1
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Olivan LA, Hand K, White RJ. Utilization of Spontaneous Alkyne-Gold Self-Assembly Chemistry as an Alternative Method for Fabricating Electrochemical Aptamer-Based Sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:12117-12123. [PMID: 38826127 DOI: 10.1021/acs.langmuir.4c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Electrochemical aptamer-based (E-AB) sensors are a promising class of biosensors which use structure-switching redox-labeled oligonucleotides (aptamers) codeposited with passivating alkanethiol monolayers on electrode surfaces to specifically bind and detect target analytes. Signaling in E-AB sensors is an outcome of aptamer conformational changes upon target binding, with the sequence of the aptamer imparting specificity toward the analyte of interest. The change in conformation translates to a change in electron transfer between the redox label attached to the aptamer and the underlying electrode and is related to analyte concentration, allowing specific electrochemical detection of nonelectroactive analytes. E-AB sensor measurements are reagentless with time resolutions of seconds or less and may be miniaturized into the submicron range. Traditionally these sensors are fabricated using thiol-on-gold chemistry. Here we present an alternate immobilization chemistry, gold-alkyne binding, which results in an increase in sensor lifetimes under ideal conditions by up to ∼100%. We find that gold-alkyne binding is spontaneous and supports efficient E-AB sensor signaling with analytical performance characteristics similar to those of thiol generated monolayers. The surface modification differs from gold-thiol binding only in the time and aptamer concentration required to achieve similar aptamer surface coverages. In addition, alkynated aptamers differ from their thiolated analogues only by their chemical handle for surface attachment, so any existing aptamers can be easily adapted to utilize this attachment strategy.
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Affiliation(s)
- Lars Alexander Olivan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0171, United States
| | - Kaitlyn Hand
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0171, United States
| | - Ryan J White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0171, United States
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, Ohio 45221, United States
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2
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [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: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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3
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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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4
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Smiljanic M, Bleteau P, Papageorgiou A, Goffart N, Adam C, Doneux T. Introducing common oxazine fluorophores as new redox labels for electrochemical DNA sensors. Bioelectrochemistry 2024; 155:108582. [PMID: 37806117 DOI: 10.1016/j.bioelechem.2023.108582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/10/2023]
Abstract
The electrochemical properties of three oxazine fluorophores, ATTO655, ATTO680 and ATTO700 have been investigated at gold electrodes. They display a reversible or quasi-reversible voltammetric behaviour involving either a 2e-, 2H+ or a 2e-, 1H+ redox process depending on the pH, at a formal potential located in the stability range of thiolate self-assembled monolayers (E°' ≈ -0.33 V vs. Ag|AgCl|3M KCl at pH 7.2). The performance of ATTO655 as redox label for electrochemical nucleic acid sensing was evaluated in a typical E-DNA configuration. The redox label has no detrimental impact on the folding of DNA, as shown with the i-motif forming sequence investigated here. An electron transfer rate constant around 40 s-1 was determined, which is comparable to the values reported for the popular methylene blue label. Hybridisation experiments show a significant signal variation between ssDNA and dsDNA, though it is emphasised that the sign and amplitude of the variation are highly dependent on the electrochemical parameters such as the frequency in square wave voltammetry.
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Affiliation(s)
- Milutin Smiljanic
- Chemistry of Surfaces, Interfaces and Nanomaterials (ChemSIN), Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 2, CP 255, B-1050 Bruxelles, Belgium; Department of Materials Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Pierre Bleteau
- Chemistry of Surfaces, Interfaces and Nanomaterials (ChemSIN), Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 2, CP 255, B-1050 Bruxelles, Belgium; Université de Paris-Cité, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - Alexia Papageorgiou
- Chemistry of Surfaces, Interfaces and Nanomaterials (ChemSIN), Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 2, CP 255, B-1050 Bruxelles, Belgium
| | - Nathan Goffart
- Chemistry of Surfaces, Interfaces and Nanomaterials (ChemSIN), Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 2, CP 255, B-1050 Bruxelles, Belgium
| | - Catherine Adam
- Chemistry of Surfaces, Interfaces and Nanomaterials (ChemSIN), Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 2, CP 255, B-1050 Bruxelles, Belgium
| | - Thomas Doneux
- Chemistry of Surfaces, Interfaces and Nanomaterials (ChemSIN), Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 2, CP 255, B-1050 Bruxelles, Belgium.
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5
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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: 2] [Impact Index Per Article: 2.0] [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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6
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Li S, Coffinier Y, Lagadec C, Cleri F, Nishiguchi K, Fujiwara A, Kim SH, Clément N. Single-Cell Electrochemical Aptasensor Array. ACS Sens 2023; 8:2921-2926. [PMID: 37431846 DOI: 10.1021/acssensors.3c00570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Despite several demonstrations of electrochemical devices with limits of detection (LOD) of 1 cell/mL, the implementation of single-cell bioelectrochemical sensor arrays has remained elusive due to the challenges of scaling up. In this study, we show that the recently introduced nanopillar array technology combined with redox-labeled aptamers targeting epithelial cell adhesion molecule (EpCAM) is perfectly suited for such implementation. Combining nanopillar arrays with microwells determined for single cell trapping directly on the sensor surface, single target cells are successfully detected and analyzed. This first implementation of a single-cell electrochemical aptasensor array, based on Brownian-fluctuating redox species, opens new opportunities for large-scale implementation and statistical analysis of early cancer diagnosis and cancer therapy in clinical settings.
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Affiliation(s)
- Shuo Li
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo 4-6-1 Komaba, Meguro-ku 153-8505, Tokyo, Japan
| | - Yannick Coffinier
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincare, BP 60069, Villeneuve d'Ascq cedex 59652, France
| | - Chann Lagadec
- Univ. Lille, CNRS, Inserm, CHU Lille, Centre Oscar Lambret, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille F-59000, France
| | - Fabrizio Cleri
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincare, BP 60069, Villeneuve d'Ascq cedex 59652, France
| | - Katsuhiko Nishiguchi
- 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
| | - Soo Hyeon Kim
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo 4-6-1 Komaba, Meguro-ku 153-8505, Tokyo, Japan
| | - Nicolas Clément
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo 4-6-1 Komaba, Meguro-ku 153-8505, Tokyo, Japan
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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: 4] [Impact Index Per Article: 4.0] [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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Ma T, Grzȩdowski AJ, Doneux T, Bizzotto D. Redox-Controlled Energy Transfer Quenching of Fluorophore-Labeled DNA SAMs Enables In Situ Study of These Complex Electrochemical Interfaces. J Am Chem Soc 2022; 144:23428-23437. [PMID: 36516982 DOI: 10.1021/jacs.2c09474] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Interfaces modified by a molecular monolayer can be challenging to study, particularly in situ, requiring novel approaches. Coupling electrochemical and optical approaches can be useful when signals are correlated. Here we detail a methodology that uses redox electrochemistry to control surface-based fluorescence intensity for detecting DNA hybridization and studying the uniformity of the surface response. A mixed composition single-strand DNA SAM was prepared using potential-assisted thiol exchange with two alkylthiol-modified ssDNAs that were either labeled with a fluorophore (AlexaFluor488) or a methylene blue (MB) redox tag. A significant change in fluorescence was observed when reducing MB to colorless leuco-MB. In situ fluorescence microscopy on a single-crystal gold bead electrode showed that fluorescence intensity depended on (1) the potential controlling the oxidation state of MB, (2) the surface density of DNA, (3) the MB:AlexFluor488 ratio in the DNA SAM, and (4) the local environment around the DNA SAM. MB efficiently quenched AlexaFluor488 fluorescence. Reduction of MB showed a significant increase in fluorescence resulting from a decrease in quenching or energy transfer efficiency. Hybridization of DNA SAMs with its unlabeled complement showed a large increase in fluorescence due to MB reduction for surfaces with sufficient DNA coverage. Comparing electrochemical-fluorescence measurements to electrochemical (SWV) measurements showed an improvement in detection of a small fraction of hybridized DNA SAM for surfaces with optimal DNA SAM composition and coverage. Additionally, this coupled electrochemical redox-fluorescence microscopy method can measure the spatial heterogeneity of electron-transfer kinetics and the influence of the local interfacial environment.
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Affiliation(s)
- Tianxiao Ma
- AMPEL and Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, CanadaV6T1Z4
| | - Adrian Jan Grzȩdowski
- AMPEL and Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, CanadaV6T1Z4
| | - Thomas Doneux
- Chemistry of Surfaces, Interfaces and Nanomaterials (ChemSIN), Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe 2, CP 255, B-1050Bruxelles, Belgium
| | - Dan Bizzotto
- AMPEL and Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, CanadaV6T1Z4
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9
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Zhou H, Lin H, Wang Q, Hao T, Hu Y, Wang S, Guo Z. Tunneling or Hopping? A Direct Electrochemical Observation of Electron Transfer in DNA. Anal Chem 2022; 94:15324-15331. [DOI: 10.1021/acs.analchem.2c02794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huiqian Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, PR China
| | - Han Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, PR China
| | - Qi Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, PR China
| | - Tingting Hao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, PR China
| | - Yufang Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, PR China
| | - Sui Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, PR China
| | - Zhiyong Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Material Science and Chemical Engineering, Ningbo University, Ningbo315211, PR China
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10
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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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11
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Zhang Y, Zhao C, Zhang H, Lu Q, Zhou J, Liu R, Wang S, Pu Y, Yin L. Trans-generational effects of copper on nerve damage in Caenorhabditis elegans. CHEMOSPHERE 2021; 284:131324. [PMID: 34225113 DOI: 10.1016/j.chemosphere.2021.131324] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 05/15/2023]
Abstract
The potential toxicity of copper has received great attention for a long time, however, trans-generational effects of copper have not been extensively investigated. Caenorhabditis elegans (C. elegans) was used to evaluate the trans-generational toxicities of copper several physiological endpoints: growth, head thrashes and body bends and degree of neuronal damage. Copper significantly inhibited growth, body bends, head thrashes and caused degeneration of dopaminergic neurons in a concentration-dependent manner in parental worms. Further we found oxidative damage was to underlying the onset of neuron degeneration. In our study copper promoted ROS accumulation, and led to an increased expression of the oxidative stress response-related genes sod-3 and a decreased expression of metal detoxification genes mtl-1 and mtl-2. Moreover, copper increased the fluorescence intensity of the transgenic strain that encodes the antioxidant enzyme SOD-3. Gradually decline in copper-induced impairments were observed in the filial generations without exposure. No growth impairment was shown in F3, the trend of head thrashes recovery gradually appeared in F2 and no growth impairment was shown in F3, the body bends impairment caused by the parental copper exposure was recovery until F4 and no growth impairment was shown in F5. Besides, dopamine neurons revealed damage related to neurobehavioral endpoints, with hereditary effects in the progeny together. In addition, sequencing results suggested that copper exposure could cause epigenetic changes. QRT-PCR results showed that differentially expressed genes can also be passed on to offspring.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Chao Zhao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Hu Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Qiang Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Jingjing Zhou
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
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12
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Skiba J, Kowalczyk A, Trzybiński D, Woźniak K, Vrček V, Gapińska M, Kowalski K. Stereo‐Defined Ferrocenyl Glycol Nucleic Acid (Fc‐GNA) Constituents: Synthesis, Electrochemistry, Mechanism of Formation, and Anticancer Activity Studies. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Joanna Skiba
- Faculty of Chemistry Department of Organic Chemistry University of Łódź Tamka 12 91-403 Łódź Poland
| | - Aleksandra Kowalczyk
- Department of Molecular Microbiology Institute of Microbiology Biotechnology and Immunology Faculty of Biology and Environmental Protection University of Łódź Banacha 12/16 90-237 Łódź Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre Department of Chemistry University of Warsaw Żwirki i Wigury 101 02-089 Warszawa Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre Department of Chemistry University of Warsaw Żwirki i Wigury 101 02-089 Warszawa Poland
| | - Valerije Vrček
- Faculty of Pharmacy and Biochemistry University of Zagreb Ante Kovačića 1 10000 Zagreb Croatia
| | - Magdalena Gapińska
- Laboratory of Microscopic Imaging and Specialized Biological Techniques Faculty of Biology and Environmental Protection,/> University of Łódź Banacha 12/16 90-237 Łódź Poland
| | - Konrad Kowalski
- Faculty of Chemistry Department of Organic Chemistry University of Łódź Tamka 12 91-403 Łódź Poland
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13
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Su S, Ma J, Xu Y, Pan H, Zhu D, Chao J, Weng L, Wang L. Electrochemical Analysis of Target-Induced Hairpin-Mediated Aptamer Sensors. ACS APPLIED MATERIALS & INTERFACES 2020; 12:48133-48139. [PMID: 32955243 DOI: 10.1021/acsami.0c12897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The state of probe DNA at the biosensing interface greatly affects the detection performance of electrochemical DNA biosensors. Herein, we constructed a target-induced hairpin-mediated biosensing interface to study the effect of probe DNA on the analytical performance of adenosine triphosphate aptamer (ATPA) and adenosine triphosphate (ATP) detection. Moreover, we also explored the electrochemical contribution of the coexisting hairpin and double-stranded DNA (dsDNA) to this sensing interface. Experimental results suggested that the molecular recognition ability and detection performance of the biosensing interface were majorly dependent on the surface density of methylene blue (MB)-labeled probe hairpin DNA and partly affected by the spatial state of the formed dsDNA. When the surface density of hairpin DNA was moderate (5.72 pmol cm-2), this sensing interface determined as low as 0.74 fM ATPA and 5.04 pM ATP with high selectivity and excellent regeneration, respectively. Furthermore, we calculated that the formed dsDNA had a 31.87% contribution in the total electrochemical signal for 10 pM ATPA detection. Based on the above results, we designed an XOR logic gate based on the biosensing interface for ATPA and ATP detection.
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Affiliation(s)
- Shao Su
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jianfeng Ma
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yongqiang Xu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Hemeng Pan
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Dan Zhu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lixing Weng
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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14
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Piotrowicz M, Kowalczyk A, Trzybiński D, Woźniak K, Kowalski K. Redox-Active Glycol Nucleic Acid (GNA) Components: Synthesis and Properties of the Ferrocenyl-GNA Nucleoside, Phosphoramidite, and Semicanonical Dinucleoside Phosphate. Organometallics 2020. [DOI: 10.1021/acs.organomet.9b00851] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michał Piotrowicz
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland
| | - Aleksandra Kowalczyk
- Faculty of Biology and Environmental Protection, Department of Microbial Genetics, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Damian Trzybiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Konrad Kowalski
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland
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15
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Ferapontova EE. Electron Transfer in DNA at Electrified Interfaces. Chem Asian J 2019; 14:3773-3781. [PMID: 31545875 DOI: 10.1002/asia.201901024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/22/2019] [Indexed: 12/24/2022]
Abstract
The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, 8000, Aarhus C, Denmark
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16
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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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17
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Electrocatalysis of ferricyanide reduction mediated by electron transfer through the DNA duplex: Kinetic analysis by thin layer voltammetry. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.06.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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18
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Kamal A, Sharma R, She Z, Kraatz HB. Hg(ii) interactions with T-rich regions in oligonucleotides: effects of positional variations on the electrochemical properties. Analyst 2019; 143:2844-2850. [PMID: 29786706 DOI: 10.1039/c8an00232k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hg(ii) binding to thymine-rich oligonucleotides (ODNs) is investigated electrochemically. The focus of this study is to probe the effects of position on the electrochemical response. For this purpose, three oligonucleotides were investigated in which the position of a hexa-thymine repeat is varied within a surface-supported oligonucleotide. The hexa repeats were placed in the top, middle, and bottom positions within the strand with respect to the gold surface. The effects were monitored by electrochemical impedance spectroscopy and scanning electrochemical microscopy. Using charge transfer resistance (RCT) and tip current (I) as a measure, it was possible to monitor the effects of Hg(ii) binding to the ds-oligonucleotide. The extent of film resistance reduces as the T-rich region moves from the bottom to top position within the film. The T-rich region closer to the gold surface probably builds less flexible and more rigid T-Hg(ii)-T basepairs compared to the other two positions and is expected to stay in the upright orientation on the surface. This in turn results in significant differences in the electrochemical readout, demonstrating that the position of T-rich sequences within an oligonucleotide strand matters.
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Affiliation(s)
- Ajar Kamal
- Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto M1C 1A4, Canada
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19
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Dauphin-Ducharme P, Arroyo-Currás N, Plaxco KW. High-Precision Electrochemical Measurements of the Guanine-, Mismatch-, and Length-Dependence of Electron Transfer from Electrode-Bound DNA Are Consistent with a Contact-Mediated Mechanism. J Am Chem Soc 2019; 141:1304-1311. [PMID: 30605323 DOI: 10.1021/jacs.8b11341] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Despite 25 years' effort, serious questions remain regarding the mechanism(s) underlying electron transfer through (or from) electrode-bound double-stranded DNA. In part this is because a control experiment regarding the putatively critical role of guanine bases in the most widely proposed transport mechanism (hopping from guanine to guanine through the π-stack) appears to be lacking from the prior literature. In response, we have employed chronoamperometry, which allows for high-precision determination of electron transfer rates, to characterize transfer to a redox reporter appended onto electrode-bound DNA duplexes. Specifically, we have measured the effects of guanines and base mismatches on the electron transfer rate associated with such constructs. Upon doing so, we find that, counter to prior reports, the transfer rate is, to within relatively tight experimental confidence intervals, unaffected by either. Parallel studies of the dependence of the electron transfer rate on the length of the DNA suggest that transfer from this system obeys a "collision" mechanism in which the redox reporter physically contacts the electrode surface prior to the exchange of electrons.
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Affiliation(s)
- Philippe Dauphin-Ducharme
- Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry , University of California Santa Barbara , Santa Barbara , California 93106 , United States.,Center for Bioengineering , University of California Santa Barbara , Santa Barbara , California 93106 , United States
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20
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Kékedy-Nagy L, Ferapontova EE. Sequence-Specific Electron Transfer Mediated by DNA Duplexes Attached to Gold through the Alkanethiol Linker. J Phys Chem B 2018; 122:10077-10085. [DOI: 10.1021/acs.jpcb.8b07505] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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21
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Silva SM, Hoque S, Gonçales VR, Gooding JJ. The Impact of the Position of the Redox Label on Charge Transfer and Hybridization Efficiency at DNA Interfaces. ELECTROANAL 2018. [DOI: 10.1002/elan.201800197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Saimon Moraes Silva
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
| | - Sharmin Hoque
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
| | - Vinicius R. Gonçales
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
| | - J. Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
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22
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On possible role of DNA electrodynamics in chromatin regulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 134:50-54. [DOI: 10.1016/j.pbiomolbio.2017.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/23/2022]
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23
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Bizzotto D, Burgess IJ, Doneux T, Sagara T, Yu HZ. Beyond Simple Cartoons: Challenges in Characterizing Electrochemical Biosensor Interfaces. ACS Sens 2018; 3:5-12. [PMID: 29282982 DOI: 10.1021/acssensors.7b00840] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Design and development of surface-based biosensors is challenging given the multidisciplinary nature of this enterprise, which is certainly the case for electrochemical biosensors. Self-assembly approaches are used to modify the surface with capture probes along with electrochemical methods for detection. Complex surface structures are created to improve the probe-target interaction. These multicomponent surface structures are usually idealized in schematic representations. Many rely on the analytical performance of the sensor surface as an indication of the quality of the surface modification strategy. While directly linked to the eventual device, arguments for pursuing a more extensive characterization of the molecular environments at the surface are presented as a path to understanding how to make electrochemical sensors that are more robust, reliable with improved sensitivity. This is a complex task that is most often accomplished using methods that only report the average characteristics of the surface. Less often applied are methods that are sensitive to the probe (or adsorbate) present in nonideal configurations (e.g., aggregates, clusters, nonspecifically adsorbed). Though these structures may compose a small fraction of the overall modified surface, they have an uncertain impact on sensor performance and reliability. Addressing this issue requires application of imaging methods over a variety of length scales (e.g., optical microscopy and/or scanning probe microscopy) that provide valuable insight into the diversity of surface structures and molecular environments present at the sensing interface. Furthermore, using in situ analytical methods, while complex, can be more relevant to the sensing environment. Reliable measurements of the nature and extent of these features are required to assess the impact of these nonideal configurations on the sensing process. The development and use of methods that can characterize complex surface based biosensors is arguably required, highlighting the need for a multidisciplinary approach toward the preparation and analysis of the biosensor surface. In many ways, representing the surface without reliance on overly simplified cartoons will highlight these important considerations for improving sensor characteristics.
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Affiliation(s)
- Dan Bizzotto
- Department
of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ian J. Burgess
- Department
of Chemistry, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada
| | - Thomas Doneux
- Chimie
Analytique et Chimie des Interfaces, Faculté des Sciences, Université libre de Bruxelles (ULB), 1050 Bruxelles, Belgium
| | - Takamasa Sagara
- Division
of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, Nagasaki, Nagasaki 852-8131, Japan
| | - Hua-Zhong Yu
- Department
of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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24
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Steentjes T, Jonkheijm P, Huskens J. Electron Transfer Processes in Ferrocene-Modified Poly(ethylene glycol) Monolayers on Electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11878-11883. [PMID: 28977744 PMCID: PMC5677253 DOI: 10.1021/acs.langmuir.7b02160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Electrochemistry is a powerful tool to study self-assembled monolayers. Here, we modified cystamine-functionalized electrodes with different lengths of linear poly(ethylene glycol) (PEG) polymers end-functionalized with a redox-active ferrocene (Fc) group. The electron transport properties of the Fc probes were studied using cyclic voltammetry. The Fc moiety attached to the shortest PEG (Mn = 250 Da) behaved as a surface-confined species, and the homogeneous electron transfer rate constants were determined. The electron transfer of the ferrocene group on the longer PEGs (Mn = 3.4, 5, and 10 kDa) was shown to be driven by diffusion. For low surface densities, where the polymer exists in the mushroom conformation, the diffusion coefficients (D) and rate constants were increasing with polymer length. In the loose brush conformation, where the polymers are close enough to interact with each other, the thickness of the layers (e) was unknown and a parameter D1/2/e was determined. This parameter showed no dependence on surface density and an increase with polymer length.
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25
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Abstract
A number of electrochemical DNA sensors based on the target-induced change in the conformation and/or flexibility of surface-bound oligonucleotides have been developed in recent years. These sensors, which are often termed E-DNA sensors, are comprised of an oligonucleotide probe modified with a redox label (e.g., methylene blue) at one terminus and attached to a gold electrode via a thiol-gold bond at the other. Binding of the target to the DNA probe changes its structure and dynamics, which, in turn, influences the efficiency of electron transfer to the interrogating electrode. Since electrochemically active contaminants are less common, these sensors are resistant to false-positive signals arising from the nonspecific adsorption of contaminants and perform well even when employed directly in serum, whole blood, and other realistically complex sample matrices. Moreover, because all of the sensor components are chemisorbed to the electrode, the E-DNA sensors are essentially label-free and readily reusable. To date, these sensors have achieved state-of-the-art sensitivity, while offering the unprecedented selectivity, reusability, and the operational convenience of direct electrochemical detection. This chapter reviews the recent advances in the development of both "signal-off" and "signal-on" E-DNA sensors. Critical aspects that dictate the stability and performance of these sensors are also addressed so as to provide a realistic overview of this oligonucleotide detection platform.
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Affiliation(s)
- Rebecca Y Lai
- University of Nebraska-Lincoln, Lincoln, NE, United States.
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26
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Álvarez-Martos I, Kartashov A, Ferapontova EE. Electron Transfer in Methylene-Blue-Labeled G3 Dendrimers Tethered to Gold. ChemElectroChem 2016. [DOI: 10.1002/celc.201600417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Isabel Álvarez-Martos
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
| | - Andrey Kartashov
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
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27
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Ferapontova EE. Hybridization Biosensors Relying on Electrical Properties of Nucleic Acids. ELECTROANAL 2016. [DOI: 10.1002/elan.201600593] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO); Center for DNA Nanotechnology (CDNA); Aarhus University; Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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28
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Wardrip AG, Mazaheripour A, Hüsken N, Jocson J, Bartlett A, Lopez RC, Frey N, Markegard CB, Kladnik G, Cossaro A, Floreano L, Verdini A, Burke AM, Dickson MN, Kymissis I, Cvetko D, Morgante A, Sharifzadeh S, Nguyen HD, Gorodetsky AA. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angew Chem Int Ed Engl 2016; 55:14267-14271. [DOI: 10.1002/anie.201605411] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/14/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Austin G. Wardrip
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Nina Hüsken
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Robert C. Lopez
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Nathan Frey
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Cade B. Markegard
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Gregor Kladnik
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
| | | | | | | | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Ioannis Kymissis
- Department of Electrical Engineering Columbia University New York NY 10027 USA
| | - Dean Cvetko
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
- Institut J. Stefan Jamova 39 1000 Ljubljana Slovenia
| | - Alberto Morgante
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Department of Physics University of Trieste Trieste 34128 Italy
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Alon A. Gorodetsky
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
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29
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Wardrip AG, Mazaheripour A, Hüsken N, Jocson J, Bartlett A, Lopez RC, Frey N, Markegard CB, Kladnik G, Cossaro A, Floreano L, Verdini A, Burke AM, Dickson MN, Kymissis I, Cvetko D, Morgante A, Sharifzadeh S, Nguyen HD, Gorodetsky AA. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Austin G. Wardrip
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Nina Hüsken
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Robert C. Lopez
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Nathan Frey
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Cade B. Markegard
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Gregor Kladnik
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
| | | | | | | | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Ioannis Kymissis
- Department of Electrical Engineering Columbia University New York NY 10027 USA
| | - Dean Cvetko
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
- Institut J. Stefan Jamova 39 1000 Ljubljana Slovenia
| | - Alberto Morgante
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Department of Physics University of Trieste Trieste 34128 Italy
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Alon A. Gorodetsky
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
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30
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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: 127] [Impact Index Per Article: 15.9] [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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31
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Longo E, Wright K, Caruso M, Gatto E, Palleschi A, Scarselli M, De Crescenzi M, Crisma M, Formaggio F, Toniolo C, Venanzi M. Peptide flatlandia: a new-concept peptide for positioning of electroactive probes in proximity to a metal surface. NANOSCALE 2015; 7:15495-15506. [PMID: 26274368 DOI: 10.1039/c5nr03549j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A helical hexapeptide was designed to link in a rigid parallel orientation to a gold surface. The peptide sequence of the newly synthesized compound is characterized by the presence of two 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) residues (positions 1 and 4) to promote a bidentate interaction with the gold surface, two L-Ala residues (positions 2 and 5) and two-aminoisobutyric acid (Aib) residues (positions 3 and 6) to favor a high population of the 310-helix conformation. Furthermore, a ferrocenoyl (Fc) probe was inserted at the N-terminus to investigate the electronic conduction properties of the peptide. X-Ray photoelectron spectroscopy and scanning tunneling microscopy techniques were used to characterize the binding of the peptide to the gold surface and the morphology of the peptide layer, respectively. Several electrochemical (cyclic voltammetry, chronoamperometry, square wave voltammetry) techniques were applied to analyze the electrochemical activity of the Fc probe, along with the influence of the peptide 3D-structure and the peptide layer morphology on electron transfer processes.
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Affiliation(s)
- Edoardo Longo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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32
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Aoki H. Electrochemical Label-Free Nucleotide Sensors. Chem Asian J 2015; 10:2560-73. [PMID: 26227073 DOI: 10.1002/asia.201500449] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/20/2015] [Indexed: 11/10/2022]
Abstract
Numerous researchers have devoted a great deal of effort over the last few decades to the development of electrochemical oligonucleotide detection techniques, owing to their advantages of simple design, inherently small dimensions, and low power requirements. Their simplicity and rapidity of detection makes label-free oligonucleotide sensors of great potential use as first-aid screening tools in the analytical field of environmental measurements and healthcare management. This review article covers label-free oligonucleotide sensors, focusing specifically on topical electrochemical techniques, including intrinsic redox reaction of bases, conductive polymers, the use of electrochemical indicators, and highly ordered probe structures.
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Affiliation(s)
- Hiroshi Aoki
- Environmental Management Research Institute, National Institute of Advanced Industrial, Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
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33
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Das P, Zafar S. Mechanistic Influence of Nanometer Length-Scale Surface Chemistry on DNA Hybridization. ACS NANO 2015; 9:7466-7478. [PMID: 26051361 DOI: 10.1021/acsnano.5b02530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hybridization of surface-immobilized oligonucleotides to their complementary counterparts is central to the rational design of novel nanodevices and DNA sensors. In this study, we have adopted a unified approach of combining sensing experiments with molecular dynamics simulations to characterize the hybridization of a 23 nucleotide long single-strand probe DNA tethered to a gold surface. Experiments indicate significant conformational changes of DNA in close vicinity (∼1 nm) of the gold surface upon hybridization and also conformational heterogeneity within hybridized DNA, consistent with simulation results. Simulations show that the conformational heterogeneity on a gold surface arises due to stabilization of surface-adsorbed partial and full duplexes, resulting in impeded hybridization in comparison to what observed on a repulsive surface. Furthermore, these simulations indicate that hybridization could be improved by tuning the nonspecific adsorption on a nanopatterned surface with an optimal patterning length. Simulations were performed on the probe tethered to gold nanodots of varying (2-8 nm) diameter. An improved hybridization of the present probe sequence was only observed for the 6 nm gold dots patterned on a repulsive surface. Results reveal that the 2D nanoconfinement provided by the 6 nm gold dot is optimal for reducing conformational heterogeneity for the specific sequence used in this study. Thus, improved DNA hybridization can be achieved on a gold nanodot patterned repulsive surface, where the optimal dot diameter will depend on the probe length and sequence. In summary, this study provides mechanistic insights onto hybridization on gold and offers a unique method toward improved hybridization on a nanopatterned surface with an optimized patterning length.
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Affiliation(s)
| | - Sufi Zafar
- ‡IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
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34
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Chiba J, Aoki S, Yamamoto J, Iwai S, Inouye M. Deformable nature of various damaged DNA duplexes estimated by an electrochemical analysis on electrodes. Chem Commun (Camb) 2015; 50:11126-8. [PMID: 25105179 DOI: 10.1039/c4cc04513k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We report bending flexibility of damaged duplexes possessing an apurinic/apyrimidinic (AP) site analogue, a cyclobutane pyrimidine dimer (CPD), and a pyrimidine(6-4)pyrimidone photoproduct (6-4PP). Based on the electrochemical evaluation on electrodes, the duplex flexibilities of the lesions increased in the following order: CPD < AP < 6-4PP. We discussed the possibility that the emerging local flexibility might be a good sign for UV-damaged DNA-binding proteins on duplexes.
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Affiliation(s)
- J Chiba
- Graduate School of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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35
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Steuwe C, Erdelyi M, Szekeres G, Csete M, Baumberg JJ, Mahajan S, Kaminski CF. Visualizing electromagnetic fields at the nanoscale by single molecule localization. NANO LETTERS 2015; 15:3217-3223. [PMID: 25915093 DOI: 10.1021/acs.nanolett.5b00405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Coupling of light to the free electrons at metallic surfaces allows the confinement of electric fields to subwavelength dimensions, far below the optical diffraction limit. While this is routinely used to manipulate light at the nanoscale, in electro-optic devices and enhanced spectroscopic techniques, no characterization technique for imaging the underlying nanoscopic electromagnetic fields exists, which does not perturb the field or employ complex electron beam imaging. Here, we demonstrate the direct visualization of electromagnetic fields on patterned metallic substrates at nanometer resolution, exploiting a strong "autonomous" fluorescence-blinking behavior of single molecules within the confined fields allowing their localization. Use of DNA-constructs for precise positioning of fluorescence dyes on the surface induces this distance-dependent autonomous blinking thus completely obviating the need for exogenous agents or switching methods. Mapping such electromagnetic field distributions at nanometer resolution aids the rational design of nanometals for diverse photonic applications.
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Affiliation(s)
- Christian Steuwe
- †Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA, U.K
- ‡Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Miklos Erdelyi
- †Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA, U.K
| | - G Szekeres
- §Department of Optics and Quantum Electronics, University of Szeged, H-6720 Szeged, Dóm tér 9, Hungary
| | - M Csete
- §Department of Optics and Quantum Electronics, University of Szeged, H-6720 Szeged, Dóm tér 9, Hungary
| | - Jeremy J Baumberg
- ‡Nanophotonics Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Sumeet Mahajan
- ∥Institute for Life Sciences and Department of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K
| | - Clemens F Kaminski
- †Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA, U.K
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Zamfir LG, Fortgang P, Farre C, Ripert M, De Crozals G, Jaffrezic-Renault N, Bala C, Temple-Boyer P, Chaix C. Synthesis and electroactivated addressing of ferrocenyl and azido-modified stem-loop oligonucleotides on an integrated electrochemical device. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.02.167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Tavallaie R, Darwish N, Brynn Hibbert D, Justin Gooding J. Nucleic-acid recognition interfaces: how the greater ability of RNA duplexes to bend towards the surface influences electrochemical sensor performance. Chem Commun (Camb) 2015; 51:16526-9. [DOI: 10.1039/c5cc05450h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Faster electron transfer kinetics were observed for redox labelled nucleic-acids duplexes containing RNA, suggesting a more flexibility, compared to DNA/DNA.
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Affiliation(s)
- Roya Tavallaie
- School of Chemistry
- The University of New South Wales
- Sydney
- Australia
- Australian Centre for NanoMedicine
| | - Nadim Darwish
- School of Chemistry
- The University of New South Wales
- Sydney
- Australia
| | - D. Brynn Hibbert
- School of Chemistry
- The University of New South Wales
- Sydney
- Australia
| | - J. Justin Gooding
- School of Chemistry
- The University of New South Wales
- Sydney
- Australia
- Australian Centre for NanoMedicine
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38
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Tymoczko J, Schuhmann W, Gebala M. Electrical potential-assisted DNA hybridization. How to mitigate electrostatics for surface DNA hybridization. ACS APPLIED MATERIALS & INTERFACES 2014; 6:21851-21858. [PMID: 25102381 DOI: 10.1021/am5027902] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Surface-confined DNA hybridization reactions are sensitive to the number and identity of DNA capture probes and experimental conditions such as the nature and the ionic strength of the electrolyte solution. When the surface probe density is high or the concentration of bulk ions is much lower than the concentration of ions within the DNA layer, hybridization is significantly slowed down or does not proceed at all. However, high-density DNA monolayers are attractive for designing high-sensitivity DNA sensors. Thus, circumventing sluggish DNA hybridization on such interfaces allows a high surface concentration of target DNA and improved signal/noise ratio. We present potential-assisted hybridization as a strategy in which an external voltage is applied to the ssDNA-modified interface during the hybridization process. Results show that a significant enhancement of hybridization can be achieved using this approach.
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Affiliation(s)
- Jakub Tymoczko
- Analytical Chemistry, Center for Electrochemical Sciences (CES), Ruhr-Universität Bochum , Universitätsstrasse 150, 44780 Bochum, Germany
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39
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Su Q, Wesner D, Schönherr H, Nöll G. Molecular beacon modified sensor chips for oligonucleotide detection with optical readout. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:14360-14367. [PMID: 25363421 DOI: 10.1021/la504105x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Three different surface bound molecular beacons (MBs) were investigated using surface plasmon fluorescence spectroscopy (SPFS) as an optical readout technique. While MB1 and MB2, both consisting of 36 bases, differed only in the length of the linker for surface attachment, the significantly longer MB3, consisting of 56 bases, comprised an entirely different sequence. For sensor chip preparation, the MBs were chemisorbed on gold via thiol anchors together with different thiol spacers. The influence of important parameters, such as the length of the MBs, the length of the linker between the MBs and the gold surface, the length and nature of the thiol spacers, and the ratio between the MBs and the thiol spacers was studied. After hybridization with the target, the fluorophore of the longer MB3 was oriented close to the surface, and the shorter MBs were standing more or less upright, leading to a larger increase in fluorescence intensity. Fluorescence microscopy revealed a homogeneous distribution of the MBs on the surface. The sensor chips could be used for simple and fast detection of target molecules with a limit of detection in the larger picomolar range. The response time was between 5 and 20 min. Furthermore, it was possible to distinguish between fully complementary and singly mismatched targets. While rinsing with buffer solution after hybridization with target did not result in any signal decrease, complete dehybridization could be carried out by intense rinsing with pure water. The MB modified sensor chips could be prepared in a repeatable manner and reused many times without significant decrease in performance.
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Affiliation(s)
- Qiang Su
- Nöll Junior Research Group, Organic Chemistry, Department of Chemistry and Biology, Faculty IV, Siegen University , Adolf-Reichwein-Strasse 2, 57068 Siegen, Germany
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40
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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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41
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Tang Y, Ge B, Sen D, Yu HZ. Functional DNA switches: rational design and electrochemical signaling. Chem Soc Rev 2014; 43:518-29. [PMID: 24169924 DOI: 10.1039/c3cs60264h] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent developments in nanoscience research have demonstrated that DNA switches (rationally designed DNA nanostructures) constitute a class of versatile building blocks for the fabrication and assembly of electronic devices and sensors at the nanoscale. Functional DNA sequences and structures such as aptamers, DNAzymes, G-quadruplexes, and i-motifs can be readily prepared in vitro, and subsequently adapted to an electrochemical platform by coupling with redox reporters. The conformational or conduction switching of such electrode-bound DNA modules in response to an external stimulus can then be monitored by conventional voltammetric measurements. In this review, we describe how we are able to design and examine functional DNA switches, particularly those systems that utilize electrochemical signaling. We also discuss different available options for labeling functional DNA with redox reporters, and comment on the function-oriented signaling pathways.
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Affiliation(s)
- Yiting Tang
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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42
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Abi A, Lin M, Pei H, Fan C, Ferapontova EE, Zuo X. Electrochemical switching with 3D DNA tetrahedral nanostructures self-assembled at gold electrodes. ACS APPLIED MATERIALS & INTERFACES 2014; 6:8928-8931. [PMID: 24802004 DOI: 10.1021/am501823q] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanomechanical switching of functional three-dimensional (3D) DNA nanostructures is crucial for nanobiotechnological applications such as nanorobotics or self-regulating sensor and actuator devices. Here, DNA tetrahedral nanostructures self-assembled onto gold electrodes were shown to undergo the electronically addressable nanoswitching due to their mechanical reconfiguration upon external chemical stimuli. That enables construction of robust surface-tethered electronic nanodevices based on 3D DNA tetrahedra. One edge of the tetrahedron contained a partially self-complementary region with a stem-loop hairpin structure, reconfigurable upon hybridization to a complementary DNA (stimulus DNA) sequence. A non-intercalative ferrocene (Fc) redox label was attached to the reconfigurable tetrahedron edge in such a way that reconfiguration of this edge changed the distance between the electrode and Fc.
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Affiliation(s)
- Alireza Abi
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, ‡Center for DNA Nanotechnology (CDNA) at iNANO, and §Sino-Danish Centre for Education and Research (SDC) at iNANO, Aarhus University , Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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43
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Yin X, Wierzbinski E, Lu H, Bezer S, de Leon AR, Davis KL, Achim C, Waldeck DH. A three-step kinetic model for electrochemical charge transfer in the hopping regime. J Phys Chem A 2014; 118:7579-89. [PMID: 24813905 DOI: 10.1021/jp502826e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-step nonadiabatic electron tunneling models are widely used to analyze electrochemical rates through self-assembled monolayer films (SAMs). For some systems, such as nucleic acids, long-range charge transfer can occur in a "hopping" regime that involves multiple charge transfer events and intermediate states. This report describes a three-step kinetic scheme to model charge transfer in this regime. Some of the features of the three-step model are probed experimentally by changing the chemical composition of the SAM. This work uses the three-step model and a temperature dependence of the charge transfer rate to extract the charge injection barrier for a SAM composed of a 10-mer peptide nucleic acid that operates in the hopping regime.
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Affiliation(s)
- Xing Yin
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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44
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Duprey JLHA, Tucker JHR. Metal–Carbon Bonds in Biopolymer Conjugates: Bioorganometallic Nucleic Acid Chemistry. CHEM LETT 2014. [DOI: 10.1246/cl.131019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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45
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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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46
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Langer A, Kaiser W, Svejda M, Schwertler P, Rant U. Molecular Dynamics of DNA–Protein Conjugates on Electrified Surfaces: Solutions to the Drift-Diffusion Equation. J Phys Chem B 2014; 118:597-607. [DOI: 10.1021/jp410640z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- A. Langer
- Walter Schottky Institute and Chemistry Department, Technische Universität München, 85748 Garching, Germany
- Dynamic
Biosensors
GmbH, 82152 Munich, Germany
| | - W. Kaiser
- Walter Schottky Institute and Chemistry Department, Technische Universität München, 85748 Garching, Germany
- Dynamic
Biosensors
GmbH, 82152 Munich, Germany
| | - M. Svejda
- Walter Schottky Institute and Chemistry Department, Technische Universität München, 85748 Garching, Germany
| | - P. Schwertler
- Walter Schottky Institute and Chemistry Department, Technische Universität München, 85748 Garching, Germany
| | - U. Rant
- Walter Schottky Institute and Chemistry Department, Technische Universität München, 85748 Garching, Germany
- Dynamic
Biosensors
GmbH, 82152 Munich, Germany
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47
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Grabowska I, Stachyra A, Góra-Sochacka A, Sirko A, Olejniczak AB, Leśnikowski ZJ, Radecki J, Radecka H. DNA probe modified with 3-iron bis(dicarbollide) for electrochemical determination of DNA sequence of Avian Influenza Virus H5N1. Biosens Bioelectron 2014; 51:170-6. [DOI: 10.1016/j.bios.2013.07.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/01/2013] [Accepted: 07/11/2013] [Indexed: 10/26/2022]
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48
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Williams K, Kim CS, Kim JR, Levicky R. Multimodal electrochemical sensing of transcription factor–operator complexes. Analyst 2014; 139:1463-71. [DOI: 10.1039/c3an02128a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Changes in diffusive movements, surface potential, and interfacial impedance of DNA monolayers are combined to analyze binding of unlabeled transcription factors.
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Affiliation(s)
- Keeshan Williams
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
| | - Chung-Sei Kim
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
| | - Jin Ryoun Kim
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
| | - Rastislav Levicky
- Department of Chemical & Biomolecular Engineering
- Polytechnic Institute of New York University
- Brooklyn, USA
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49
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Doneux T, De Rache A, Triffaux E, Meunier A, Steichen M, Buess-Herman C. Optimization of the Probe Coverage in DNA Biosensors by a One-Step Coadsorption Procedure. ChemElectroChem 2013. [DOI: 10.1002/celc.201300145] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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50
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Tavallaie R, Darwish N, Gebala M, Hibbert DB, Gooding JJ. The Effect of Interfacial Design on the Electrochemical Detection of DNA and MicroRNA Using Methylene Blue at Low-Density DNA Films. ChemElectroChem 2013. [DOI: 10.1002/celc.201300136] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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