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Gu K, Lin S. Advances in the Dynamics of Adsorbate Diffusion on Metal Surfaces: Focus on Hydrogen and Oxygen. Chemphyschem 2024; 25:e202400083. [PMID: 38511509 DOI: 10.1002/cphc.202400083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/26/2024] [Accepted: 03/21/2024] [Indexed: 03/22/2024]
Abstract
Adsorbates on metal surfaces are typically formed from the dissociative chemisorption of molecules occurring at gas-solid interfaces. These adsorbed species exhibit unique diffusion behaviors on metal surfaces, which are influenced by their translational energy. They play crucial roles in various fields, including heterogeneous catalysis and corrosion. This review examines recent theoretical advancements in understanding the diffusion dynamics of adsorbates on metal surfaces, with a specific emphasis on hydrogen and oxygen atoms. The diffusion processes of adsorbates on metal surfaces involve two energy transfer mechanisms: surface phonons and electron-hole pair excitations. This review also surveys new theoretical methods, including the characterization of the electron-hole pair excitation within electronic friction models, the acceleration of quantum chemistry calculations through machine learning, and the treatment of atomic nuclear motion from both quantum mechanical and classical perspectives. Furthermore, this review offers valuable insights into how energy transfer, nuclear quantum effects, supercell sizes, and the topography of potential energy surfaces impact the diffusion behavior of hydrogen and oxygen species on metal surfaces. Lastly, some preliminary research proposals are presented.
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Affiliation(s)
- Kaixuan Gu
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Sen Lin
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
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2
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Zheng Z, Grall S, Kim SH, Chovin A, Clement N, Demaille C. Activationless Electron Transfer of Redox-DNA in Electrochemical Nanogaps. J Am Chem Soc 2024; 146:6094-6103. [PMID: 38407938 DOI: 10.1021/jacs.3c13532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Our recent discovery of decreased reorganization energy in electrode-tethered redox-DNA systems prompts inquiries into the origin of this phenomenon and suggests its potential use to lower the activation energy of electrochemical reactions. Here, we show that the confinement of the DNA chain in a nanogap amplifies this effect to an extent to which it nearly abolishes the intrinsic activation energy of electron transfer. Employing electrochemical atomic force microscopy (AFM-SECM), we create sub-10 nm nanogaps between a planar electrode surface bearing end-anchored ferrocenylated DNA chains and an incoming microelectrode tip. The redox cycling of the DNA's ferrocenyl (Fc) moiety between the surface and the tip generates a measurable current at the scale of ∼10 molecules. Our experimental findings are rigorously interpreted through theoretical modeling and original molecular dynamics simulations (Q-Biol code). Several intriguing findings emerge from our investigation: (i) The electron transport resulting from DNA dynamics is many times faster than predicted by simple diffusion considerations. (ii) The current in the nanogap is solely governed by the electron transfer rate at the electrodes. (iii) This rate rapidly saturates as overpotentials applied to the nanogap electrodes increase, implying near-complete suppression of the reorganization energy for the oxidation/reduction of the Fc heads within confined DNA. Furthermore, evidence is presented that this may constitute a general, previously unforeseen, behavior of redox polymer chains in electrochemical nanogaps.
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Affiliation(s)
- Zhiyong Zheng
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
| | - Simon Grall
- IIS, LIMMS/CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8505 Tokyo, Japan
| | - Soo Hyeon Kim
- IIS, LIMMS/CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8505 Tokyo, Japan
| | - Arnaud Chovin
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
| | - Nicolas Clement
- IIS, LIMMS/CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8505 Tokyo, Japan
- LAAS, 7 avenue du Colonel Roche, 31400 Toulouse, France
| | - Christophe Demaille
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
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3
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Gurukandure A, Somasundaram S, Kurian ASN, Khuda N, Easley CJ. Building a Nucleic Acid Nanostructure with DNA-Epitope Conjugates for a Versatile Approach to Electrochemical Protein Detection. Anal Chem 2023; 95:18122-18129. [PMID: 38032341 PMCID: PMC10720615 DOI: 10.1021/acs.analchem.3c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023]
Abstract
The recent surge of effort in nucleic-acid-based electrochemical (EC) sensors has been fruitful, yet there remains a need for more generalizable EC platforms for sensing multiple classes of clinically relevant targets. We recently reported a nucleic acid nanostructure for simple, economical, and more generalizable EC readout of a range of analytes, including small molecules, peptides, proteins, and antibodies. The nanostructure is built through on-electrode enzymatic ligation of three oligonucleotides for attachment, binding, and signaling. However, the generalizable detection of larger proteins remains a challenge. Here, we adapted the sensor to quantify larger proteins in a more generic manner through conjugating the protein's minimized antibody-binding epitope to the central DNA strand. This concept was verified using creatine kinase (CK-MM), a biomarker of muscle damage and several disorders for which rapid clinical sensing is important. DNA-epitope conjugates permitted a competitive immunoassay for the CK protein at the electrode via square-wave voltammetry (SWV). Sensing through a signal-off mechanism, the anti-CK antibody limit of detection (LOD) was 5 nM with a response time as low as 3 min. Antibody displacement by native protein analytes gave a signal-on response with the CK sensing range from the LOD of 14 nM up to 100 nM, overlapping with the normal (nonelevated) human clinical range (3-37 nM), and the sensor was validated in 98% human serum. While a need for improved DNA-epitope conjugate purification was identified, overall, this approach allows the quantification of a generic protein- or peptide-binding antibody and should facilitate future quantitative EC readouts of clinically relevant proteins that were previously inaccessible to EC techniques.
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Affiliation(s)
- Asanka Gurukandure
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Subramaniam Somasundaram
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Amanda S. N. Kurian
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Niamat Khuda
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Christopher J. Easley
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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4
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Madrid I, Zheng Z, Gerbelot C, Fujiwara A, Li S, Grall S, Nishiguchi K, Kim SH, Chovin A, Demaille C, Clement N. Ballistic Brownian Motion of Nanoconfined DNA. ACS NANO 2023; 17:17031-17040. [PMID: 37700490 DOI: 10.1021/acsnano.3c04349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Theoretical treatments of polymer dynamics in liquid generally start with the basic assumption that motion at the smallest scale is heavily overdamped; therefore, inertia can be neglected. We report on the Brownian motion of tethered DNA under nanoconfinement, which was analyzed by molecular dynamics simulation and nanoelectrochemistry-based single-electron shuttle experiments. Our results show a transition into the ballistic Brownian motion regime for short DNA in sub-5 nm gaps, with quality coefficients as high as 2 for double-stranded DNA, an effect mainly attributed to a drastic increase in stiffness. The possibility for DNA to enter the underdamped regime could have profound implications on our understanding of the energetics of biomolecular engines such as the replication machinery, which operates in nanocavities that are a few nanometers wide.
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Affiliation(s)
- Ignacio Madrid
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Zhiyong Zheng
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Cedric Gerbelot
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Akira Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Shuo Li
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Simon Grall
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Katsuhiko Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Soo Hyeon Kim
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Arnaud Chovin
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Christophe Demaille
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Nicolas Clement
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
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5
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Grall S, Li S, Jalabert L, Kim SH, Chovin A, Demaille C, Clément N. Electrochemical Shot Noise of a Redox Monolayer. PHYSICAL REVIEW LETTERS 2023; 130:218001. [PMID: 37295112 DOI: 10.1103/physrevlett.130.218001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/25/2023] [Indexed: 06/12/2023]
Abstract
Redox monolayers are the base for a wide variety of devices including high-frequency molecular diodes or biomolecular sensors. We introduce a formalism to describe the electrochemical shot noise of such a monolayer, confirmed experimentally at room temperature in liquid. The proposed method, carried out at equilibrium, avoids parasitic capacitance, increases the sensitivity, and allows us to obtain quantitative information such as the electronic coupling (or standard electron transfer rates), its dispersion, and the number of molecules. Unlike in solid-state physics, the homogeneity in energy levels and transfer rates in the monolayer yields a Lorentzian spectrum. This first step for shot noise studies in molecular electrochemical systems opens perspectives for quantum transport studies in a liquid environment at room temperature as well as highly sensitive measurements for bioelectrochemical sensors.
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Affiliation(s)
- Simon Grall
- IIS, LIMMS/CNRS-IIS IRL2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - Shuo Li
- IIS, LIMMS/CNRS-IIS IRL2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - Laurent Jalabert
- IIS, LIMMS/CNRS-IIS IRL2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - Soo Hyeon Kim
- IIS, LIMMS/CNRS-IIS IRL2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - Arnaud Chovin
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
| | - Christophe Demaille
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
| | - Nicolas Clément
- IIS, LIMMS/CNRS-IIS IRL2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
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6
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Rahbarimehr E, Chao HP, Churcher ZR, Slavkovic S, Kaiyum YA, Johnson PE, Dauphin-Ducharme P. Finding the Lost Dissociation Constant of Electrochemical Aptamer-Based Biosensors. Anal Chem 2023; 95:2229-2237. [PMID: 36638814 DOI: 10.1021/acs.analchem.2c03566] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Electrochemical aptamer-based (E-AB) biosensors afford real-time measurements of the concentrations of molecules directly in complex matrices and in the body, offering alternative strategies to develop innovative personalized medicine tools. While different electroanalytical techniques have been used to interrogate E-AB sensors (i.e., cyclic voltammetry, electrochemical impedance spectroscopy, and chronoamperometry) to resolve the change in electron transfer of the aptamer's covalently attached redox reporter, square-wave voltammetry remains a widely used technique due to its ability to maximize the redox reporter's faradic contribution to the measured current. Several E-AB sensors interrogated with this technique, however, show lower aptamer affinity (i.e., μM-mM) even in the face of employing aptamers that have high affinities (i.e., nM-μM) when characterized using solution techniques such as isothermal titration calorimetry (ITC) or fluorescence spectroscopy. Given past reports showing that E-AB sensor's response is dependent on square-wave interrogation parameters (i.e., frequency and amplitude), we hypothesized that the difference in dissociation constants measured with solution techniques stemmed from the electrochemical interrogation technique itself. In response, we decided to compare six dissociation constants of aptamers when characterized in solution with ITC and when interrogated on electrodes with electrochemical impedance spectroscopy, a technique able to, in contrast to square-wave voltammetry, deconvolute and quantify E-AB sensors' contributions to the measured current. In doing so, we found that we were able to measure dissociation constants that were either separated by 2-3-fold or within experimental errors. These results are in contrast with square-wave voltammetry-measured dissociation constants that are at the most separated by 2-3 orders of magnitude from ones measured by ITC. We thus envision that the versatility and time scales covered by electrochemical impedance spectroscopy offer the highest sensitivity to measure target binding in electrochemical biosensors relying on changes in electron-transfer rates.
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Affiliation(s)
- Erfan Rahbarimehr
- Département de chimie, Université de Sherbrooke, Sherbrooke, QuébecJ1K 2R1, Canada
| | - Hoi Pui Chao
- Department of Chemistry, York University, 4700 Keele Street, Toronto, OntarioM3J 1P3, Canada
| | - Zachary R Churcher
- Department of Chemistry, York University, 4700 Keele Street, Toronto, OntarioM3J 1P3, Canada
| | - Sladjana Slavkovic
- Department of Chemistry, York University, 4700 Keele Street, Toronto, OntarioM3J 1P3, Canada
| | - Yunus A Kaiyum
- Department of Chemistry, York University, 4700 Keele Street, Toronto, OntarioM3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry, York University, 4700 Keele Street, Toronto, OntarioM3J 1P3, Canada
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7
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Zheng Z, Kim SH, Chovin A, Clement N, Demaille C. Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics. Chem Sci 2023; 14:3652-3660. [PMID: 37006693 PMCID: PMC10055828 DOI: 10.1039/d3sc00320e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
We demonstrate, using high scan rate cyclic voltammetry and molecular dynamics simulations, that the electrochemical response of electrode-attached redox DNA is governed by low reorganization energy electron transfer kinetics.
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Affiliation(s)
- Zhiyong Zheng
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
| | - Soo Hyeon Kim
- IIS, LIMMS/CNRS-IIS UMI2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Arnaud Chovin
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
| | - Nicolas Clement
- IIS, LIMMS/CNRS-IIS UMI2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Christophe Demaille
- Université Paris Cité, CNRS, Laboratoire d'Electrochimie Moléculaire, F-75013 Paris, France
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8
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Sykes KS, White RJ. Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7322-7330. [PMID: 35639972 PMCID: PMC10150402 DOI: 10.1021/acs.langmuir.2c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The cation condensation-induced collapse of electrode-bound nucleic acids and the resulting change in the electrochemical signal is a useful tool to predict the structure and redox probe location of heterogeneous structures of surface-tethered DNA probes─a common architecture employed in the development of electrochemical sensors. In this paper, we measure the faradaic current of an appended redox molecule at the 3' position of the nucleic acid using cyclic voltammetry before and after nucleic acid collapse for various nucleic acid architectures and heterogeneous mixtures on the same electrode surface. The voltammetric peak current change with collapse correlates with the proximity of the redox molecules from the surface. For stem-loop probes, the terminal methylene blue is initially held closer to the surface, such that inducing collapse, by reducing the dielectric permittivity of the interrogation solution, results in a ∼30% increase in current. However, when incorporating pseudoknot probes that hold methylene blue further away from the electrode surface, the current change is much larger (∼120%), indicating a larger conformation change. Upon a 50:50 ratio of the two, we observe a change in current that relates to the ratiometric distribution of the probe used to make the surfaces. Additionally, using cyclic voltammetry, we find that the change between diffusion-limited and diffusion-independent peak currents is dependent upon the distinct structural characteristics of DNA probes on the surface (stem-loop or pseudoknot), as well as the ratios of different DNA probes on the surface. Thus, we demonstrate that the heterogeneous nature of DNA probes governs the corresponding electrochemical signals, which can lead to a better understanding on how to predict the structures of functional nucleic acids on electrode surfaces and how this affects surface-to-surface variability and electrochemical response.
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Affiliation(s)
- Kiana S. Sykes
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Corresponding Author:
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9
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Khuda N, Somasundaram S, Easley CJ. Electrochemical Sensing of the Peptide Drug Exendin-4 Using a Versatile Nucleic Acid Nanostructure. ACS Sens 2022; 7:784-789. [PMID: 35180342 PMCID: PMC8985241 DOI: 10.1021/acssensors.1c02336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although endogenous peptides and peptide-based therapeutics are both highly relevant to human health, there are few approaches for sensitive biosensing of this class of molecules with minimized workflow. In this work, we have further expanded on the generalizability of our recently developed DNA nanostructure architecture by applying it to electrochemical (EC) peptide quantification. While DNA-small molecule conjugates were used in a prior work to make sensors for small molecule and protein analytes, here DNA-peptide conjugates were incorporated into the nanostructure at the electrode surfaces, and antibody displacement permitted rapid peptide sensing. Interestingly, multivalent DNA-peptide conjugates were found to be detrimental to the assay readout, yet these effects could be minimized by solution-phase bioconjugation. The final biosensor was validated for quantifying exendin-4 (4.2 kDa)─a human glucagon-like peptide-1 receptor agonist important in diabetes therapy─for the first time using EC methods with minimal workflow. The sensor was functional in 98% human serum, and the low nanomolar assay range lies between the injected dose concentration and the therapeutic range, boding well for future applications in therapeutic drug monitoring.
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10
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Tan J, Li H, Ji C, Zhang L, Zhao C, Tang L, Zhang C, Sun Z, Tan W, Yuan Q. Electron transfer-triggered imaging of EGFR signaling activity. Nat Commun 2022; 13:594. [PMID: 35105871 PMCID: PMC8807759 DOI: 10.1038/s41467-022-28213-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
In vivo electron transfer processes are closely related to the activation of signaling pathways, and, thus, affect various life processes. Indeed, the signaling pathway activation of key molecules may be associated with certain diseases. For example, epidermal growth factor receptor (EGFR) activation is related to the occurrence and development of tumors. Hence, monitoring the activation of EGFR-related signaling pathways can help reveal the progression of tumor development. However, it is challenging for current detection methods to monitor the activation of specific signaling pathways in complex biochemical reactions. Here we designed a highly sensitive and specific nanoprobe that enables in vivo imaging of electronic transfer over a broad range of spatial and temporal scales. By using the ferrocene-DNA polymer “wire”, the electrons transferred in a biochemical reaction can flow to persistent luminescent nanoparticles and change their electron distribution, thereby altering the optical signal of the particles. This electron transfer-triggered imaging probe enables mapping the activation of EGFR-related signaling pathways in a temporally and spatially precise manner. By offering precise visualization of signaling activity, this approach may offer a general platform not only for understanding molecular mechanisms in various biological processes but also for promoting disease therapies and drug evaluation. Here, the authors design a nanoprobe for in vivo imaging of electronic transfer, consisting of a ferrocene-DNA polymer to transfer electrons to luminescent nanoparticles, changing their optical signal. Using this probe, they map activation of EGFR signalling during tumour treatment.
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Affiliation(s)
- Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Hao Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Chenxuan Zhao
- Department of Chemistry, ZJU-NHU United R&D Center, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liming Tang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Caixin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Zhijun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China.
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China. .,The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.
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11
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Ma T, Bizzotto D. Improved Thermal Stability and Homogeneity of Low Probe Density DNA SAMs Using Potential-Assisted Thiol-Exchange Assembly Methods. Anal Chem 2021; 93:15973-15981. [PMID: 34813297 DOI: 10.1021/acs.analchem.1c03353] [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
Methods for producing DNA SAM-based sensors with improved thermal stability and control over the homogeneity of low DNA probe density will enable advanced sensor development. The thermal stability of low-coverage DNA SAMs was studied for surfaces prepared using potential-assisted thiol exchange (Edep) and compared to DNA SAMs prepared without control over the substrate potential (OCPdep). Both surface preparation methods were studied using in situ fluorescence microscopy and electrochemistry with fluorophore or redox-modified DNA SAMs on a single-crystal gold bead electrode. Fluorescence microscopy showed that the influence of the underlying surface crystallography was important in both cases. The highest thermal stability was realized for square or rectangular surface atomic structure (e.g., surfaces from 110 to 100). The 111 and related surfaces were the least thermally stable. The low DNA coverage surfaces prepared by Edep had better thermal stability and higher DNA probe mobility as compared to OCPdep-prepared surfaces with the similar coverage. These results were correlated with methylene blue redox-tagged DNA probes, which directly measured the average DNA coverage. Both methods indicated that Edep DNA SAMs were more uniformly distributed across the electrode surface, while the surfaces prepared via OCPdep assembled into clusters with reduced mobility. The potential-assisted thiol-exchange approach to preparing low-coverage DNA SAMs was shown to quickly create modified surfaces that were consistent, had mobility characteristics which should yield superior DNA hybridization efficiencies, and having greater thermal stability which will translate into a longer shelf-life.
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Affiliation(s)
- Tianxiao Ma
- AMPEL, University of British Columbia, Vancouver V6T 1Z4, Canada.,Department of Chemistry, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Dan Bizzotto
- AMPEL, University of British Columbia, Vancouver V6T 1Z4, Canada.,Department of Chemistry, University of British Columbia, Vancouver V6T 1Z4, Canada
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12
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Sykes KS, White RJ. Nucleic Acid Identity, Structure, and Flexibility Affect the Electrochemical Signal of Tethered Redox Molecules upon Biopolymer Collapse. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12466-12475. [PMID: 34644498 PMCID: PMC10150403 DOI: 10.1021/acs.langmuir.1c02161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We demonstrate that cation condensation can induce the collapse of surface-bound nucleic acids and that the electrochemical signal from a tethered redox molecule (methylene blue) upon collapse reports on nucleic acid identity, structure, and flexibility. Furthermore, the correlation of the electrochemical signal and structure is consistent with theoretical considerations of nucleic acid collapse. Changes in solution dielectric permittivity or the concentration of trivalent cations cause the structure of nucleic acids to become more compact due to an increase in attractive electrostatic interactions between the charged biopolymer backbone and multivalent ions in the solution. Consequently, the compaction of nucleic acids results in a change in the dynamics and location of the terminally appended redox marker, which is reflected in the faradaic current measured using cyclic voltammetry. In comparison to ssDNA, nucleic acid duplexes (dsDNA, DNA/peptide nucleic acid, and dsRNA) require nucleic-acid-composition-specific solution conditions for the collapse to occur. Moreover, the magnitude of current increase observed after the collapse is different for each nucleic structure, and we find here that these changes are dictated by physical parameters of the nucleic acids including the axial charge spacing and the periodicity of the helix. The work here aims to provide quantitative and predicative measures of the effects of the nucleic acid structure on the electrochemical signal produced from distal-end appended redox markers. This architecture is commonly employed in functional nucleic acid sensors and a better understanding of structure-to-signal correlations will enable the rational design of sensitive sensing architectures.
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Affiliation(s)
- Kiana S. Sykes
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Corresponding Author
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13
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Ahmed JU, Lutkenhaus JA, Alam MS, Marshall I, Paul DK, Alvarez JC. Dynamics of Collisions and Adsorption in the Stochastic Electrochemistry of Emulsion Microdroplets. Anal Chem 2021; 93:7993-8001. [PMID: 34043322 DOI: 10.1021/acs.analchem.1c01027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Current-time recordings of emulsified toluene microdroplets containing 20 mM Ferrocene (Fc), show electrochemical oxidation peaks from individual adsorption events on disk microelectrodes (5 μm diameter). The average droplet diameter (∼0.7 μm) determined from peak area integration was close to Dynamic Light Scattering measurements (∼1 μm). Random walk simulations were performed deriving equations for droplet electrolysis using the diffusion and thermal velocity expressions from Einstein. The simulations show that multiple droplet-electrode collisions, lasting ∼0.11 μs each, occur before a droplet wanders away. Updating the Fc-concentration at every collision shows that a droplet only oxidizes ∼0.58% of its content in one collisional journey. In fact, it would take ∼5.45 × 106 collisions and ∼1.26 h to electrolyze the Fc in one droplet with the collision frequency derived from the thermal velocity (∼0.52 cm/s) of a 1 μm-droplet. To simulate adsorption, the droplet was immobilized at first contact with the electrode while the electrolysis current was computed. This approach along with modeling of instrumental filtering, produced the best match of experimental peaks, which were attributed to electrolysis from single adsorption events instead of multiple consecutive collisions. These results point to a heightened sensitivity and speed when relying on adsorption instead of collisions. The electrochemical current for the former is limited by the probability of adsorption per collision, whereas for the latter, the current depends on the collision frequency and the probability of electron transfer per collision (J. Am. Chem. Soc. 2017, 139, 16923-16931).
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Affiliation(s)
- Junaid U Ahmed
- Chemistry Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - John A Lutkenhaus
- Chemistry Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Muhammad S Alam
- Electrical and Computer Engineering, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Ivan Marshall
- Maggie L. Walker Governor's School, Richmond, Virginia 23220, United States
| | - Dilip K Paul
- Intel Corporation, Hillsboro, Oregon 97124, United States
| | - Julio C Alvarez
- Chemistry Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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14
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Reagentless biomolecular analysis using a molecular pendulum. Nat Chem 2021; 13:428-434. [PMID: 33686229 DOI: 10.1038/s41557-021-00644-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
The development of reagentless sensors that can detect molecular analytes in biological fluids could enable a broad range of applications in personalized health monitoring. However, only a limited set of molecular inputs can currently be detected using reagentless sensors. Here, we report a sensing mechanism that is compatible with the analysis of proteins that are important physiological markers of stress, allergy, cardiovascular health, inflammation and cancer. The sensing method is based on the motion of an inverted molecular pendulum that exhibits field-induced transport modulated by the presence of a bound analyte. We measure the sensor's electric field-mediated transport using the electron-transfer kinetics of an attached reporter molecule. Using time-resolved electrochemical measurements that enable unidirectional motion of our sensor, the presence of an analyte bound to our sensor complex can be tracked continuously in real time. We show that this sensing approach is compatible with making measurements in blood, saliva, urine, tears and sweat and that the sensors can collect data in situ in living animals.
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15
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Pellitero MA, Curtis SD, Arroyo-Currás N. Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids. ACS Sens 2021; 6:1199-1207. [PMID: 33599479 DOI: 10.1021/acssensors.0c02455] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electrochemical, aptamer-based (E-AB) sensors support continuous, real-time measurements of specific molecular targets in complex fluids such as undiluted serum. They achieve these measurements by using redox-reporter-modified, electrode-attached aptamers that undergo target binding-induced conformational changes which, in turn, change electron transfer between the reporter and the sensor surface. Traditionally, E-AB sensors are interrogated via pulse voltammetry to monitor binding-induced changes in transfer kinetics. While these pulse techniques are sensitive to changes in electron transfer, they also respond to progressive changes in the sensor surface driven by biofouling or monolayer desorption and, consequently, present a significant drift. Moreover, we have empirically observed that differential voltage pulsing can accelerate monolayer desorption from the sensor surface, presumably via field-induced actuation of aptamers. Here, in contrast, we demonstrate the potential advantages of employing cyclic voltammetry to measure electron-transfer changes directly. In our approach, the target concentration is reported via changes in the peak-to-peak separation, ΔEP, of cyclic voltammograms. Because the magnitude of ΔEP is insensitive to variations in the number of aptamer probes on the electrode, ΔEP-interrogated E-AB sensors are resistant to drift and show decreased batch-to-batch and day-to-day variability in sensor performance. Moreover, ΔEP-based measurements can also be performed in a few hundred milliseconds and are, thus, competitive with other subsecond interrogation strategies such as chronoamperometry but with the added benefit of retaining sensor capacitance information that can report on monolayer stability over time.
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Affiliation(s)
- Miguel Aller Pellitero
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
| | - Samuel D. Curtis
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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16
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Vogiazi V, de la Cruz A, Heineman WR, White RJ, Dionysiou DD. Effects of Experimental Conditions on the Signaling Fidelity of Impedance-Based Nucleic Acid Sensors. Anal Chem 2021; 93:812-819. [PMID: 33395261 DOI: 10.1021/acs.analchem.0c03269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electrochemical impedance spectroscopy (EIS), an extremely sensitive analytical technique, is a widely used signal transduction method for the electrochemical detection of target analytes in a broad range of applications. The use of nucleic acids (aptamers) for sequence-specific or molecular detection in electrochemical biosensor development has been extensive, and the field continues to grow. Although nucleic acid-based sensors using EIS offer exceptional sensitivity, signal fidelity is often linked to the physical and chemical properties of the electrode-solution interface. Little emphasis has been placed on the stability of nucleic acid self-assembled monolayers (SAMs) over repeated voltammetric and impedimetric analyses. We have studied the stability and performance of electrochemical biosensors with mixed SAMs of varying length thiolated nucleic acids and short mercapto alcohols on gold surfaces under repeated electrochemical interrogation. This systematic study demonstrates that signal fidelity is linked to the stability of the SAM layer and nucleic acid structure and the packing density of the nucleic acid on the surface. A decrease in packing density and structural changes of nucleic acids significantly influence the signal change observed with EIS after routine voltammetric analysis. The goal of this article is to improve our understanding of the effect of multiple factors on EIS signal response and to optimize the experimental conditions for development of sensitive and reproducible sensors. Our data demonstrate a need for rigorous control experiments to ensure that the measured change in impedance is unequivocally a result of a specific interaction between the target analyte and nucleic recognition element.
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Affiliation(s)
- Vasileia Vogiazi
- Environmental Engineering and Science Program, Department of Chemical and Environmental Engineering (ChEE), University of Cincinnati, Cincinnati, Ohio 45221-0012, United States
| | - Armah de la Cruz
- Office of Research and Development, US Environmental Protection Agency, Cincinnati, Ohio 45268-0001, United States
| | - William R Heineman
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ryan J White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States.,Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221-0030, United States
| | - Dionysios D Dionysiou
- Environmental Engineering and Science Program, Department of Chemical and Environmental Engineering (ChEE), University of Cincinnati, Cincinnati, Ohio 45221-0012, United States
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17
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Wu Y, Ali S, White RJ. Electrocatalytic Mechanism for Improving Sensitivity and Specificity of Electrochemical Nucleic Acid-Based Sensors with Covalent Redox Tags-Part I. ACS Sens 2020; 5:3833-3841. [PMID: 33296188 DOI: 10.1021/acssensors.0c02362] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The design and development of advanced electrocatalysis have been extensively explored for efficient energy conversion and electrochemical biosensing. Both ferricyanide (Fe(CN)63-) and methylene blue (MB) have been widely used in the development of electrochemical biosensing strategies. However, the electrocatalytic mechanism between nucleic acid-tethered MB and Fe(CN)63- remains unexplored. In this manuscript, we aim to provide readers in our community molecular insights into the electrocatalytic mechanism. The exploration of the electrocatalytic mechanism starts with a kinetic zone diagram for a one-electron homogeneous electrocatalytic reaction. Two factors-the excess factor γ and the kinetic parameter λ-are important for a homogeneous electrocatalytic reaction; as such, we studied both. The excess factor parameter was controlled by applying Fe(CN)63- with various concentrations (50, 100, and 200 μM), and the kinetic parameter effect on the electrocatalytic process was examined by varying scan rates of cyclic voltammetry (CV) or frequencies of square-wave voltammetry (SWV). Moreover, we discovered that the probe dynamics of the nucleic acid tether is the third rate-limiting factor for the electrocatalytic reaction. As the probe dynamics switch of electrode-bound nucleic acid is often utilized as a mechanism in electrochemical nucleic acid-based sensors, we believe the electrocatalysis between nucleic acid-tethered MB and Fe(CN)63- is capable of enhancing sensitivity and specificity of electrochemical nucleic acid-based sensors with covalent redox tags.
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Affiliation(s)
- Yao Wu
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Sufyaan Ali
- Walnut Hills High School, Cincinnati, Ohio 45207, United States
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
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18
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Kutovyi Y, Madrid I, Zadorozhnyi I, Boichuk N, Kim SH, Fujii T, Jalabert L, Offenhaeusser A, Vitusevich S, Clément N. Noise suppression beyond the thermal limit with nanotransistor biosensors. Sci Rep 2020; 10:12678. [PMID: 32728030 PMCID: PMC7391715 DOI: 10.1038/s41598-020-69493-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/08/2020] [Indexed: 01/04/2023] Open
Abstract
Transistor biosensors are mass-fabrication-compatible devices of interest for point of care diagnosis as well as molecular interaction studies. While the actual transistor gates in processors reach the sub-10 nm range for optimum integration and power consumption, studies on design rules for the signal-to-noise ratio (S/N) optimization in transistor-based biosensors have been so far restricted to 1 µm2 device gate area, a range where the discrete nature of the defects can be neglected. In this study, which combines experiments and theoretical analysis at both numerical and analytical levels, we extend such investigation to the nanometer range and highlight the effect of doping type as well as the noise suppression opportunities offered at this scale. In particular, we show that, when a single trap is active near the conductive channel, the noise can be suppressed even beyond the thermal limit by monitoring the trap occupancy probability in an approach analog to the stochastic resonance effect used in biological systems.
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Affiliation(s)
- Yurii Kutovyi
- Bioelectronics (IBI-3), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Ignacio Madrid
- LIMMS-CNRS/IIS, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Ihor Zadorozhnyi
- Bioelectronics (IBI-3), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Nazarii Boichuk
- Bioelectronics (IBI-3), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Soo Hyeon Kim
- LIMMS-CNRS/IIS, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Teruo Fujii
- LIMMS-CNRS/IIS, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Laurent Jalabert
- LIMMS-CNRS/IIS, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | | | | | - Nicolas Clément
- LIMMS-CNRS/IIS, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan.
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19
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Veselinovic J, AlMashtoub S, Nagella S, Seker E. Interplay of Effective Surface Area, Mass Transport, and Electrochemical Features in Nanoporous Nucleic Acid Sensors. Anal Chem 2020; 92:10751-10758. [PMID: 32600033 DOI: 10.1021/acs.analchem.0c02104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Electrochemical biosensors transduce biochemical events (e.g., DNA hybridization) to electrical signals and can be readily interfaced with electronic instrumentation for portability. Nanostructuring the working electrode enhances sensor performance via augmented effective surface area that increases the capture probability of an analyte. However, increasing the effective surface area via thicker nanostructured electrodes hinders the analyte's permeation into the nanostructured volume and limits its access to deeper electrode surfaces. Here, we use nanoporous gold (np-Au) with various thicknesses and pore morphologies coupled with a methylene blue (MB) reporter-tagged DNA probe for DNA target detection as a model system to study the influence of electrode features on electrochemical sensing performance. Independent of the DNA target concentration, the hybridization current (surrogate for detection sensitivity) increases with the surface enhancement factor (EF), until an EF of ∼5, after which the sensor performance deteriorates. Electrochemical and fluorometric quantification of a desorbed DNA probe suggest that DNA permeation is severely limited for higher EFs. In addition, undesirable capacitive currents disguise the faradaic currents from the MB reporter at larger EFs that require higher square wave voltammetry (SWV) frequencies. Finally, a real-time hybridization study reveals that expanding the effective surface area beyond EFs of ∼5 decreases sensor performance.
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Affiliation(s)
- Jovana Veselinovic
- Department of Chemical Engineering, University of California-Davis, Davis, California 95616, United States
| | - Suzan AlMashtoub
- Department of Chemical Engineering, University of California-Davis, Davis, California 95616, United States
| | - Sachit Nagella
- Department of Chemical Engineering, University of California-Davis, Davis, California 95616, United States
| | - Erkin Seker
- Department of Electrical and Computer Engineering, University of California-Davis, Davis, California 95616, United States
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20
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Holtan MD, Somasundaram S, Khuda N, Easley CJ. Nonfaradaic Current Suppression in DNA-Based Electrochemical Assays with a Differential Potentiostat. Anal Chem 2019; 91:15833-15839. [PMID: 31718147 DOI: 10.1021/acs.analchem.9b04149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One of the key factors limiting sensitivity in many electrochemical assays is the nonfaradaic or capacitive current. This is particularly true in modern assay systems based on DNA monolayers at gold electrode surfaces, which have shown great promise for bioanalysis in complex milieu such as whole blood or serum. While various changes in analytical parameters, redox reporter molecules, DNA structures, probe coverage, and electrode surface area have been shown useful, background reduction by hardware subtraction has not yet been explored for these assays. Here, we introduce new electrochemistry hardware that considerably suppresses nonfaradaic currents through real-time analog subtraction during current-to-voltage conversion in the potentiostat. This differential potentiostat (DiffStat) configuration is shown to suppress or remove capacitance currents in chronoamperometry, cyclic voltammetry, and square-wave voltammetry measurements applied to nucleic acid hybridization assays at the electrode surface. The DiffStat makes larger electrodes and higher sensitivity settings accessible to the user, providing order-of-magnitude improvements in sensitivity, and it also significantly simplifies data processing to extract faradaic currents in square-wave voltammetry (SWV). Because two working electrodes are used for differential measurements, unique arrangements are introduced such as converting signal-OFF assays to signal-ON assays or background drift correction in 50% human serum. Overall, this new potentiostat design should be helpful not only in improving the sensitivity of most electrochemical assays, but it should also better support adaptation of assays to the point-of-care by circumventing complex data processing.
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Affiliation(s)
- Mark D Holtan
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Subramaniam Somasundaram
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Niamat Khuda
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Christopher J Easley
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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21
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Sykes KS, Oliveira LFL, Stan G, White RJ. Electrochemical Studies of Cation Condensation-Induced Collapse of Surface-Bound DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:12962-12970. [PMID: 31509702 PMCID: PMC6823840 DOI: 10.1021/acs.langmuir.9b02299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this paper, we demonstrate the ability to control and electrochemically monitor nucleic acid conformation by inducing collapse of short, surface-bound nucleotides (7-28 nucleotides). More specifically, we monitored changes in a 5'-electrode-bound DNA structure via changes in the faradaic current related to the reduction/oxidation of a 3'-terminal-appended redox molecule. Reversible DNA collapse was induced by cation condensation achieved by either reducing the dielectric permittivity of the interrogation solution or by the addition of multivalent cations such as the polyamine spermidine (3+). Additionally, we find that while the change in electrochemical signal associated with surface bound DNA collapse is dependent on nucleic acid length and surface packing density, the solution conditions (e.g., dielectric permittivity) required for collapse remain constant. As such, we find that collapse of the short DNA strands occurs when the effective charge of the DNA backbone is ∼73-89% neutralized by cations in solution/buffer, according to Manning's theory on cation condensation. This work provides new insight into the structure function relationship of surface-bound nucleic acids and how this is manifested in electrochemical signaling.
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Affiliation(s)
- Kiana S. Sykes
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | | | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, USA
- Corresponding author: Ryan J. White
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22
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Somasundaram S, Easley CJ. A Nucleic Acid Nanostructure Built through On-Electrode Ligation for Electrochemical Detection of a Broad Range of Analytes. J Am Chem Soc 2019; 141:11721-11726. [PMID: 31257869 DOI: 10.1021/jacs.9b06229] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For an assay to be most effective in point-of-care clinical analysis, it needs to be economical, simple, generalizable, and free from tedious workflows. While electrochemistry-based DNA sensors reduce instrumental costs and eliminate complicated procedures, there remains a need to address probe costs and generalizability, as numerous probes with multiple conjugations are needed to quantify a wide range of biomarkers. In this work, we have opened a route to circumvent complicated multiconjugation schemes using enzyme-catalyzed probe construction directly on the surface of the electrode. With this, we have created a versatile DNA nanostructure probe and validated its effectiveness by quantification of proteins (streptavidin, anti-digoxigenin, anti-tacrolimus) and small molecules (biotin, digoxigenin, tacrolimus) using the same platform. Tacrolimus, a widely prescribed immunosuppressant drug for organ transplant patients, was directly quantified with electrochemistry for the first time, with the assay range matching the therapeutic index range. Finally, the stability and sensitivity of the probe was confirmed in a background of minimally diluted human serum.
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Affiliation(s)
- Subramaniam Somasundaram
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Christopher J Easley
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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23
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Santos-Cancel M, Simpson LW, Leach JB, White RJ. Direct, Real-Time Detection of Adenosine Triphosphate Release from Astrocytes in Three-Dimensional Culture Using an Integrated Electrochemical Aptamer-Based Sensor. ACS Chem Neurosci 2019; 10:2070-2079. [PMID: 30754968 PMCID: PMC6469990 DOI: 10.1021/acschemneuro.9b00033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In this manuscript, we describe the development and application of electrochemical aptamer-based (E-AB) sensors directly interfaced with astrocytes in three-dimensional (3D) cell culture to monitor stimulated release of adenosine triphosphate (ATP). The aptamer-based sensor couples specific detection of ATP, selective performance directly in cell culture media, and seconds time resolution using squarewave voltammetry for quantitative ATP-release measurements. More specifically, we demonstrate the ability to quantitatively monitor ATP release into the extracellular environment after stimulation by the addition of calcium (Ca2+), ionomycin, and glutamate. The sensor response is confirmed to be specific to ATP and requires the presence of astrocytes in culture. For example, PC12 cells do not elicit a sensor response after stimulation with the same stimulants. In addition, we confirmed cell viability in the collagen matrix for all conditions tested. Our hydrogel-sensor interface offers the potential to study the release of small molecule messengers in 3D environments. Given the generality of electrochemical aptamer-based sensors and the demonstrated successful interfacing of sensors with tissue scaffold material, in the long term, we anticipate our sensors will be able to translate from in vitro to in vivo small molecule recordings.
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Affiliation(s)
| | - Laura W. Simpson
- Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Jennie B. Leach
- Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, USA
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24
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Santos-Cancel M, Lazenby RA, White RJ. Rapid Two-Millisecond Interrogation of Electrochemical, Aptamer-Based Sensor Response Using Intermittent Pulse Amperometry. ACS Sens 2018; 3:1203-1209. [PMID: 29762016 DOI: 10.1021/acssensors.8b00278] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this manuscript, we employ the technique intermittent pulse amperometry (IPA) to interrogate equilibrium and kinetic target binding to the surface of electrochemical, aptamer-based (E-AB) sensors, achieving as fast as 2 ms time resolution. E-AB sensors comprise an electrode surface modified with a flexible nucleic acid aptamer tethered at the 3'-terminus with a redox-active molecule. The introduction of a target changes the conformation and flexibility of the nucleic acid, which alters the charge transfer rate of the appended redox molecule. Typically, changes in charge transfer rate within this class of sensor are monitored via voltammetric methods. Here, we demonstrate that the use of IPA enables the detection of changes in charge transfer rates (i.e., current) at times <100 μs after the application of a potential pulse. Changes in sensor current are quantitatively related to target analyte concentration and can be used to create binding isotherms. Furthermore, the application of IPA enables rapid probing of the electrochemical surface with a time resolution equivalent to as low as twice the applied potential pulse width, not previously demonstrated with traditional voltammetric techniques employed with E-AB sensors (alternating current, square wave, cyclic). To visualize binding, we developed false-color plots analogous to those used in the field of fast-scan cyclic voltammetry. The use of IPA is universal, as demonstrated with two representative small molecule E-AB sensors directed against the aminoglycoside antibiotic tobramycin and adenosine triphosphate (ATP). Intermittent pulse amperometry exhibits an unprecedented sub-microsecond temporal response and is a general method for measuring rapid sensor performance.
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Affiliation(s)
- Mirelis Santos-Cancel
- Department of Chemistry and ‡Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Robert A. Lazenby
- Department of Chemistry and ‡Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ryan J. White
- Department of Chemistry and ‡Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
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25
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Daniel J, Fetter L, Jett S, Rowland TJ, Bonham AJ. Electrochemical Aptamer Scaffold Biosensors for Detection of Botulism and Ricin Proteins. Methods Mol Biol 2018; 1600:9-23. [PMID: 28478553 DOI: 10.1007/978-1-4939-6958-6_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Electrochemical DNA (E-DNA) biosensors enable the detection and quantification of a variety of molecular targets, including oligonucleotides, small molecules, heavy metals, antibodies, and proteins. Here we describe the design, electrode preparation and sensor attachment, and voltammetry conditions needed to generate and perform measurements using E-DNA biosensors against two protein targets, the biological toxins ricin and botulinum neurotoxin. This method can be applied to generate E-DNA biosensors for the detection of many other protein targets, with potential advantages over other systems including sensitive detection limits typically in the nanomolar range, real-time monitoring, and reusable biosensors.
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Affiliation(s)
- Jessica Daniel
- Department of Chemistry, Metropolitan State University of Denver, 890 Auraria Parkway, Denver, CO, 80220, USA
| | - Lisa Fetter
- Department of Chemistry, Metropolitan State University of Denver, 890 Auraria Parkway, Denver, CO, 80220, USA
| | - Susan Jett
- Department of Chemistry, Metropolitan State University of Denver, 890 Auraria Parkway, Denver, CO, 80220, USA
| | - Teisha J Rowland
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado Denver Anschutz Medical Campus, 12700 E 19th Ave, Aurora, 80045, CO, USA
| | - Andrew J Bonham
- Department of Chemistry, Metropolitan State University of Denver, 890 Auraria Parkway, Denver, CO, 80220, USA.
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26
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Somasundaram S, Holtan MD, Easley CJ. Understanding Signal and Background in a Thermally Resolved, Single-Branched DNA Assay Using Square Wave Voltammetry. Anal Chem 2018; 90:3584-3591. [PMID: 29385341 DOI: 10.1021/acs.analchem.8b00036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrochemical bioanalytical sensors with oligonucleotide transducer molecules have been recently extended for quantifying a wide range of biomolecules, from small drugs to large proteins. Short DNA or RNA strands have gained attention recently due to the existence of circulating oligonucleotides in human blood, yet challenges remain for adequately sensing these targets at electrode surfaces. In this work, we have developed a quantitative electrochemical method which uses target-induced proximity of a single-branched DNA structure to drive hybridization at an electrode surface, with readout by square-wave voltammetry (SWV). Using custom instrumentation, we first show that precise control of temperature can provide both electrochemical signal amplification and background signal depreciation in SWV readout of small oligonucleotides. Next, we thoroughly compared 25 different combinations of binding energies by their signal-to-background ratios and differences. These data served as a guide to select the optimal parameters of binding energy, SWV frequency, and assay temperature. Finally, the influence of experimental workflow on the sensitivity and limit of detection (LOD) of the sensor is demonstrated. This study highlights the importance of precisely controlling temperature and SWV frequency in DNA-driven assays on electrode surfaces while also presenting a novel instrumental design for fine-tuning of such systems.
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Affiliation(s)
- Subramaniam Somasundaram
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Mark D Holtan
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Christopher J Easley
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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27
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Robinson DA, Liu Y, Edwards MA, Vitti NJ, Oja SM, Zhang B, White HS. Collision Dynamics during the Electrooxidation of Individual Silver Nanoparticles. J Am Chem Soc 2017; 139:16923-16931. [PMID: 29083174 DOI: 10.1021/jacs.7b09842] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent high-bandwidth recordings of the oxidation and dissolution of 35 nm radius Ag nanoparticles at a Au microelectrode show that these nanoparticles undergo multiple collisions with the electrode, generating multiple electrochemical current peaks. In the time interval between observed current peaks, the nanoparticles diffuse in the solution near the electrolyte/electrode interface. Here, we demonstrate that simulations of random nanoparticle motion, coupled with electrochemical kinetic parameters, quantitatively reproduce the experimentally observed multicurrent peak behavior. Simulations of particle diffusion are based on the nanoparticle-mass-based thermal nanoparticle velocity and the Einstein diffusion relations, while the electron-transfer rate is informed by the literature exchange current density for the Ag/Ag+ redox system. Simulations indicate that tens to thousands of particle-electrode collisions, each lasting ∼6 ns or less (currently unobservable on accessible experimental time scales), contribute to each experimentally observed current peak. The simulation provides a means to estimate the instantaneous current density during a collision (∼500-1000 A/cm2), from which we estimate a rate constant between ∼5 and 10 cm/s for the electron transfer between Ag nanoparticles and the Au electrode. This extracted rate constant is approximately equal to the thermal collisional velocity of the Ag nanoparticle (4.6 cm/s), the latter defining the theoretical upper limit of the electron-transfer rate constant. Our results suggest that only ∼1% of the surface atoms on the Ag nanoparticles are oxidized per instantaneous collision. The combined simulated and experimental results underscore the roles of Brownian motion and collision frequency in the interpretation of heterogeneous electron-transfer reactions involving nanoparticles.
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Affiliation(s)
- Donald A Robinson
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Yuwen Liu
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States.,College of Chemistry and Molecular Sciences, Wuhan University , Wuhan, 430072, China
| | - Martin A Edwards
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Nicholas J Vitti
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Stephen M Oja
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Bo Zhang
- Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States
| | - Henry S White
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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28
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Rodríguez-Guerra Pedregal J, Sciortino G, Guasp J, Municoy M, Maréchal JD. GaudiMM: A modular multi-objective platform for molecular modeling. J Comput Chem 2017; 38:2118-2126. [PMID: 28605037 DOI: 10.1002/jcc.24847] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 01/16/2023]
Abstract
GaudiMM (for Genetic Algorithms with Unrestricted Descriptors for Intuitive Molecular Modeling) is here presented as a modular platform for rapid 3D sketching of molecular systems. It combines a Multi-Objective Genetic Algorithm with diverse molecular descriptors to overcome the difficulty of generating candidate models for systems with scarce structural data. Its grounds consist in transforming any molecular descriptor (i.e. those generally used for analysis of data) as a guiding objective for PES explorations. The platform is written in Python with flexibility in mind: the user can choose which descriptors to use for each problem and is even encouraged to code custom ones. Illustrative cases of its potential applications are included to demonstrate the flexibility of this approach, including metal coordination of multidentate ligands, peptide folding, and protein-ligand docking. GaudiMM is available free of charge from https://github.com/insilichem/gaudi. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autónoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Jordi Guasp
- Departament de Química, Universitat Autónoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Martí Municoy
- Departament de Química, Universitat Autónoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autónoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
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29
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Santos-Cancel M, White RJ. Collagen Membranes with Ribonuclease Inhibitors for Long-Term Stability of Electrochemical Aptamer-Based Sensors Employing RNA. Anal Chem 2017; 89:5598-5604. [PMID: 28440619 PMCID: PMC5653965 DOI: 10.1021/acs.analchem.7b00766] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Electrochemical aptamer-based (E-AB) sensors offer advantageous analytical detection abilities due to their rapid response time (seconds to minutes), specificity to a target, and selectivity to function in complex media. Ribonucleic acid (RNA) aptamers employed in this class of sensor offer favorable binding characteristics resulting from the ability of RNA to form stable tertiary folds aided by long-range intermolecular interactions. As a result, RNA aptamers can fold into three-dimensional structures more complex than those of their DNA counterparts and consequently exhibit better binding ability to target analytes. Unfortunately, RNA aptamers are susceptible to degradation by nucleases, and for this reason, RNA-based sensors are scarce or require significant sample pretreatment before use in clinically relevant media. Here, we combine the usefulness of a collagen I hydrogel membrane with entrapped ribonuclease inhibitors (RI) to protect small molecule RNA E-AB sensors from endogenous nucleases in complex media. More specifically, the biocompatibility of the naturally polymerized hydrogel with encapsulated RI promotes the protection of an aminoglycoside-binding RNA E-AB sensor up to 6 h, enabling full sensor function in nuclease-rich environments (undiluted serum) without the need for prior sample preparation or oligonucleotide modification. The use of collagen as a biocompatible membrane represents a general approach to compatibly interface E-AB sensors with complex biological samples.
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Affiliation(s)
- Mirelis Santos-Cancel
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland 21250
| | - Ryan J. White
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland 21250
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30
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Steentjes T, Sarkar S, Jonkheijm P, Lemay SG, Huskens J. Electron Transfer Mediated by Surface-Tethered Redox Groups in Nanofluidic Devices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1603268. [PMID: 27982518 DOI: 10.1002/smll.201603268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/11/2016] [Indexed: 06/06/2023]
Abstract
Electrochemistry provides a powerful sensor transduction and amplification mechanism that is highly suited for use in integrated, massively parallelized assays. Here, the cyclic voltammetric detection of flexible, linear poly(ethylene glycol) polymers is demonstrated, which have been functionalized with redox-active ferrocene (Fc) moieties and surface-tethered inside a nanofluidic device consisting of two microscale electrodes separated by a gap of <100 nm. Diffusion of the surface-bound polymer chains in the aqueous electrolyte allows the redox groups to repeatedly shuttle electrons from one electrode to the other, resulting in a greatly amplified steady-state electrical current. Variation of the polymer length provides control over the current, as the activity per Fc moiety appears to depend on the extent to which the polymer layers of the opposing electrodes can interpenetrate each other and thus exchange electrons. These results outline the design rules for sensing devices that are based on changing the polymer length, flexibility, and/or diffusivity by binding an analyte to the polymer chain. Such a nanofluidic enabled configuration provides an amplified and highly sensitive alternative to other electrochemical detection mechanisms.
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Affiliation(s)
- Tom Steentjes
- Molecular NanoFabrication, MESA + Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, The Netherlands
| | - Sahana Sarkar
- NanoIonics, MESA + Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, The Netherlands
| | - Pascal Jonkheijm
- Molecular NanoFabrication, MESA + Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, The Netherlands
| | - Serge G Lemay
- NanoIonics, MESA + Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular NanoFabrication, MESA + Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, The Netherlands
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31
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Lin CN, Ren ST, Ye LP, Chen CH, Zhan SZ. Synthesis and electrocatalytic properties of a nickel(II) complex supported by bis(diphenylphosphino)methane. INORG CHEM COMMUN 2016. [DOI: 10.1016/j.inoche.2016.04.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Schoukroun-Barnes LR, Macazo FC, Gutierrez B, Lottermoser J, Liu J, White RJ. Reagentless, Structure-Switching, Electrochemical Aptamer-Based Sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:163-81. [PMID: 27070185 PMCID: PMC5627773 DOI: 10.1146/annurev-anchem-071015-041446] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The development of structure-switching, electrochemical, aptamer-based sensors over the past ∼10 years has led to a variety of reagentless sensors capable of analytical detection in a range of sample matrices. The crux of this methodology is the coupling of target-induced conformation changes of a redox-labeled aptamer with electrochemical detection of the resulting altered charge transfer rate between the redox molecule and electrode surface. Using aptamer recognition expands the highly sensitive detection ability of electrochemistry to a range of previously inaccessible analytes. In this review, we focus on the methods of sensor fabrication and how sensor signaling is affected by fabrication parameters. We then discuss recent studies addressing the fundamentals of sensor signaling as well as quantitative characterization of the analytical performance of electrochemical aptamer-based sensors. Although the limits of detection of reported electrochemical aptamer-based sensors do not often reach that of gold-standard methods such as enzyme-linked immunosorbent assays, the operational convenience of the sensor platform enables exciting analytical applications that we address. Using illustrative examples, we highlight recent advances in the field that impact important areas of analytical chemistry. Finally, we discuss the challenges and prospects for this class of sensors.
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Affiliation(s)
- Lauren R Schoukroun-Barnes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Florika C Macazo
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Brenda Gutierrez
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Justine Lottermoser
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Juan Liu
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Ryan J White
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
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33
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Affiliation(s)
- Pradyumna S. Singh
- Intel
Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Serge G. Lemay
- MESA+
Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
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34
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Zaitouna AJ, Maben AJ, Lai RY. Incorporation of extra amino acids in peptide recognition probe to improve specificity and selectivity of an electrochemical peptide-based sensor. Anal Chim Acta 2015; 886:157-64. [PMID: 26320648 DOI: 10.1016/j.aca.2015.05.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
We investigated the effect of incorporating extra amino acids (AA) at the n-terminus of the thiolated and methylene blue-modified peptide probe on both specificity and selectivity of an electrochemical peptide-based (E-PB) HIV sensor. The addition of a flexible (SG)3 hexapeptide is, in particular, useful in improving sensor selectivity, whereas the addition of a highly hydrophilic (EK)3 hexapeptide has shown to be effective in enhancing sensor specificity. Overall, both E-PB sensors fabricated using peptide probes with the added AA (SG-EAA and EK-EAA) showed better specificity and selectivity, especially when compared to the sensor fabricated using a peptide probe without the extra AA (EAA). For example, the selectivity factor recorded in the 50% saliva was ∼2.5 for the EAA sensor, whereas the selectivity factor was 7.8 for both the SG-EAA and EK-EAA sensors. Other sensor properties such as the limit of detection and dynamic range were minimally affected by the addition of the six AA sequence. The limit of detection was 0.5 nM for the EAA sensor and 1 nM for both SG-EAA and EK-EAA sensors. The saturation target concentration was ∼200 nM for all three sensors. Unlike previously reported E-PB HIV sensors, the peptide probe functions as both the recognition element and antifouling passivating agent; this modification eliminates the need to include an additional antifouling diluent, which simplifies the sensor design and fabrication protocol.
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Affiliation(s)
- Anita J Zaitouna
- University of Nebraska-Lincoln, 651 Hamilton Hall, Lincoln, NE 68588-0304, USA
| | - Alex J Maben
- University of Nebraska-Lincoln, 651 Hamilton Hall, Lincoln, NE 68588-0304, USA
| | - Rebecca Y Lai
- University of Nebraska-Lincoln, 651 Hamilton Hall, Lincoln, NE 68588-0304, USA.
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35
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Macazo F, Karpel RL, White RJ. Monitoring cooperative binding using electrochemical DNA-based sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:868-75. [PMID: 25517392 PMCID: PMC4303326 DOI: 10.1021/la504083c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/15/2014] [Indexed: 05/20/2023]
Abstract
Electrochemical DNA-based (E-DNA) sensors are utilized to detect a variety of targets including complementary DNA, small molecules, and proteins. These sensors typically employ surface-bound single-stranded oligonucleotides that are modified with a redox-active molecule on the distal 3' terminus. Target-induced flexibility changes of the DNA probe alter the efficiency of electron transfer between the redox active methylene blue and the electrode surface, allowing for quantitative detection of target concentration. While numerous studies have utilized the specific and sensitive abilities of E-DNA sensors to quantify target concentration, no studies to date have demonstrated the ability of this class of collision-based sensors to elucidate biochemical-binding mechanisms such as cooperativity. In this study, we demonstrate that E-DNA sensors fabricated with various lengths of surface-bound oligodeoxythymidylate [(dT)n] sensing probes are able to quantitatively distinguish between cooperative and noncooperative binding of a single-stranded DNA-binding protein. Specifically, we demonstrate that oligo(dT) E-DNA sensors are able to quantitatively detect nM levels (50 nM-4 μM) of gene 32 protein (g32p). Furthermore, the sensors exhibit signal that is able to distinguish between the cooperative binding of the full-length g32p and the noncooperative binding of the core domain (*III) fragment to single-stranded DNA. Finally, we demonstrate that this binding is both probe-length- and ionic-strength-dependent. This study illustrates a new quantitative property of this powerful class of biosensor and represents a rapid and simple methodology for understanding protein-DNA binding mechanisms.
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Affiliation(s)
- Florika
C. Macazo
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Richard L. Karpel
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Ryan J. White
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
- E-mail:
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36
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Campos R, Kotlyar A, Ferapontova EE. DNA-mediated electron transfer in DNA duplexes tethered to gold electrodes via phosphorothioated dA tags. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:11853-11857. [PMID: 25267302 DOI: 10.1021/la502766g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The efficiency of DNA-based bioelectronic devices strongly depends on the way DNA molecules are linked to the electronic component. Commonly, DNA is tethered to metal electrodes via an alkanethiol linker representing an additional barrier for electron transport. Here we demonstrate that the replacement of the alkanethiol linker for a phosphorothioated adenosine tag increases the rate of DNA-mediated electron transfer (ET) up to 259 s(-1), representing the highest hitherto reported rate of electrochemically-modulated ET, and improves the stability of DNA-electrode surface binding. Both results offer pronounced technological and scientific benefits for DNA-based electronics.
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Affiliation(s)
- Rui Campos
- Interdisciplinary Nanoscience Center (iNANO) and ‡Center for DNA Nanotechnology (CDNA) at iNANO, Science and Technology, Aarhus University , Gustav Wieds Vej 14, 8000 Aarhus, Denmark
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37
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Wu Y, Lai RY. Effects of DNA Probe and Target Flexibility on the Performance of a “Signal-on” Electrochemical DNA Sensor. Anal Chem 2014; 86:8888-95. [DOI: 10.1021/ac5027226] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yao Wu
- 651 Hamilton Hall, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Rebecca Y. Lai
- 651 Hamilton Hall, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
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38
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Hu J, Yu Y, Brooks JC, Godwin LA, Somasundaram S, Torabinejad F, Kim J, Shannon C, Easley CJ. A reusable electrochemical proximity assay for highly selective, real-time protein quantitation in biological matrices. J Am Chem Soc 2014; 136:8467-74. [PMID: 24827871 PMCID: PMC4193296 DOI: 10.1021/ja503679q] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
Rapid
and specific quantitation of a variety of proteins over a
wide concentration range is highly desirable for biosensing at the
point-of-care, in clinical laboratories, and in research settings.
Our recently developed electrochemical proximity assay (ECPA) is a
target-flexible, DNA-directed, direct-readout protein quantitation
method with detection limits in the low femtomolar range, making it
particularly amenable to point-of-care detection. However, consistent
quantitation in more complex matrices is required at the point-of-care,
and improvements in measurement speed are needed for clinical and
research settings. Here, we address these concerns with a reusable
ECPA, where a gentle regeneration of the surface DNA monolayer (used
to capture the proximity complex) is achieved enzymatically through
a novel combination of molecular biology and electrochemistry. Strategically
placed uracils in the DNA sequence trigger selective cleavage of the
backbone, releasing the assembled proximity complex. This allows repeated
protein quantitation by square-wave voltammetry (SWV)—as quickly
as 3 min between runs. The process can be repeated up to 19 times
on a single electrode without loss of assay sensitivity, and currents
are shown to be highly repeatable with similar calibrations using
seven different electrodes. The utility of reusable ECPA is demonstrated
through two important applications in complex matrices: (1) direct,
quantitative monitoring of hormone secretion in real time from as
few as five murine pancreatic islets and (2) standard addition experiments
in unspiked serum for direct quantitation of insulin at clinically
relevant levels. Results from both applications distinguish ECPA as
an exceptional tool in protein quantitation.
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Affiliation(s)
- Jiaming Hu
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
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39
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Yu ZG, Zaitouna AJ, Lai RY. Effect of redox label tether length and flexibility on sensor performance of displacement-based electrochemical DNA sensors. Anal Chim Acta 2014; 812:176-83. [DOI: 10.1016/j.aca.2013.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/19/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
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