Alaa A. Oughli
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - John S. McCaskill
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
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28
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Li Z, Zhang L, Mo H, Peng Y, Zhang H, Xu Z, Zheng C, Lu Z. Size-fitting effect for hybridization of DNA/mercaptohexanol mixed monolayers on gold. Analyst 2014; 139:3137-45. [DOI: 10.1039/c4an00280f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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29
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Doneux T, De Rache A, Triffaux E, Meunier A, Steichen M, Buess-Herman C. Optimization of the Probe Coverage in DNA Biosensors by a One-Step Coadsorption Procedure. ChemElectroChem 2013. [DOI: 10.1002/celc.201300145] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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30
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Pastré D, Joshi V, Curmi PA, Hamon L. Detection of single DNA molecule hybridization on a surface by atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3630-3638. [PMID: 23674511 DOI: 10.1002/smll.201300546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Indexed: 06/02/2023]
Abstract
Improving the detection of DNA hybridization is a critical issue for several challenging applications encountered in microarray and biosensor domains. Herein, it is demonstrated that hybridization between complementary single-stranded DNA (ssDNA) molecules loosely adsorbed on a mica surface can be achieved thanks to fine-tuning of the composition of the hybridization buffer. Single-molecule DNA hybridization occurs in only a few minutes upon encounters of freely diffusing complementary strands on the mica surface. Interestingly, the specific hybridization between complementary ssDNA is not altered in the presence of large amounts of nonrelated DNA. The detection of single-molecule DNA hybridization events is performed by measuring the contour length of DNA in atomic force microscopy images. Besides the advantage provided by facilitated diffusion, which promotes hybridization between probes and targets on mica, the present approach also allows the detection of single isolated DNA duplexes and thus requires a very low amount of both probe and target molecules.
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Affiliation(s)
- David Pastré
- Inserm U829, Laboratoire Structure-Activité des, Biomolécules Normales et Pathologiques, Université d'Evry-Val d'Essonne, Evry 91025, France
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31
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Ngo HT, Wang HN, Fales AM, Vo-Dinh T. Label-free DNA biosensor based on SERS Molecular Sentinel on Nanowave chip. Anal Chem 2013; 85:6378-83. [PMID: 23718777 PMCID: PMC4022286 DOI: 10.1021/ac400763c] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development of a rapid, cost-effective, label-free biosensor for DNA detection is important for many applications in clinical diagnosis, homeland defense, and environment monitoring. A unique label-free DNA biosensor based on Molecular Sentinel (MS) immobilized on a plasmonic 'Nanowave' chip, which is also referred to as a metal film over nanosphere (MFON), is presented. Its sensing mechanism is based upon the decrease of the surface-enhanced Raman scattering (SERS) intensity when Raman label tagged at one end of MS is physically separated from the MFON's surface upon DNA hybridization. This method is label-free as the target does not have to be labeled. The MFON fabrication is relatively simple and low-cost with high reproducibility based on depositing a thin shell of gold over close-packed arrays of nanospheres. The sensing process involves a single hybridization step between the DNA target sequences and the complementary MS probes on the Nanowave chip without requiring secondary hybridization or posthybridization washing, thus resulting in rapid assay time and low reagent usage. The usefulness and potential application of the biosensor for medical diagnostics is demonstrated by detecting the human radical S-adenosyl methionine domain containing 2 (RSAD2) gene, a common inflammation biomarker.
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Affiliation(s)
- Hoan Thanh Ngo
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Hsin-Neng Wang
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Andrew M. Fales
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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32
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Wang H, Wang D, Peng Z, Tang W, Li N, Liu F. Assembly of DNA-functionalized gold nanoparticles on electrospun nanofibers as a fluorescent sensor for nucleic acids. Chem Commun (Camb) 2013; 49:5568-70. [DOI: 10.1039/c3cc41753k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Zheng YB, Payton JL, Song TB, Pathem BK, Zhao Y, Ma H, Yang Y, Jensen L, Jen AKY, Weiss PS. Surface-enhanced Raman spectroscopy to probe photoreaction pathways and kinetics of isolated reactants on surfaces: flat versus curved substrates. NANO LETTERS 2012; 12:5362-5368. [PMID: 22978482 DOI: 10.1021/nl302750d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We identify and control the photoreaction paths of self-assembled monolayers (SAMs) of thiolate-linked anthracene phenylethynyl molecules on Au substrate surfaces, and study the effects of nanoscale morphology of substrates on regioselective photoreactions. Two types of morphologies, atomically flat and curved, are produced on Au surfaces by controlling substrate structure and metal deposition. We employ surface-enhanced Raman spectroscopy (SERS), combined with Raman mode analyses using density functional theory, to identify the different photoreaction paths and to track the photoreaction kinetics and efficiencies of molecules in monolayers. The SAMs on curved surfaces exhibit dramatically lower regioselective photoreaction kinetics and efficiencies than those on atomically flat surfaces. This result is attributed to the increased intermolecular distances and variable orientations on the curved surfaces. Better understanding of the morphological effects of substrates will enable control of nanoparticle functionalization in ligand exchange in targeted delivery of therapeutics and theranostics and in catalysis.
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Affiliation(s)
- Yue Bing Zheng
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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34
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Adams NM, Jackson SR, Haselton FR, Wright DW. Design, synthesis, and characterization of nucleic-acid-functionalized gold surfaces for biomarker detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1068-82. [PMID: 21905721 PMCID: PMC4211628 DOI: 10.1021/la2028862] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nucleic-acid-functionalized gold surfaces have been used extensively for the development of biological sensors. The development of an effective biomarker detection assay requires careful design, synthesis, and characterization of probe components. In this Feature Article, we describe fundamental probe development constraints and provide a critical appraisal of the current methodologies and applications in the field. We discuss critical issues and obstacles that impede the sensitivity and reliability of the sensors to underscore the challenges that must be met to advance the field of biomarker detection.
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Affiliation(s)
- Nicholas M. Adams
- VU Station B 351822, Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA. VU Station B 351631, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Stephen R. Jackson
- VU Station B 351822, Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Frederick R. Haselton
- VU Station B 351631, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
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35
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Hong X, Hall EAH. Contribution of gold nanoparticles to the signal amplification in surface plasmon resonance. Analyst 2012; 137:4712-9. [DOI: 10.1039/c2an35742a] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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36
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Huang K, Martí AA. Recent trends in molecular beacon design and applications. Anal Bioanal Chem 2011; 402:3091-102. [PMID: 22159461 DOI: 10.1007/s00216-011-5570-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/26/2022]
Abstract
A molecular beacon (MB) is a hairpin-structured oligonucleotide probe containing a photoluminescent species (PLS) and a quencher at different ends of the strand. In a recognition and detection process, the hybridization of MBs with target DNA sequences restores the strong photoluminescence, which is quenched before hybridization. Making better MBs involves reducing the background photoluminescence and increasing the brightness of the PLS, which therefore involves the development of new PLS and quenchers, as well as innovative PLS-quencher systems. Heavy-metal complexes, nanocrystals, pyrene compounds, and other materials with excellent photophysical properties have been applied as PLS of MBs. Nanoparticles, nanowires, graphene, metal films, and many other media have also been introduced to quench photoluminescence. On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides.
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Affiliation(s)
- Kewei Huang
- Department of Chemistry, Rice University, 6100 South Main Street, Houston, TX 77005, USA
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37
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Day BS, Fiegland LR, Vint ES, Shen W, Morris JR, Norton ML. Thiolated dendrimers as multi-point binding headgroups for DNA immobilization on gold. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12434-12442. [PMID: 21916426 DOI: 10.1021/la202444s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The synthesis of multithiolated DNA molecules that can be used to produce self-assembled monolayers of single-stranded DNA oligonucleotides on gold substrates is described. Generation 3 polyamidoamine (PAMAM) dendrimers were conjugated to DNA oligomers and functionalized with ~30 protected thiol groups. The protected thiol groups-thioacetate groups-allowed the dendrimer-DNA constructs to be stored in a buffer solution for at least 2 months before deprotection without any observable decrease in their ability to assemble into functional layers. The monolayers formed using these multithiolated DNA probe strands demonstrate target capture efficiencies comparable to those of analogous monolayers assembled with DNA functionalized with single thiol groups. A functional advantage of using dendrimer headgroups is the resistance to probe strand loss in prolonged exposure to buffer solutions at a high temperature (95 °C).
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Affiliation(s)
- B Scott Day
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, USA.
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