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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Mirbagheri N, Campos R, Ferapontova EE. Electrocatalytic Oxidation of Water by OH
−
‐ and H
2
O‐Capped IrO
x
Nanoparticles Electrophoretically Deposited on Graphite and Basal Plane HOPG: Effect of the Substrate Electrode**. ChemElectroChem 2021. [DOI: 10.1002/celc.202100317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Naghmehalsadat Mirbagheri
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
- Department of Microsystems Engineering – IMTEK University of Freiburg Georges-Koehler-Allee 103 79110 Freiburg Germany
| | - Rui Campos
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
- AXES research group and NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerpen Belgium
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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3
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Naik SG, Rabinal MHK. Compositional tuning of negative differential resistance in a bulk silver iodide memristor. NEW J CHEM 2021. [DOI: 10.1039/d0nj05427e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Silver iodide a negative differential resistance (NDR) memristor
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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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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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6
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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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7
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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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8
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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9
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Tang MSL, Shiu SCC, Godonoga M, Cheung YW, Liang S, Dirkzwager RM, Kinghorn AB, Fraser LA, Heddle JG, Tanner JA. An aptamer-enabled DNA nanobox for protein sensing. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1161-1168. [PMID: 29410111 DOI: 10.1016/j.nano.2018.01.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
Abstract
DNA nanostructures can show dynamic responses to molecular triggers for a wide variety of applications. While DNA sequence signal triggers are now well-established, there is a critical need for a broader diversity of molecular triggers to drive dynamic responses in DNA nanostructures. DNA aptamers are ideal; they can both seamlessly integrate into DNA nanostructure scaffolds and transduce molecular recognition into functional responses. Here, we report construction and optimization of a DNA origami nanobox locked by a pair of DNA double strands where one strand is a DNA aptamer targeting the malaria biomarker protein Plasmodium falciparum lactate dehydrogenase. The protein acts as the key which enables box opening. We observe highly specific protein-mediated box opening by both transmission electron microscopy and fluorescence. Aptamer-enabled DNA boxes have significant potential for enabling direct responses to proteins and other biomolecules in nanoscale diagnostics, drug delivery and sensing devices.
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Affiliation(s)
- Marco S L Tang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maia Godonoga
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shaolin Liang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Roderick M Dirkzwager
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewis A Fraser
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jonathan G Heddle
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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10
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Majikes JM, Ferraz LCC, LaBean TH. pH-Driven Actuation of DNA Origami via Parallel I-Motif Sequences in Solution and on Surfaces. Bioconjug Chem 2017; 28:1821-1825. [PMID: 28616969 DOI: 10.1021/acs.bioconjchem.7b00288] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As bottom up DNA nanofabrication creates increasingly complex and dynamic mechanisms, the implementation of actuators within the DNA nanotechnology toolkit has grown increasingly important. One such actuator, the I-motif, is fairly simple in that it consists solely of standard DNA sequences and does not require any modification chemistry or special purification beyond that typical for DNA oligomer synthesis. This study presents a new implementation of parallel I-motif actuators, emphasizing their future potential as drivers of complex internal motion between substructures. Here we characterize internal motion between DNA origami substructures via AFM and image analysis. Such parallel I-motif design and quantification of actuation provide a useful step toward more complex and effective molecular machines.
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Affiliation(s)
- Jacob M Majikes
- North Carolina State University , Raleigh, North Carolina 27695, United States
| | | | - Thomas H LaBean
- North Carolina State University , Raleigh, North Carolina 27695, United States
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11
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Ricardo KB, Xu A, Salim M, Zhou F, Liu H. Deposition of DNA Nanostructures on Highly Oriented Pyrolytic Graphite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3991-3997. [PMID: 28406032 DOI: 10.1021/acs.langmuir.6b03836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report the deposition of DNA origami nanostructures on highly oriented pyrolytic graphite (HOPG). The DNA origami goes through a structural rearrangement and the DNA base is exposed to interact with the graphite surface. Exposure to ambient air, which is known to result in a hydrophilic-to-hydrophobic wetting transition of HOPG, does not significantly impact the deposition yield or the shape deformation of DNA nanostructures. The deposited DNA nanostructures maintain their morphology for at least a week and promote site-selective chemical vapor deposition of SiO2. This process is potentially useful for a range of applications that include but are not limited to nanostructure fabrication, sensing, and electronic and surface engineering.
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Affiliation(s)
- Karen B Ricardo
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Anqin Xu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Muhammad Salim
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Feng Zhou
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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12
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Kékedy-Nagy L, Ferapontova EE, Brand I. Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials. J Phys Chem B 2017; 121:1552-1565. [PMID: 28177253 DOI: 10.1021/acs.jpcb.6b12363] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT)25 or cytosine-guanine (dGdC)20 base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C6 alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT)25 molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC)20 helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.
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Affiliation(s)
- László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus-C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus-C, Denmark
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg , 26111 Oldenburg, Germany
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13
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Majikes JM, Nash JA, LaBean TH. Search for effective chemical quenching to arrest molecular assembly and directly monitor DNA nanostructure formation. NANOSCALE 2017; 9:1637-1644. [PMID: 28074960 DOI: 10.1039/c6nr08433h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structural DNA nanotechnology has demonstrated both versatility and potential as a molecular manufacturing tool; the formation and processing of DNA nanostructures has therefore been subject to much interest. Characterization of the formation process itself is vital to understanding the role of design in production yield. We present our search for a robust new technique, chemical quenching, to arrest molecular folding in DNA systems for subsequent characterization. Toward this end we will introduce two miniM13 origami designs based on a 2.4 kb scaffold, each with diametrically opposed scaffold routing strategies (maximized scaffold crossovers versus maximized staple crossovers) to examine the relevance of design in the folding process. By chemically rendering single strand DNA inert and unable to hybridize, we probe the folding pathway of several scaffolded DNA origami structures.
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Affiliation(s)
- J M Majikes
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
| | - J A Nash
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
| | - T H LaBean
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
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14
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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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