1
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Jamal RB, Vitasovic T, Gosewinkel U, Ferapontova EE. Detection of E.coli 23S rRNA by electrocatalytic "off-on" DNA beacon assay with femtomolar sensitivity. Biosens Bioelectron 2023; 228:115214. [PMID: 36906990 DOI: 10.1016/j.bios.2023.115214] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
Prevention of food spoilage, environmental bio-contamination, and pathogenic infections requires rapid and sensitive bacterial detection systems. Among microbial communities, the bacterial strain of Escherichia coli is most widespread, with pathogenic and non-pathogenic strains being biomarkers of bacterial contamination. Here, we have developed a fM-sensitive, simple, and robust electrocatalytically-amplified assay facilitating specific detection of E.coli 23S ribosomal rRNA, in the total RNA sample, after its site-specific cleavage by RNase H enzyme. Gold screen-printed electrodes (SPE) were electrochemically pre-treated to be productively modified with a methylene-blue (MB) - labelled hairpin DNA probes, which hybridization with the E. coli-specific DNA placed MB in the top region of the DNA duplex. The formed duplex acted as an electrical wire, mediating electron transfer from the gold electrode to the DNA-intercalated MB, and further to ferricyanide in solution, enabling its electrocatalytic reduction otherwise impeded on the hairpin-modified SPEs. The assay facilitated 20 min 1 fM detection of both synthetic E. coli DNA and 23S rRNA isolated from E.coli (equivalent to 15 CFU mL-1), and can be extended to fM analysis of nucleic acids isolated from any other bacteria.
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Affiliation(s)
- Rimsha B Jamal
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Toni Vitasovic
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
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2
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Deng M, Ren Z, Zhang H, Li Z, Xue C, Wang J, Zhang D, Yang H, Wang X, Li J. Unamplified and Real-Time Label-Free miRNA-21 Detection Using Solution-Gated Graphene Transistors in Prostate Cancer Diagnosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205886. [PMID: 36480308 PMCID: PMC9896035 DOI: 10.1002/advs.202205886] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/15/2022] [Indexed: 06/17/2023]
Abstract
The incidence of prostate cancer (PCa) in men globally increases as the standard of living improves. Blood serum biomarker prostate-specific antigen (PSA) detection is the gold standard assay that do not meet the requirements of early detection. Herein, a solution-gated graphene transistor (SGGT) biosensor for the ultrasensitive and rapid quantification detection of the early prostate cancer-relevant biomarker, miRNA-21 is reported. The designed single-stranded DNA (ssDNA) probes immobilized on the Au gate can hybridize effectively with the miRNA-21 molecules targets and induce the Dirac voltage shifts of SGGT transfer curves. The limit of detection (LOD) of the sensor can reach 10-20 M without amplification and any chemical or biological labeling. The detection linear range is from 10-20 to 10-12 M. The sensor can realize real-time detection of the miRNA-21 molecules in less than 5 min and can well distinguish one-mismatched miRNA-21 molecule. The blood serum samples from the patients without RNA extraction and amplification are measured. The results demonstrated that the biosensor can well distinguish the cancer patients from the control group and has higher sensitivity (100%) than PSA detection (58.3%). Contrastingly, it can be found that the PSA level is not directly related to PCa.
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Affiliation(s)
- Minghua Deng
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
| | - Zhanpeng Ren
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
| | - Huibin Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
| | - Ziqin Li
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
| | - Chenglong Xue
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
| | - Jianying Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
| | - Dan Zhang
- School of Computer Science and Information EngineeringHubei UniversityWuhan430062P. R. China
| | - Huan Yang
- Department of UrologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030P. R. China
| | - Xianbao Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
| | - Jinhua Li
- Hubei Collaborative Innovation Center for Advanced Organic Chemical MaterialsKey Laboratory for the Green Preparation and Application of Functional MaterialsMinistry of EducationHubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062P. R. China
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3
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Bonnet H, Coche-Guérente L, Defrancq E, Spinelli N, Van der Heyden A, Dejeu J. Negative SPR Signals during Low Molecular Weight Analyte Recognition. Anal Chem 2021; 93:4134-4140. [PMID: 33577288 DOI: 10.1021/acs.analchem.1c00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface plasmon resonance (SPR) is a powerful technique for studying biomolecular interactions mainly due to its sensitivity and real-time and label free advantages. While SPR signals are usually positive, only a few studies have reported sensorgrams with negative signals. The aim of the present work is to investigate and to explain the observation of negative SPR signals with the hypothesis that it reflects major changes in ligand conformation resulting from target binding. We demonstrated that these negative unconventional signals were due to the negative complex (ligand/analyte) refractive index increment (RII) deviation from the sum of the RII of the individual entities which counterbalanced the theoretical increase of the signal triggered by the target recognition and the ligand folding. We also found that the conformation change of biomolecules can induce a negative or a positive complex RII deviation depending on its sequence and immobilization mode.
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Affiliation(s)
- H Bonnet
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - L Coche-Guérente
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - E Defrancq
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - N Spinelli
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - A Van der Heyden
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - J Dejeu
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
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4
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Reprint of "Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces". J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Cui J, Han H, Piao J, Shi H, Zhou D, Gong X, Chang J. Construction of a Novel Biosensor Based on the Self-assembly of Dual-Enzyme Cascade Amplification-Induced Copper Nanoparticles for Ultrasensitive Detection of MicroRNA153. ACS APPLIED MATERIALS & INTERFACES 2020; 12:34130-34136. [PMID: 32627523 DOI: 10.1021/acsami.0c06032] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
MicroRNAs (miRNAs) have received extensive attention because of their potential as biomarkers for cancer diagnosis and monitoring, and their effective detection is very significant. Here, a specific, one-pot, rapid, femtomolar sensitive miRNAs detection biosensor was developed based on the target-triggered three-way junction (3-WJ) and terminal deoxynucleotide transferase (TDT)/Nt.BspQI in combination with activated copper nanoparticles (CuNPs) self-assembly. To this end, a 3-WJ hairpin probe and helper probe were designed to selectively identify the target miRNA, so as to form a stable 3-WJ structure that further triggered the double-enzyme cycling to produce poly T to activate the self-assembly of CuNPs. Based on the simplicity of CuNPs generation, the poly T template fluorescence CuNPs can detect the minimum detection limit of 1 fm within 1.75 h. In addition, the applicability of this method in complex samples was demonstrated by analyzing the whole-blood RNA extraction from Parkinson patients, consisting of the results of commercial miRNA kits. The developed strategy performs powerful implications for miRNA detection, which may be beneficial for the effective diagnostic assays and biological research of Parkinson's disease.
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Affiliation(s)
- Jingyu Cui
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin 300072, China
| | - Houyu Han
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin 300072, China
| | - Jiafang Piao
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin 300072, China
| | - Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, China
| | - Dianming Zhou
- Department of Toxicology, Tianjin Center for Disease Control and Prevention, Tianjin 300011, China
| | - Xiaoqun Gong
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin 300072, China
| | - Jin Chang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin 300072, China
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6
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Milioni D, Mateos-Gil P, Papadakis G, Tsortos A, Sarlidou O, Gizeli E. Acoustic Methodology for Selecting Highly Dissipative Probes for Ultrasensitive DNA Detection. Anal Chem 2020; 92:8186-8193. [PMID: 32449355 DOI: 10.1021/acs.analchem.0c00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The objective of this work is to present a methodology for the selection of nanoparticles such as liposomes to be used as acoustic probes for the detection of very low concentrations of DNA. Liposomes, applied in the past as mass amplifiers and detected through frequency measurement, are employed in the current work as probes for energy-dissipation enhancement. Because the dissipation signal is related to the structure of the sensed nanoentity, a systematic investigation of the geometrical features of the liposome/DNA complex was carried out. We introduce the parameter of dissipation capacity by which several sizes of liposome and DNA structures were compared with respect to their ability to dissipate acoustic energy at the level of a single molecule/particle. Optimized 200 nm liposomes anchored to a dsDNA chain led to an improvement of the limit of detection (LoD) by 3 orders of magnitude when compared to direct DNA detection, with the new LoD being 1.2 fmol (or 26 fg/μL or 2 pM). Dissipation monitoring was also shown to be 8 times more sensitive than the corresponding frequency response. The high versatility of this new methodology is demonstrated in the detection of genetic biomarkers down to 1-2 target copies in real samples such as blood. This study offers new prospects in acoustic detection with potential use in real-world diagnostics.
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Affiliation(s)
- Dimitra Milioni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Pablo Mateos-Gil
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Olga Sarlidou
- Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece.,Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
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7
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Nguyen TTV, Xie X, Xu J, Wu Y, Hong M, Liu X. Plasmonic bimetallic nanodisk arrays for DNA conformation sensing. NANOSCALE 2019; 11:19291-19296. [PMID: 31560008 DOI: 10.1039/c9nr06101k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The integration of large-scale 2D bimetallic Ag/Au nanodisk arrays with gold nanoparticles is developed for sensing DNA conformation with the assistance of 3D finite-difference time-domain simulation. The optimized system comprising Ag/Au nanodisk arrays and gold nanoparticles offers a more than 6-fold enhancement in surface plasmon resonance shift, enabling the feasibility for sensitive DNA detection with a detection limit down to 100 femtomolar. Importantly, owing to the distance-dependent nature of the surface plasmon signal, sensitive differentiation of DNA conformations can be achieved with a conventional optical measurement. This platform could provide new exciting capabilities for a reliable, reproducible, and label-free assay analysis for investigating the conformations of DNA and other biological molecules.
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Affiliation(s)
- Thanh Thi Van Nguyen
- Advanced Materials for Micro- and Nano-Systems Programme, Singapore-MIT Alliance, 117576, Singapore
| | - Xiaoji Xie
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Jiahui Xu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Yiming Wu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Minghui Hong
- Department of Electrical and Computer Engineering, National University of Singapore, 117576, Singapore
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore. and The N.1 Institute for Health, National University of Singapore, 28 Medical Dr. #05-COR, 117456, Singapore and Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Fuzhou, 350207, P. R. China
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9
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Ferapontova EE. Electron Transfer in DNA at Electrified Interfaces. Chem Asian J 2019; 14:3773-3781. [PMID: 31545875 DOI: 10.1002/asia.201901024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/22/2019] [Indexed: 12/24/2022]
Abstract
The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, 8000, Aarhus C, Denmark
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10
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Kékedy-Nagy L, Sørensen KD, Ferapontova EE. Picomolar sensitive and SNP-selective “Off-On” hairpin genosensor based on structure-tunable redox indicator signals. Biosens Bioelectron 2018; 117:444-449. [DOI: 10.1016/j.bios.2018.06.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 01/10/2023]
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11
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Papadakis G, Murasova P, Hamiot A, Tsougeni K, Kaprou G, Eck M, Rabus D, Bilkova Z, Dupuy B, Jobst G, Tserepi A, Gogolides E, Gizeli E. Micro-nano-bio acoustic system for the detection of foodborne pathogens in real samples. Biosens Bioelectron 2018; 111:52-58. [DOI: 10.1016/j.bios.2018.03.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/21/2018] [Accepted: 03/26/2018] [Indexed: 01/30/2023]
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12
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Ganesan VV, Dhanasekaran M, Thangavel N, Dhathathreyan A. Elastic compliance of fibrillar assemblies in type I collagen. Biophys Chem 2018; 240:15-24. [PMID: 29857170 DOI: 10.1016/j.bpc.2018.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 11/17/2022]
Abstract
Fibrillary assemblies of Type I collagen find important applications in tissue engineering and as matrices for biophysical studies. The mechanical and structural properties of these structures are governed by factors such as protein concentration, temperature, pH and ionic strength. This study reports on an impedance based analysis of the elastic compliance of fibrillary assemblies of Type I collagen using quartz crystal microbalance with dissipation (QCM-D) at a fundamental frequency of 5 MHz and overtones (n = 3,5,7,9,11). Here, In situ partial fibrillation of the adsorbing collagen followed by its fibrillary assemblies on hydrophilic gold coated quartz surface have been crosslinked using Gallic acid (GA), Chromium (III) gallate (Cr-GA), Catechin (Cat), Tetrakis(hydroxymethyl)phosphonium sulfate (THPS) and Oxazolidine (Ox). This approach allows direct comparison of how viscoelastic properties track the structural evolution of the fiber and network length scales. The collagen crosslinking shows significant positive impact on the protein's mechanical behaviour and on the type of crosslinking agents used. The elastic modulus increases as collagen <GA < THPS < Cr-GA < Cat < Ox. Atomic force microscopic studies on the adsorbed collagen after cross linking confirmed the presence of fibrous assemblies. The results indicate stabilization and reinforcement through strong physical entanglement between the molecules of collagen as well as chemical interaction between collagen matrix and fibrils during cross linking. The elastic compliance evaluated from ΔDissipation/Δfreq. from QCM-D showed that cross linking with GA, Cr-GA and Ox resulted in flexible fibrillary network while agents like THPS and Cat showed elastic moduli similar to that of pure collagen. Results suggest that optimal collagen-crosslinking agent ratio and degree of crosslinking of collagen can help tailor the mechanical properties for specific applications in design of bio-materials of these composites.
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13
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Characterization and electrochemical response of DNA functionalized 2nm gold nanoparticles confined in a nanochannel array. Bioelectrochemistry 2018; 121:169-175. [PMID: 29454941 DOI: 10.1016/j.bioelechem.2018.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/02/2018] [Accepted: 02/07/2018] [Indexed: 11/21/2022]
Abstract
Polyvalent gold nanoparticle oligonucleotide conjugates are subject of intense research. Even though 2nm diameter AuNPs have been previously modified with DNA, little is known about their structure and electrochemical behavior. In this work, we examine the influence of different surface modification strategies on the interplay between the meso-organization and the molecular recognition properties of a 27-mer DNA strand. This DNA strand is functionalized with different sulfur-containing moieties and immobilized on 2nm gold nanoparticles confined on a nanoporous alumina, working the whole system as an electrode array. Surface coverages were determined by EXAFS and the performance as recognition elements for impedance-based sensors is evaluated. Our results prove that low DNA coverages on the confined nanoparticles prompt to a more sensitive response, showing the relevance in avoiding the DNA strand overcrowding. The system was able to determine a concentration as low as 100pM of the complementary strand, thus introducing the foundations for the construction of label-free genosensors at the nanometer scale.
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14
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Dunn KE, Trefzer MA, Johnson S, Tyrrell AM. Characterizing Surface-Immobilized DNA Structures and Devices Using a Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D). Methods Mol Biol 2018; 1811:101-114. [PMID: 29926448 DOI: 10.1007/978-1-4939-8582-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A quartz crystal microbalance with dissipation monitoring can be used to study the mass and structure of surface-immobilized layers of molecules, in real time. Here we describe the use of the technique to study DNA structures and devices.
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Affiliation(s)
- Katherine E Dunn
- Department of Electronic Engineering, University of York, Heslington, York, UK.
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Martin A Trefzer
- Department of Electronic Engineering, University of York, Heslington, York, UK
| | - Steven Johnson
- Department of Electronic Engineering, University of York, Heslington, York, UK
| | - Andy M Tyrrell
- Department of Electronic Engineering, University of York, Heslington, York, UK
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15
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Papadakis G, Friedt JM, Eck M, Rabus D, Jobst G, Gizeli E. Optimized acoustic biochip integrated with microfluidics for biomarkers detection in molecular diagnostics. Biomed Microdevices 2017; 19:16. [DOI: 10.1007/s10544-017-0159-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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16
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Milioni D, Tsortos A, Velez M, Gizeli E. Extracting the Shape and Size of Biomolecules Attached to a Surface as Suspended Discrete Nanoparticles. Anal Chem 2017; 89:4198-4203. [DOI: 10.1021/acs.analchem.7b00206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitra Milioni
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, C/Marie Curie 2, 28049 Madrid, Spain
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department
of Biology, University of Crete, Heraklion 71110, Greece
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17
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Dunn KE, Leake MC, Wollman AJM, Trefzer MA, Johnson S, Tyrrell AM. An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160767. [PMID: 28405363 PMCID: PMC5383820 DOI: 10.1098/rsos.160767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/23/2017] [Indexed: 05/05/2023]
Abstract
DNA has been used to construct a wide variety of nanoscale molecular devices. Inspiration for such synthetic molecular machines is frequently drawn from protein motors, which are naturally occurring and ubiquitous. However, despite the fact that rotary motors such as ATP synthase and the bacterial flagellar motor play extremely important roles in nature, very few rotary devices have been constructed using DNA. This paper describes an experimental study of the putative mechanism of a rotary DNA nanomotor, which is based on strand displacement, the phenomenon that powers many synthetic linear DNA motors. Unlike other examples of rotary DNA machines, the device described here is designed to be capable of autonomous operation after it is triggered. The experimental results are consistent with operation of the motor as expected, and future work on an enhanced motor design may allow rotation to be observed at the single-molecule level. The rotary motor concept presented here has potential applications in molecular processing, DNA computing, biosensing and photonics.
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Affiliation(s)
- K. E. Dunn
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
- Author for correspondence: K. E. Dunn e-mail:
| | - M. C. Leake
- Biological Physical Sciences Institute, Departments of Physics and Biology, University of York, Heslington, York YO10 5DD, UK
| | - A. J. M. Wollman
- Biological Physical Sciences Institute, Departments of Physics and Biology, University of York, Heslington, York YO10 5DD, UK
| | - M. A. Trefzer
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
| | - S. Johnson
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
| | - A. M. Tyrrell
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
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18
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Papadakis G, Palladino P, Chronaki D, Tsortos A, Gizeli E. Sample-to-answer acoustic detection of DNA in complex samples. Chem Commun (Camb) 2017; 53:8058-8061. [DOI: 10.1039/c6cc10175e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The present study demonstrates the sensitive and label-free acoustic detection of dsDNA amplicons produced from whole Salmonella Thyphimurium cells without employing any DNA extraction and/or purification step, in the presence of the lysed bacterial cells and in a hybridization-free assay.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
| | | | - Dimitra Chronaki
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
- Dept. of Biology
- Univ. of Crete
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
- Dept. of Biology
- Univ. of Crete
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19
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Wu C, Sun Z, Liu LS. Quantitative control of CaCO3 growth on quartz crystal microbalance sensors as a signal amplification method. Analyst 2017; 142:2547-2551. [DOI: 10.1039/c7an00335h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantitative control of mass growth on QCM sensor surfaces was realized, providing a potential signal amplification method.
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Affiliation(s)
- Congcong Wu
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Shandong Normal University
- Jinan 250014
- China
- Shandong Province Key Laboratory of Detection Technology of Tumor Markers
| | - Zhaomei Sun
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Shandong Normal University
- Jinan 250014
- China
- Shandong Province Key Laboratory of Detection Technology of Tumor Markers
| | - Li-Shang Liu
- Shandong Province Key Laboratory of Detection Technology of Tumor Markers
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
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20
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Chronaki D, Stratiotis DI, Tsortos A, Anastasiadou E, Gizeli E. Screening between normal and cancer human thyroid cells through comparative adhesion studies using the Quartz Crystal Microbalance. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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21
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Ferapontova EE. Hybridization Biosensors Relying on Electrical Properties of Nucleic Acids. ELECTROANAL 2016. [DOI: 10.1002/elan.201600593] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO); Center for DNA Nanotechnology (CDNA); Aarhus University; Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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22
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Dunn KE, Trefzer MA, Johnson S, Tyrrell AM. Investigating the dynamics of surface-immobilized DNA nanomachines. Sci Rep 2016; 6:29581. [PMID: 27387252 PMCID: PMC4937388 DOI: 10.1038/srep29581] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/20/2016] [Indexed: 11/08/2022] Open
Abstract
Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors.
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Affiliation(s)
- Katherine E. Dunn
- Department of Electronics, University of York, Heslington, York, YO10 5DD, UK
| | - Martin A. Trefzer
- Department of Electronics, University of York, Heslington, York, YO10 5DD, UK
| | - Steven Johnson
- Department of Electronics, University of York, Heslington, York, YO10 5DD, UK
| | - Andy M. Tyrrell
- Department of Electronics, University of York, Heslington, York, YO10 5DD, UK
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23
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - George Papadakis
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
- Department
of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion, Greece
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24
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Maslakci NN, Danas FD, Oksuz AU. QCM-DNA biosensor based on plasma modified PT/TiO2nanocomposites. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2016. [DOI: 10.1080/10601325.2016.1151651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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25
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Mateos-Gil P, Tsortos A, Vélez M, Gizeli E. Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA. Chem Commun (Camb) 2016; 52:6541-4. [DOI: 10.1039/c6cc02127a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of structural changes in an intrinsically disordered protein attached on a QCM-D, with a sensitivity of 1.8 nm or better.
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Affiliation(s)
- Pablo Mateos-Gil
- Instituto de Catálisis y Petroleoquímica (ICP-CSIC)
- 28049 Madrid
- Spain
| | | | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica (ICP-CSIC)
- 28049 Madrid
- Spain
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology
- Heraklion
- Greece
- Department of Biology
- University of Crete
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26
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Huang Y, Tian Z, Sun LP, Sun D, Li J, Ran Y, Guan BO. High-sensitivity DNA biosensor based on optical fiber taper interferometer coated with conjugated polymer tentacle. OPTICS EXPRESS 2015; 23:26962-26968. [PMID: 26480357 DOI: 10.1364/oe.23.026962] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A sensitive bio-probe to in situ detect unlabeled single-stranded DNA targets based on optical microfiber taper interferometer coated by a high ordered pore arrays conjugated polymer has been presented. The polymer coating serves as tentacles to catch single-stranded DNA molecules by π-π conjugated interaction and varies the surface refractive index of the optical microfiber. The microfiber taper interferometer translates the refractive index information into wavelength shift of the interference fringe. The sensor exhibits DNA concentration sensitivity of 2.393 nm/log M and the lowest detection ability of 10(-10) M or even lower.
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27
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Şeker Ş, Elçin AE, Elçin YM. Real-time monitoring of mesenchymal stem cell responses to biomaterial surfaces and to a model drug by using quartz crystal microbalance. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2015; 44:1722-32. [DOI: 10.3109/21691401.2015.1089255] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Zhang X, Daaboul GG, Spuhler PS, Freedman DS, Yurt A, Ahn S, Avci O, Ünlü MS. Nanoscale characterization of DNA conformation using dual-color fluorescence axial localization and label-free biosensing. Analyst 2015; 139:6440-9. [PMID: 25340741 DOI: 10.1039/c4an01425a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantitative determination of the density and conformation of DNA molecules tethered to the surface can help optimize and understand DNA nanosensors and nanodevices, which use conformational or motional changes of surface-immobilized DNA for detection or actuation. We present an interferometric sensing platform that combines (i) dual-color fluorescence spectroscopy for precise axial co-localization of two fluorophores attached at different nucleotides of surface-immobilized DNA molecules and (ii) independent label-free quantification of biomolecule surface density at the same site. Using this platform, we examined the conformation of DNA molecules immobilized on a three-dimensional polymeric surface and demonstrated simultaneous detection of DNA conformational change and binding in real-time. These results demonstrate that independent quantification of both surface density and molecular nanoscale conformation constitutes a versatile approach for nanoscale solid-biochemical interface investigations and molecular binding assays.
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Affiliation(s)
- Xirui Zhang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
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29
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Osypova A, Thakar D, Dejeu J, Bonnet H, Van der Heyden A, Dubacheva GV, Richter RP, Defrancq E, Spinelli N, Coche-Guérente L, Labbé P. Sensor Based on Aptamer Folding to Detect Low-Molecular Weight Analytes. Anal Chem 2015; 87:7566-74. [PMID: 26122480 DOI: 10.1021/acs.analchem.5b01736] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aptamers have emerged as promising biorecognition elements in the development of biosensors. The present work focuses on the application of quartz crystal microbalance with dissipation monitoring (QCM-D) for the enantioselective detection of a low molecular weight target molecule (less than 200 Da) by aptamer-based sensors. While QCM-D is a powerful technique for label-free, real-time characterization and quantification of molecular interactions at interfaces, the detection of small molecules interacting with immobilized receptors still remains a challenge. In the present study, we take advantage of the aptamer conformational changes upon the target binding that induces displacement of water acoustically coupled to the sensing layer. As a consequence, this phenomenon leads to a significant enhancement of the detection signal. The methodology is exemplified with the enantioselective recognition of a low molecular weight model compound, L-tyrosinamide (L-Tym). QCM-D monitoring of L-Tym interaction with the aptamer monolayer leads to an appreciable signal that can be further exploited for analytical purposes or thermodynamics studies. Furthermore, in situ combination of QCM-D with spectroscopic ellipsometry unambiguously demonstrates that the conformational change induces a nanometric decrease of the aptamer monolayer thickness. Since QCM-D is sensitive to the whole mass of the sensing layer including water that is acoustically coupled, a decrease in thickness of the highly hydrated aptamer layer induces a sizable release of water that can be easily detected by QCM-D.
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Affiliation(s)
- Alina Osypova
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Dhruv Thakar
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Jérôme Dejeu
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Hugues Bonnet
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Angéline Van der Heyden
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | | | - Ralf P Richter
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France.,§CIC biomaGUNE, 20009 Donostia-San Sebastian, Spain.,∥Max-Planck-Institute for Intelligent Systems, 70569 Stuttgart, Germany
| | - Eric Defrancq
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Nicolas Spinelli
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Liliane Coche-Guérente
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Pierre Labbé
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
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30
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Peinetti AS, Ceretti H, Mizrahi M, González GA, Ramírez SA, Requejo FG, Montserrat JM, Battaglini F. Confined gold nanoparticles enhance the detection of small molecules in label-free impedance aptasensors. NANOSCALE 2015; 7:7763-7769. [PMID: 25838116 DOI: 10.1039/c5nr01429h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A controlled architecture of nanoelectrodes, of a similar size to small molecule-binding aptamers, is synthesized inside nanoporous alumina. Gold nanoparticles with a controlled size (about 2 nm) are electrogenerated in the alumina cavities, showing a fast electron transfer process toward ferrocyanide. These uncapped nanoparticles are easily modified with a thiol-containing aptamer for label-free detection of adenosine monophosphate by electrochemical impedance spectroscopy. Our results show that the use of a limited electrical conducting surface inside an insulating environment can be very sensitive to conformational changes, introducing a new approach to the detection of small molecules, exemplified here by the direct and selective detection of adenosine monophosphate at the nanomolar scale.
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Affiliation(s)
- Ana S Peinetti
- INQUIMAE (CONICET) - Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
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31
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Gutiérrez Sánchez C, Su Q, Schönherr H, Grininger M, Nöll G. Multi-Ligand-Binding Flavoprotein Dodecin as a Key Element for Reversible Surface Modification in Nano-biotechnology. ACS NANO 2015; 9:3491-3500. [PMID: 25738566 DOI: 10.1021/nn506993s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper the multiple (re)programming of protein-DNA nanostructures comprising generation, deletion, and reprogramming on the same flavin-DNA-modified surface is introduced. This work is based on a systematic study of the binding affinity of the multi-ligand-binding flavoprotein dodecin on flavin-terminated DNA monolayers by surface plasmon resonance and quartz crystal microbalance with dissipation (QCM-D) measurements, surface plasmon fluorescence spectroscopy (SPFS), and dynamic AFM force spectroscopy. Depending on the flavin surface coverage, a single apododecin is captured by one or more surface-immobilized flavins. The corresponding complex binding and unbinding rate constants kon(QCM) = 7.7 × 10(3) M(-1)·s(-1) and koff(QCM) = 4.5 × 10(-3) s(-1) (Kd(QCM) = 580 nM) were determined by QCM and were found to be in agreement with values for koff determined by SPFS and force spectroscopy. Even though a single apododecin-flavin bond is relatively weak, stable dodecin monolayers were formed on flavin-DNA-modified surfaces at high flavin surface coverage due to multivalent interactions between apododecin bearing six binding pockets and the surface-bound flavin-DNA ligands. If bi- or multivalent flavin ligands are adsorbed on dodecin monolayers, stable sandwich-type surface-DNA-flavin-apododecin-flavin ligand arrays are obtained. Nevertheless, the apododecin flavin complex is easily and quantitatively disassembled by flavin reduction. Binding and release of apododecin are reversible processes, which can be carried out alternatingly several times to release one type of ligand by an external redox trigger and subsequently replace it with a different ligand. Hence the versatile concept of reprogrammable functional biointerfaces with the multi-ligand-binding flavoprotein dodecin is demonstrated.
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Affiliation(s)
| | | | | | - Martin Grininger
- ∥Goethe University Frankfurt, Riedberg Campus FMLS Building, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
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32
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Rahman MM, Li XB, Lopa NS, Ahn SJ, Lee JJ. Electrochemical DNA hybridization sensors based on conducting polymers. SENSORS (BASEL, SWITZERLAND) 2015; 15:3801-29. [PMID: 25664436 PMCID: PMC4367386 DOI: 10.3390/s150203801] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/27/2015] [Indexed: 02/07/2023]
Abstract
Conducting polymers (CPs) are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective.
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Affiliation(s)
- Md Mahbubur Rahman
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
| | - Xiao-Bo Li
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
| | - Nasrin Siraj Lopa
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
| | - Sang Jung Ahn
- Center for Advanced Instrumentation, Korea Research Institute of Standards and Science (KRISS), Daejeon 305-340, Korea.
| | - Jae-Joon Lee
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
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33
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Tsortos A, Grammoustianou A, Lymbouridou R, Papadakis G, Gizeli E. The detection of multiple DNA targets with a single probe using a conformation-sensitive acoustic sensor. Chem Commun (Camb) 2015; 51:11504-7. [DOI: 10.1039/c5cc03436a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Acoustic sensing of DNA targets using a single probe that produces hybridization products of different conformations.
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34
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Quan X, Heiskanen A, Tenje M, Boisen A. In-situ monitoring of potential enhanced DNA related processes using electrochemical quartz crystal microbalance with dissipation (EQCM-D). Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.08.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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35
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Sun L, Svedhem S, Akerman B. Construction and modeling of concatemeric DNA multilayers on a planar surface as monitored by QCM-D and SPR. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8432-8441. [PMID: 24971872 DOI: 10.1021/la500716d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The sequential hybridization of a 534 base pair DNA concatemer layer was monitored by QCM-D and SPR, and the QCM-D data were analyzed by Voigt viscoelastic models. The results show that Voigt-based modeling gives a good description of the experimental data but only if shear viscosity and elasticity are allowed to depend on the shear frequency. The derived layer thickness, shear viscosity and elasticity of the growing film give a representation of the DNA film in agreement with known bulk properties of DNA, and reveal a maximum in film viscosity when the molecules in the layer contain 75 base pairs. The experimental data during construction of a 3084 bp DNA concatemer layer were compared to predictions of the QCM-D response of a 1 μm thick film of rod-like polymers. A predicted nonmonotonous variation of dissipation with frequency (added mass) is in qualitative agreement with the experiments, but with a quantitative disagreement which likely reflects that the flexibility of such long DNA molecules is not included in the model.
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Affiliation(s)
- Lu Sun
- Department of Chemical and Biological Engineering and ‡Department of Applied Physics, Chalmers University of Technology , 412 96 Gothenburg, Sweden
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36
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Papadakis G, Tsortos A, Kordas A, Tiniakou I, Morou E, Vontas J, Kardassis D, Gizeli E. Acoustic detection of DNA conformation in genetic assays combined with PCR. Sci Rep 2014; 3:2033. [PMID: 23778520 PMCID: PMC3686166 DOI: 10.1038/srep02033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 06/03/2013] [Indexed: 11/09/2022] Open
Abstract
Application of PCR to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. Alternative PCR-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. Here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target amplicons produced in the same PCR reaction. The new methodology exploits acoustic wave devices which are shown to be able to characterize in a fully quantitative manner multiple double stranded DNAs of various lengths. The generic nature of the combined acoustic/PCR platform is shown using real samples and, specifically, during the detection of SNP genotyping in Anopheles gambiae and gene expression quantification in treated mice. The method possesses significant advantages to TaqMan assay and real-time PCR regarding multiplexing capability, speed, simplicity and cost.
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Affiliation(s)
- G Papadakis
- Institute of Molecular Biology & Biotechnology, FORTH, Vassilika Vouton, 70013 Heraklion, Greece.
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37
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ZHOU JP, BAO Y, LIN Q, PANG RS, WANG LM, NIU L. A New Quartz Crystal Microbalance Measuring Method with Expansive Frequency Range and Broadband Adaptive Response Capacity. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(13)60735-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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Zheng Y, Yang C, Yang F, Yang X. Real-time study of interactions between cytosine-cytosine pairs in DNA oligonucleotides and silver ions using dual polarization interferometry. Anal Chem 2014; 86:3849-55. [PMID: 24611666 DOI: 10.1021/ac403992r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The real-time conformational changes of cytosine (C)-rich ssDNA oligonucleotides upon binding with silver ions (Ag(+)) were studied using dual polarization interferometry (DPI). Upon the addition of Ag(+), Ag(+) selectively bound to cytosine-cytosine mismatches and formed C-Ag(+)-C complexes, inducing change of the structure of the C-rich ssDNA from random coil conformation to duplex conformation, whereas the control ssDNA without cytosine-cytosine mismatches had no such signal, which was consistent with circular dichroism (CD) characterization. The conformational change of DNA was reflected on the changes of the mass, thickness, and density values resolved by DPI. The calibration curves showed that as the concentration of Ag(+) increased from 10 nM to 8 μM, the thickness and mass values increased linearly while the density values decreased linearly. Other metal ions such as K(+), Ca(2+), Na(+), Mg(2+), Zn(2+), Mn(2+), Ni(2+), and Pb(2+) did not interfere with the interaction between Ag(+) and C-rich ssDNA, indicating that this method had a good selectivity. The practical application of this biosensor was also investigated in real samples such as drinking water. Besides, cysteine could specifically capture Ag(+) from C-Ag(+)-C complexes and transformed the structure of the C-rich DNA back from rigid double-stranded conformation to random coil conformation, which allowed cysteine to be detected selectively as well. It is expected that this biosensing strategy may be utilized to study the interaction of DNA with other molecules.
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Affiliation(s)
- Yu Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
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39
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Mitsakakis K, Tsortos A, Gizeli E. Quantitative determination of protein molecular weight with an acoustic sensor; significance of specific versus non-specific binding. Analyst 2014; 139:3918-25. [DOI: 10.1039/c4an00616j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multi-analyte acoustic biosensor determines the molecular weight of proteinsviathe phase change of the acoustic signal.
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Affiliation(s)
- Konstantinos Mitsakakis
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
- Department of Materials Science & Technology
- University of Crete
| | - Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
- Department of Biology
- University of Crete
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40
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Rust P, Cereghetti D, Dual J. A micro-liter viscosity and density sensor for the rheological characterization of DNA solutions in the kilo-hertz range. LAB ON A CHIP 2013; 13:4794-4799. [PMID: 24154924 DOI: 10.1039/c3lc50857a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
When measuring the properties of fluids from biological sources, sample volumes in the micro-liter range are often desired as higher volumes may not be available or are very expensive. Miniaturized viscosity and density sensors based on a vibrating cantilever fulfill this requirement. In this paper, the possibility of measuring viscosity and density of DNA solutions at the same time using such a sensor is shown. The sensor requires a sample volume of 10 μl. By doing a titration of a solution containing 110 bp long strands of DNA in the diluted, Newtonian regime, the intrinsic viscosity can be determined to be 0.047 ml mg(-1) using the cantilever sensor. The cantilever is also tested with solutions of 10 kbp long strands with concentrations in the semi-dilute, non-Newtonian regime. The comparably small change in resonance frequency and damping observed using these solutions at 12.5 kHz is attributed to shear thinning, which is expected when extrapolating results from other groups.
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Affiliation(s)
- Philipp Rust
- Department of Mechanical and Process Engineering, Institute of Mechanical Systems, ETH Zurich, CH-8092, Zurich, Switzerland.
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Fu Y, Zou C, Bu L, Xie Q, Yao S. Novel amperometric aptasensor based on analyte-induced suppression of enzyme catalysis in polymeric bionanocomposites. ACS APPLIED MATERIALS & INTERFACES 2013; 5:934-939. [PMID: 23269073 DOI: 10.1021/am302602s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report on a novel label-free biosensing interface based on multifunctional polymeric bionanocomposites (PBNCs) and its application for sensitive detection of protein based on the analyte-induced suppression of enzymatic catalysis in PBNCs. Thrombin and its aptamer are adopted as a model system to construct an amperometric aptasensor. First, polydopamine-based PBNCs with glucose oxidase (GOx) entrapped at high load/activity and Au nanoparticles (AuNPs) dispersed in high abundance on the surface were prepared through a chemical/biochemical synthesis method, as proven by UV-vis spectrophotometry, digital imaging, and transmission electron microscopy. Then, the PBNCs were cast-coated onto an Au electrode. The PBNC-modified Au electrode presented a high chronoamperometric sensitivity of 113 ± 2 μA cm(-2) mM(-1) to glucose, as well as a high capability of immobilizing the aptamer through the surficial AuNPs to fabricate a label-free aptasensing interface. The binding of thrombin to the aptasensor surface significantly hindered the mass-transfer of the enzymatic substrates/products and thus suppressed the enzymatic catalysis efficiency, which produced obvious signal change through measuring the electrooxidation of enzymatically generated H(2)O(2). The thus-prepared aptasensor could detect thrombin with a broad detection range (1-100 nM), a detection limit down to 0.1 nM, and satisfactory specificity. The developed aptasensing method may find broad applications in the fields of clinical diagnosis, environmental protection, and food safety.
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Affiliation(s)
- Yingchun Fu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P R China.
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Abi A, Ferapontova EE. Electroanalysis of single-nucleotide polymorphism by hairpin DNA architectures. Anal Bioanal Chem 2012; 405:3693-703. [PMID: 23263518 DOI: 10.1007/s00216-012-6633-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/27/2012] [Accepted: 12/06/2012] [Indexed: 12/21/2022]
Abstract
Genetic analysis of infectious and genetic diseases and cancer diagnostics require the development of efficient tools for fast and reliable analysis of single-nucleotide polymorphism (SNP) in targeted DNA and RNA sequences often responsible for signalling disease onset. Here, we highlight the main trends in the development of electrochemical genosensors for sensitive and selective detection of SNP that are based on hairpin DNA architectures exhibiting better SNP recognition properties compared with linear DNA probes. SNP detection by electrochemical hairpin DNA beacons is discussed, and comparative analysis of the existing SNP sensing strategies based on enzymatic and nanoparticle signal amplification schemes is presented.
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Affiliation(s)
- Alireza Abi
- Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 1590-14, 8000 Aarhus C, Denmark
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Ivanov IE, Morrison AE, Cobb JE, Fahey CA, Camesano TA. Creating antibacterial surfaces with the peptide chrysophsin-1. ACS APPLIED MATERIALS & INTERFACES 2012; 4:5891-5897. [PMID: 23043421 DOI: 10.1021/am301530a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immobilization of antimicrobial peptides (AMPs) holds potential for creating surfaces with bactericidal properties. In order to successfully incorporate AMPs into desired materials, increased fundamental understanding of the relationship between AMP immobilization and the efficacy of bound peptides as antibacterial agents is required. In this study, we characterize the relationship between surface binding of the AMP and subsequent ability of the peptide to kill bacteria. Surface immobilization of the AMP chrysophsin-1 (CHY1) via a flexible linker is studied in real-time, using a quartz crystal microbalance with dissipation monitoring (QCM-D). Depending on whether the AMP is physically adsorbed to the surface or attached covalently via a zero-length or flexible cross-linker, changes could be observed in AMP orientation, surface density, flexibility, and activity against bacteria. Covalent surface binding of CHY1 led to the formation of solvated monolayers of vertically positioned peptide molecules, while the physical adsorption of CHY1 led to the deposition of rigid monolayers of horizontally positioned peptide molecules on the sensor surface. Covalently bound peptides were not removed by extensive washing and did not leach from the surface. Zero-length immobilization of the peptide decreased its ability to kill E. coli to 34% ± 7% of added bacteria, while binding via a flexible linker resulted in 82% ± 11% of bacteria being killed by the AMP.
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Affiliation(s)
- Ivan E Ivanov
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
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Wang W, Yuan X, Zhang W, Gao Q, Qi H, Zhang C. Cascade signal amplification for ultra-sensitive impedimetric detection of DNA hybridization using a hairpin DNA as probe. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Abi A, Ferapontova EE. Unmediated by DNA Electron Transfer in Redox-Labeled DNA Duplexes End-Tethered to Gold Electrodes. J Am Chem Soc 2012; 134:14499-507. [DOI: 10.1021/ja304864w] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alireza Abi
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds Vej 1590-14, DK-8000
Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds Vej 1590-14, DK-8000
Aarhus C, Denmark
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Tang W, Wang D, Xu Y, Li N, Liu F. A self-assembled DNA nanostructure-amplified quartz crystal microbalance with dissipation biosensing platform for nucleic acids. Chem Commun (Camb) 2012; 48:6678-80. [PMID: 22641067 DOI: 10.1039/c2cc32747c] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A self-assembled DNA nanostructure as an efficient signal amplifier was introduced to create a simple and label-free quartz crystal microbalance with dissipation monitoring (QCM-D) biosensing platform for highly sensitive and selective detection of nucleic acids.
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Affiliation(s)
- Wei Tang
- Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Stobiecka M, Molinero AA, Chałupa A, Hepel M. Mercury/homocysteine ligation-induced ON/OFF-switching of a T-T mismatch-based oligonucleotide molecular beacon. Anal Chem 2012; 84:4970-8. [PMID: 22524145 DOI: 10.1021/ac300632u] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A molecular beacon (MB) with stem-loop (hairpin) DNA structure and with attached fluorophore-quencher pair at the ends of the strand has been applied to study the interactions of Hg(2+) ions with a thymine-thymine (T-T) mismatch in Watson-Crick base-pairs and the ligative disassembly of MB·Hg(2+) complex by Hg(2+) sequestration with small biomolecule ligands. In this work, a five base-pair stem with configuration 5'-GGTGG...CCTCC-3' for self-hybridization of MB has been utilized. In this configuration, the four GC base-pair binding energy is not sufficient to hybridize fully at intermediate temperatures and to form a hairpin MB conformation. The T-T mismatch built-in into the stem area can effectively bind Hg(2+) ions creating a bridge, T-Hg-T. We have found that the T-Hg-T bridge strongly enhances the ability of MB to hybridize, as evidenced by an unusually large MB melting temperature shift observed on bridge formation, ΔT(m) = +15.1 ± 0.5 °C, for 100 nM MB in MOPS buffer. The observed ΔT(m) is the largest of the ΔT(m) found for other MBs and dsDNA structures. By fitting the parameters of the proposed model of reversible MB interactions to the experimental data, we have determined the T-Hg-T bridge formation constant at 25 °C, K(1) = 8.92 ± 0.42 × 10(17) M(-1) from mercury(II) titration data and K(1) = 1.04 ± 0.51 × 10(18) M(-1) from the bridge disassembly data; ΔG° = -24.53 ± 0.13 kcal/mol. We have found that the biomarker of oxidative stress and cardiovascular disease, homocysteine (Hcys), can sequester Hg(2+) ions from the T-Hg-T complex and withdraw Hg(2+) ions from MB in the form of stable Hg(Hcys)(2)H(2) complexes. Both the model fitting and independent (1)H NMR results on the thymidine-Hg-Hcys system indicate also the high importance of 1:1 complexes. The high value of K(1) for T-Hg-T bridge formation enables analytical determinations of low concentrations of Hg(2+) (limit of detection LOD = 19 nM or 3.8 ppb, based on 3σ method) and Hcys (LOD = 23 nM, 3σ method). The conditional stability constants for Hg(Hcys)H(2)(2+) and Hg(Hcys)(2)H(2) at 52 °C have been determined, β(112) = 5.37 ± 0.3 × 10(46) M(-3), β(122) = 3.80 ± 0.6 × 10(68) M(-4), respectively.
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Affiliation(s)
- Magdalena Stobiecka
- Department of Chemistry, State University of New York at Potsdam, Potsdam, New York 13676, United States
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