1
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Feng C, Liu X, Sun YF, Ren CL. Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study. ACS Macro Lett 2024:105-111. [PMID: 38190547 DOI: 10.1021/acsmacrolett.3c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xiao Liu
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Yang-Feng Sun
- Industrial Technology Center, Chengde Petroleum College, Chengde 067000, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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2
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Wittmar J, Ohle C, Kunte J, Brand I. Effect of Ectoine on the Conformation and Hybridization of dsDNA in Monolayer Films: A Spectroelectrochemical Study. ChemElectroChem 2021. [DOI: 10.1002/celc.202100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Julia Wittmar
- Department of Chemistry University of Oldenburg 26111 Oldenburg Germany
- Institute of Cell Dynamics and Imaging Westfälische Wilhelms Universität Münster 48149 Münster Germany
| | - Corina Ohle
- Division Biodeterioration and Reference Organisms Bundesanstalt für Materialforschung und -prüfung BAM 12205 Berlin Germany
- Deutsche Akkreditierungsstelle GmbH (DAkkS) Spittelmarkt 10 10117 Berlin Germany
| | - Jörg Kunte
- Division Biodeterioration and Reference Organisms Bundesanstalt für Materialforschung und -prüfung BAM 12205 Berlin Germany
| | - Izabella Brand
- Department of Chemistry University of Oldenburg 26111 Oldenburg Germany
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3
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Komorek P, Jachimska B, Brand I. Adsorption of lysozyme on gold surfaces in the presence of an external electric potential. Bioelectrochemistry 2021; 142:107946. [PMID: 34507162 DOI: 10.1016/j.bioelechem.2021.107946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/30/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Adsorbed protein films consist of essential building blocks of many biotechnological and biomedical devices. The electrostatic potential may significantly modulate the protein behaviour on surfaces, affecting their structure and biological activity. In this study, lysozyme was used to investigate the effects of applied electric potentials on adsorption and the protein structure. The pH and the surface charge determine the amount and secondary structure of adsorbed lysozyme on a gold surface. In-situ measurements using polarization modulation infrared reflection absorption spectroscopy indicated that the concentration of both the adsorbed anions and the lysozyme led to conformational changes in the protein film, which was demonstrated by a greater amount of aggregated β-sheets in films fabricated at net positive charges of the Au electrode (Eads > Epzc). The changes in secondary structure involved two parallel processes. One comprised changes in the hydration/hydrogen-bond network at helices, leading to diverse helical structures: α-, 310- and/or π-helices. In the second process β-turns, β-sheets, and random coils displayed an ability to form aggregated β-sheet structures. The study illuminates the understanding of electrical potential-dependent changes involved in the protein misfolding process.
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Affiliation(s)
- Paulina Komorek
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland.
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg, 26111 Oldenburg, Germany.
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4
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Wittmar J, Meyer S, Sieling T, Kunte J, Smiatek J, Brand I. What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute-Biopolymer Interactions. J Phys Chem B 2020; 124:7999-8011. [PMID: 32816487 DOI: 10.1021/acs.jpcb.0c05273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Compatible solutes accumulate in the cytoplasm of halophilic microorganisms, enabling their survival in a high-salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule that strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules such as lipids, proteins, and DNA. The molecular interaction between ectoine and biomolecules, in particular the interaction between ectoine and DNA, is far from being understood. In this paper, we describe molecular aspects of the interaction between ectoine and double-stranded DNA (dsDNA). Two 20 base pairs-long dsDNA fragments were immobilized on a gold surface via a thiol-tether. The interaction between the dsDNA monolayers with diluted and concentrated ectoine solutions was examined by means of X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopies (PM IRRAS). Experimental results indicate that the ability of ectoine to bind water reduces the strength of hydrogen bonds formed to the ribose-phosphate backbone in the dsDNA. In diluted (0.1 M) ectoine solution, DNA interacts predominantly with water molecules. The sugar-phosphate backbone is involved in the formation of strong hydrogen bonds to water, which, over time, leads to a reorientation of the planes of nucleic acid bases. This reorientation destabilizes the strength of hydrogen bonds between the bases and leads to a partial dehybridization of the dsDNA. In concentrated ectoine solution (2.5 M), almost all water molecules interact with ectoine. Under this condition, ectoine is able to interact directly with DNA. Density functional theory (DFT) calculations demonstrate that the direct interaction involves the nitrogen atoms in ectoine and phosphate groups in the DNA molecule. The results of the quantum-chemical calculations show that rearrangements in the ribose-phosphate backbone, caused by a direct interaction with ectoine, facilitates contacts between the O atom in the phosphate group and H atoms in a nucleic acid base. In the PM IRRA spectra, an increase in the number of IR absorption modes in the base pair frequency region proves that the hydrogen bonds between bases become weaker. Thus, a sequence of reorientations caused by interaction with ectoine leads to a breakdown of hydrogen bonds between bases in the double helix.
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Affiliation(s)
- Julia Wittmar
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Susann Meyer
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Thorben Sieling
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Jörg Kunte
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Izabella Brand
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
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5
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Alvarez-Malmagro J, Su Z, Leitch JJ, Prieto F, Rueda M, Lipkowski J. Molecular recognition between guanine and cytosine-functionalized nucleolipid hybrid bilayers supported on gold (111) electrodes. Bioelectrochemistry 2020; 132:107416. [PMID: 31981968 DOI: 10.1016/j.bioelechem.2019.107416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/17/2019] [Accepted: 11/17/2019] [Indexed: 12/16/2022]
Abstract
A hybrid bilayer lipid membrane (hBLM), constructed with a 1-hexadecanethiol self-assembled interior leaflet and a 1,2-dipalmitoyl-sn-glycero-3-cytidine nucleolipid exterior leaflet, was deposited at the surface of a gold (111) electrode. This system was used to investigate the molecular recognition reaction between the cytosine moieties of the lipid head group with guanine molecules in the bulk electrolyte solution. Electrochemical measurements and photon polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) were employed to characterize the system and determine the extent of the molecular recognition reaction. The capacitance of the hBLM-covered gold electrode was very low (~1 μF cm-2), therefore the charge density at the gold surface was small. Changing the electrode potential had a minimal effect on the complexation between the cytosine moieties and guanine molecules due to small changes in the static electric field across the membrane. This behavior favored the formation of the guanine-cytosine complex.
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Affiliation(s)
- Julia Alvarez-Malmagro
- Department of Physical Chemistry, University of Seville, C/Profesor García González no 2, 41012 Seville, Spain; Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - ZhangFei Su
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - J Jay Leitch
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Francisco Prieto
- Department of Physical Chemistry, University of Seville, C/Profesor García González no 2, 41012 Seville, Spain.
| | - Manuela Rueda
- Department of Physical Chemistry, University of Seville, C/Profesor García González no 2, 41012 Seville, Spain.
| | - Jacek Lipkowski
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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6
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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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7
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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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8
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Alvarez-Malmagro J, Su Z, Leitch JJ, Prieto F, Rueda M, Lipkowski J. Electric-Field-Driven Molecular Recognition Reactions of Guanine with 1,2-Dipalmitoyl- sn- glycero-3-cytidine Monolayers Deposited on Gold Electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9297-9307. [PMID: 31274320 DOI: 10.1021/acs.langmuir.9b01238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Monolayers of 1,2-dipalmitoyl-sn-glycero-3-cytidine were incubated with guanine in a 0.1 M NaF electrolyte at the surface of a Langmuir trough and transferred to gold (111) electrodes using the Langmuir-Schaefer technique. Chronocoulometry and photon polarization modulation infrared reflection absorption spectroscopy were employed to investigate the influence of the static electric field on the orientation and conformation of the cytidine nucleolipid molecules on the metal surface in the presence of guanine and to monitor the molecular recognition of guanine with the cytosine moiety. When the monolayer is exposed to guanine solutions, the cytosine moiety binds to the guanine residue in either a Watson-Crick complex at positively charged electrode surfaces or a noncomplexed state at negative surface charges. The positive electrostatic field causes the cytosine moiety and the cytosine-guanine complex to adopt a nearly parallel orientation with respect to the plane of the monolayer with a measured tilt angle of ∼10°. The parallel orientation is stabilized by the interactions between the permanent dipole of the cytosine moiety or the Watson-Crick complex and the static electric field. At negative charge densities, the tilt of the cytosine moiety increases by ∼15-20°, destabilizing the complex. Our results demonstrate that the static electric field has an influence on the molecular recognition reactions between nucleoside base pairs at the metal-solution interface and can be controlled by altering the surface charge at the metal.
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Affiliation(s)
- Julia Alvarez-Malmagro
- Department of Physical Chemistry , University of Seville , C/Profesor García González no. 2 , 41012 Seville , Spain
- Department of Chemistry , University of Guelph , Guelph , Ontario , Canada N1G 2W1
| | - ZhangFei Su
- Department of Chemistry , University of Guelph , Guelph , Ontario , Canada N1G 2W1
| | - J Jay Leitch
- Department of Chemistry , University of Guelph , Guelph , Ontario , Canada N1G 2W1
| | - Francisco Prieto
- Department of Physical Chemistry , University of Seville , C/Profesor García González no. 2 , 41012 Seville , Spain
| | - Manuela Rueda
- Department of Physical Chemistry , University of Seville , C/Profesor García González no. 2 , 41012 Seville , Spain
| | - Jacek Lipkowski
- Department of Chemistry , University of Guelph , Guelph , Ontario , Canada N1G 2W1
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9
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Kékedy‐Nagy L, Ferapontova EE. Directional Preference of DNA‐Mediated Electron Transfer in Gold‐Tethered DNA Duplexes: Is DNA a Molecular Rectifier? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- László Kékedy‐Nagy
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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10
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Kékedy‐Nagy L, Ferapontova EE. Directional Preference of DNA‐Mediated Electron Transfer in Gold‐Tethered DNA Duplexes: Is DNA a Molecular Rectifier? Angew Chem Int Ed Engl 2019; 58:3048-3052. [DOI: 10.1002/anie.201809559] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/26/2018] [Indexed: 12/20/2022]
Affiliation(s)
- László Kékedy‐Nagy
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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11
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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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12
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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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13
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Jaworska A, Jablonska A, Wilanowski T, Palys B, Sek S, Kudelski A. Influence of amine and thiol modifications at the 3' ends of single stranded DNA molecules on their adsorption on gold surface and the efficiency of their hybridization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 203:31-39. [PMID: 29857258 DOI: 10.1016/j.saa.2018.05.076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3' ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orientation of DNA on gold surface when using thiol linker. Also, hybridization of the layer of thiol-modified DNA containing 20 adenine bases with the respective DNA containing thymine bases leads to formation of much more organized structures than in the case of unmodified DNA or DNA with the amine linker. We conclude that the thiol-modified ssDNA is more promising for the preparation of biosensors, in comparison with the amine-modified or unmodified ssDNA. We have also found that the above-mentioned modifications at the 3' end of ssDNA significantly influence the IR spectrum (and hence the structure) of polycrystalline films formed from such compounds, even though adsorbed fragments contain less than 5% of the DNA chain. This effect should be taken into account when comparing IR spectra of various polycrystalline films formed from modified and unmodified DNA.
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Affiliation(s)
- Aleksandra Jaworska
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland.
| | - Anna Jablonska
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
| | - Tomasz Wilanowski
- Laboratory of Signal Transduction, Department of Cell Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Barbara Palys
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
| | - Slawomir Sek
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
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14
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Campos R, Kékedy-Nagy L, She Z, Sodhi R, Kraatz HB, Ferapontova EE. Electron Transfer in Spacer-Free DNA Duplexes Tethered to Gold via dA 10 Tags. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8472-8479. [PMID: 29936843 DOI: 10.1021/acs.langmuir.8b01412] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Electrical properties of DNA critically depend on the way DNA molecules are integrated within the electronics, particularly on DNA-electrode immobilization strategies. Here, we show that the rate of electron transport in DNA duplexes spacer-free tethered to gold via the adenosine terminal region (a dA10 tag) is enhanced compared to the hitherto reported DNA-metal electrode tethering chemistries. The rate of DNA-mediated electron transfer (ET) between the electrode and methylene blue intercalated into the dA10-tagged DNA duplex approached 361 s-1 at a ca. half-monolayer DNA surface coverage ΓDNA (with a linear regression limit of 670 s-1 at ΓDNA → 0), being 2.7-fold enhanced compared to phosphorothioated dA5* tethering (6-fold for the C6-alkanethiol linker representing an additional ET barrier). X-ray photoelectron spectroscopy evidenced dA10 binding to the Au surface via the purine N, whereas dA5* predominantly coordinated to the surface via sulfur atoms of phosphothioates. The latter apparently induces the DNA strand twist in the point of surface attachment affecting the local DNA conformation and, as a result, decreasing the ET rates through the duplex. Thus, a spacer-free DNA coupling to electrodes via dA10 tags thus allows a perspective design of DNA electronic circuits and sensors with advanced electronic properties and no implication from more expensive, synthetic linkers.
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Affiliation(s)
- Rui Campos
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - Zhe She
- Department of Physical and Environmental Sciences, 1095 Military Trail , University of Toronto Scarborough , Toronto , Ontario M1C 1A4 , Canada
| | - Rana Sodhi
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , Toronto , Ontario M5S 3E5 , Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, 1095 Military Trail , University of Toronto Scarborough , Toronto , Ontario M1C 1A4 , Canada
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , Toronto , Ontario M5S 3E5 , Canada
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
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15
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Ferapontova EE. DNA Electrochemistry and Electrochemical Sensors for Nucleic Acids. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:197-218. [PMID: 29894229 DOI: 10.1146/annurev-anchem-061417-125811] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark;
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16
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Barreda-García S, Miranda-Castro R, de-Los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Solid-phase helicase dependent amplification and electrochemical detection of Salmonella on highly stable oligonucleotide-modified ITO electrodes. Chem Commun (Camb) 2018; 53:9721-9724. [PMID: 28782763 DOI: 10.1039/c7cc05128j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An on-surface isothermal helicase-dependent amplification is devised for simple, point-of-need quantification of bacterial genomes. The method relies on the enzyme-extension of a thiol-modified reverse primer anchored to indium tin oxide electrodes, which shows strikingly high thermal and storage stability. Amplification and electrochemical detection of only 10 genomes are thus performed on the same platform without thermal cycling.
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Affiliation(s)
- S Barreda-García
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, Oviedo, Spain.
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17
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Harroun SG. The Controversial Orientation of Adenine on Gold and Silver. Chemphyschem 2018; 19:1003-1015. [DOI: 10.1002/cphc.201701223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Scott G. Harroun
- Department of Chemistry; Université de Montréal; Montréal Québec H3C 3J7 Canada
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