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Xing H, Zhu Y, Xu D, Wu R, Xing X, Li LS. DNA tetrahedron-mediated triplex molecular switch for extracellular pH monitoring. Anal Chim Acta 2023; 1265:341336. [PMID: 37230576 DOI: 10.1016/j.aca.2023.341336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
This study aimed to construct a novel DNA triplex molecular switch modified with DNA tetrahedron (DTMS-DT) with sensitive response to extracellular pH using a DNA tetrahedron as the anchoring unit and DNA triplex as the response unit. The results showed that the DTMS-DT had desirable pH sensitivity, excellent reversibility, outstanding anti-interference ability, and good biocompatibility. Confocal laser scanning microscopy suggested that the DTMS-DT could not only be stably anchored on the cell membrane but also be employed to dynamically monitor the change in extracellular pH. Compared with the reported probes for extracellular pH monitoring, the designed DNA tetrahedron-mediated triplex molecular switch exhibited higher cell surface stability and brought the pH-responsive unit closer to the cell membrane surface, making the results more reliable. In general, developing the DNA tetrahedron-based DNA triplex molecular switch is helpful for understanding and illustrating the pH dependent cell behaviors and disease diagnostics.
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Affiliation(s)
- Huanhuan Xing
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China
| | - Yazhen Zhu
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Dangdang Xu
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China
| | - Ruili Wu
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China
| | - Xiaojing Xing
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, 473061, China.
| | - Lin Song Li
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China.
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2
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Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
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Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
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3
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Leitner M, Brummeir J, Plaimer GO, Kefer I, Poturnayova A, Hianik T, Ebner A. DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy. Methods 2021; 197:54-62. [PMID: 33677061 DOI: 10.1016/j.ymeth.2021.02.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/13/2021] [Accepted: 02/27/2021] [Indexed: 10/22/2022] Open
Abstract
Biosensing atomic force microscopy (AFM) offers the unique feature to determine the energy landscape of a bimolecular interaction at the real single molecule level. Furthermore, simultaneous and label-free mapping of molecular recognition and the determination of sample topography at the nanoscale gets possible. A prerequisite and one of the major parts in biosensing AFM are the bio-functionalized AFM tips. In the past decades, different approaches for tip functionalization have been developed. Using these functionalization strategies, several biological highly relevant interactions at the single molecule level have been explored. For the most common approach, the use of a heterobifunctional poly(ethylenglycol) crosslinker, a broad range of linkers for different chemical coupling strategies is available. Nonetheless, the time consuming functionalization protocol as well as the broad distribution of rupture length reduces the possibility of automation and may reduce the accuracy of the results. Here we present a stable and fast forward approach based on tetra-functional DNA tetrahedra. A fast functionalization and a sharp defined distribution of rupture length gets possible with low effort and high success rate. We tested the performance on the classical avidin biotin system by using tetrahedra with three disulfide legs for stable and site directed coupling to gold coated tips and a biotinylated end at the fourth vertex. A special advantage appears when working with a DNA aptamer as sensing molecule. In this case, the fourth strand can be extended by a certain DNA sequence complementary to the linkage part of an aptamer. This AFM tip functionalization protocol was applied on thrombin using DNA aptamers directed against the fibrinogen binding side of human thrombin.
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Affiliation(s)
- Michael Leitner
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Julian Brummeir
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Gernot Oswald Plaimer
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Isabel Kefer
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Alexandra Poturnayova
- Center of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Tibor Hianik
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovakia
| | - Andreas Ebner
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria.
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4
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Stainer S, Reisetbauer S, Ahiable JEA, Ebner L, Zhu R, Reindl D, Körmöczi GF, Ebner A. Single molecule distribution of RhD binding epitopes on ultraflat erythrocyte ghosts. NANOSCALE 2020; 12:22097-22106. [PMID: 33118583 DOI: 10.1039/d0nr04393a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Rh blood group system plays a key role in transfusion and organ transplant medicine. The complex transmembrane Rh polypeptides RhD and RhCE carry numerous antigens, including the extremely immunogenic D antigen. The Rh polypeptides form multimolecular Rh complexes with certain transmembrane and skeletal proteins, with so far only incompletely understood physiological functions. Determination of the energy landscape of individual Rh binding epitopes towards their specific interaction partners as well as their localization across the red blood cell (RBC) membrane requires single molecule approaches including large area high resolution recognition imaging. Atomic force microscopy based molecular recognition force spectroscopy in combination with single molecule recognition imaging fulfills these requirements. For unbiased single molecule results, nano-mechanical influences due to cell elasticity have to be eliminated. This is realized by generation of ultra flat erythrocyte ghosts on a solid support. We developed a protocol for the preparation of complete ultraflat erythrocyte ghosts and determined the molecular binding behaviour of different anti-D antibodies towards their binding epitopes on RhD positive and negative erythrocytes. Performing optimized topography and recognition imaging at 16 Mpixel resolution allowed localisation of individual RhD molecules at the single molecule level across an entire RBC. A map of Rh antigens across integer ultraflat RBC ghosts was generated with nanometer resolution. Here we show a homogeneous distribution on rim and dimple regions with comparable receptor densities. Furthermore, differences in the energy landscape between specific monoclonal antibodies were determined at the single molecule level.
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Affiliation(s)
- Sarah Stainer
- Molecular Biosensing group, Institute of Biophysics, Johannes Kepler University Linz, Austria.
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Alunda BO, Lee YJ. Review: Cantilever-Based Sensors for High Speed Atomic Force Microscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:E4784. [PMID: 32854193 PMCID: PMC7506678 DOI: 10.3390/s20174784] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022]
Abstract
This review critically summarizes the recent advances of the microcantilever-based force sensors for atomic force microscope (AFM) applications. They are one the most common mechanical spring-mass systems and are extremely sensitive to changes in the resonant frequency, thus finding numerous applications especially for molecular sensing. Specifically, we comment on the latest progress in research on the deflection detection systems, fabrication, coating and functionalization of the microcantilevers and their application as bio- and chemical sensors. A trend on the recent breakthroughs on the study of biological samples using high-speed atomic force microscope is also reported in this review.
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Affiliation(s)
- Bernard Ouma Alunda
- School of Mines and Engineering, Taita Taveta University, P.O. Box 635-80300 Voi, Kenya;
| | - Yong Joong Lee
- School of Mechanical Engineering, Kyungpook National University, Daegu 41566, Korea
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6
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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7
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Chtcheglova LA, Hinterdorfer P. Simultaneous AFM topography and recognition imaging at the plasma membrane of mammalian cells. Semin Cell Dev Biol 2018; 73:45-56. [DOI: 10.1016/j.semcdb.2017.08.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
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8
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9
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Leitner M, Poturnayova A, Lamprecht C, Weich S, Snejdarkova M, Karpisova I, Hianik T, Ebner A. Characterization of the specific interaction between the DNA aptamer sgc8c and protein tyrosine kinase-7 receptors at the surface of T-cells by biosensing AFM. Anal Bioanal Chem 2017; 409:2767-2776. [PMID: 28229174 PMCID: PMC5366180 DOI: 10.1007/s00216-017-0238-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/18/2017] [Accepted: 01/31/2017] [Indexed: 01/10/2023]
Abstract
We studied the interaction of the specific DNA aptamer sgc8c immobilized at the AFM tip with its corresponding receptor, the protein tyrosine kinase-7 (PTK7) embedded in the membrane of acute lymphoblastic leukemia (ALL) cells (Jurkat T-cells). Performing single molecule force spectroscopy (SMFS) experiments, we showed that the aptamer sgc8c bound with high probability (38.3 ± 7.48%) and high specificity to PTK7, as demonstrated by receptor blocking experiments and through comparison with the binding behavior of a nonspecific aptamer. The determined kinetic off-rate (koff = 5.16 s−1) indicates low dissociation of the sgc8c–PTK7 complex. In addition to the pulling force experiments, simultaneous topography and recognition imaging (TREC) experiments using AFM tips functionalized with sgc8c aptamers were realized on the outer regions surface of surface-immobilized Jurkat cells for the first time. This allowed determination of the distribution of PTK7 without any labeling and at near physiological conditions. As a result, we could show a homogeneous distribution of PTK7 molecules on the outer regions of ALL cells with a surface density of 325 ± 12 PTK7 receptors (or small receptor clusters) per μm2. The specific interaction of the DNA aptamer sgc8c and protein tyrosine kinase-7 (PTK7) on acute lymphoblastic leukemia (ALL) cells was characterized. AFM based single molecule force spectroscopy (SMFS) yielded a kinetic off-rate of 5.16 s−1 of the complex. Simultaneous topography and recognition imaging (TREC) revealed a PTK7 density of 325 ± 12 molecules or clusters per μm2 in the cell membrane ![]()
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Affiliation(s)
- Michael Leitner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Alexandra Poturnayova
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska dolina F1, 842 48, Bratislava, Slovakia.,Institute of Biochemistry and Animal Genetics, Slovak Academy of Sciences, Moyzesova 61, 900 28, Ivanka pri Dunaji, Slovakia
| | - Constanze Lamprecht
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Sabine Weich
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Maja Snejdarkova
- Institute of Biochemistry and Animal Genetics, Slovak Academy of Sciences, Moyzesova 61, 900 28, Ivanka pri Dunaji, Slovakia
| | - Ivana Karpisova
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska dolina F1, 842 48, Bratislava, Slovakia
| | - Tibor Hianik
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska dolina F1, 842 48, Bratislava, Slovakia
| | - Andreas Ebner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.
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10
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Leitner M, Stock LG, Traxler L, Leclercq L, Bonazza K, Friedbacher G, Cottet H, Stutz H, Ebner A. Mapping molecular adhesion sites inside SMIL coated capillaries using atomic force microscopy recognition imaging. Anal Chim Acta 2016; 930:39-48. [PMID: 27265903 DOI: 10.1016/j.aca.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/29/2016] [Accepted: 05/01/2016] [Indexed: 10/21/2022]
Abstract
Capillary zone electrophoresis (CZE) is a powerful analytical technique for fast and efficient separation of different analytes ranging from small inorganic ions to large proteins. However electrophoretic resolution significantly depends on the coating of the inner capillary surface. High technical efforts like Successive Multiple Ionic Polymer Layer (SMIL) generation have been taken to develop stable coatings with switchable surface charges fulfilling the requirements needed for optimal separation. Although the performance can be easily proven in normalized test runs, characterization of the coating itself remains challenging. Atomic force microscopy (AFM) allows for topographical investigation of biological and analytical relevant surfaces with nanometer resolution and yields information about the surface roughness and homogeneity. Upgrading the scanning tip to a molecular biosensor by adhesive molecules (like partly inverted charged molecules) allows for performing topography and recognition imaging (TREC). As a result, simultaneously acquired sample topography and adhesion maps can be recorded. We optimized this technique for electrophoresis capillaries and investigated the charge distribution of differently composed and treated SMIL coatings. By using the positively charged protein avidin as a single molecule sensor, we compared these SMIL coatings with respect to negative charges, resulting in adhesion maps with nanometer resolution. The capability of TREC as a functional investigation technique at the nanoscale was successfully demonstrated.
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Affiliation(s)
- Michael Leitner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Lorenz G Stock
- Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Lukas Traxler
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Laurent Leclercq
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier, France
| | - Klaus Bonazza
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna, Austria
| | - Gernot Friedbacher
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna, Austria
| | - Hervé Cottet
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier, France
| | - Hanno Stutz
- Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Andreas Ebner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria.
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Tan X, Litau S, Zhang X, Müller J. Single-Molecule Force Spectroscopy of an Artificial DNA Duplex Comprising a Silver(I)-Mediated Base Pair. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11305-11310. [PMID: 26421907 DOI: 10.1021/acs.langmuir.5b03183] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule force spectroscopy measurements of a DNA duplex comprising an artificial metal-mediated base pair are reported. The measurements reveal that DNA duplexes comprising one central imidazole:imidazole mispair rupture at lower forces than a related duplex with canonical base pairs only. In contrast, DNA duplexes with one central imidazole-Ag(+)-imidazole base pair (formed by the addition of Ag(+) to the aforementioned duplex with the mispair) rupture at higher forces. These measurements indicate for the first time that the increase in thermal stability of a nucleic acid duplex that is observed upon the formation of a metal-mediated base pair is accompanied by a concomitant mechanical stabilization. In fact, the mechanical stabilization even exceeds the thermal one. This result indicates that nucleic acids with metal-mediated base pairs should be ideal building blocks for rigid functionalized DNA nano-objects.
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Affiliation(s)
- Xinxin Tan
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Stefanie Litau
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster , Corrensstr. 28/30, 48149 Münster, Germany
| | - Xi Zhang
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster , Corrensstr. 28/30, 48149 Münster, Germany
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12
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Roy D, Park JW. Spatially nanoscale-controlled functional surfaces toward efficient bioactive platforms. J Mater Chem B 2015; 3:5135-5149. [PMID: 32262587 DOI: 10.1039/c5tb00529a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interest in well-defined surface architectures has shown a steady increase, particularly among those involved in biological applications where the reactivity of functional groups on the surface is desired to be close to that of the solution phase. Recent research has demonstrated that utilizing the self-assembly process is an attractive and viable choice for the fabrication of two-dimensional nanoscale-controlled architectures. This review highlights representative examples for controlling the spatial placement of reactive functional groups in the optimization of bioactive surfaces. While the selection is not comprehensive, it becomes evident that surface architecture is one of the key components in allowing efficient biomolecular interactions with surfaces and that the optimized lateral spacing between the immobilized molecules is crucial and even critical in some cases.
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Affiliation(s)
- Dhruvajyoti Roy
- Nanogea Inc., 6162 Bristol Parkway, Culver City, CA 90230, USA
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13
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Burns JR, Al-Juffali N, Janes SM, Howorka S. Membrane-spanning DNA nanopores with cytotoxic effect. Angew Chem Int Ed Engl 2014; 53:12466-70. [PMID: 25294680 PMCID: PMC4282124 DOI: 10.1002/anie.201405719] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/10/2014] [Indexed: 01/24/2023]
Abstract
DNA-based cytotoxic agents: Nanopores composed of folded DNA featuring a hydrophobic belt of ethyl phosphorothioate groups insert into bilayer membranes and kill cancer cells. The mode by which the pores achieve cell killing is elucidated with confocal microscopy.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, University College London, Institute of Structural and Molecular Biology, 20 Gordon StreetLondon WC1H OAJ (UK)
| | - Noura Al-Juffali
- Lungs for Living Research Centre, Division of Medicine, University College LondonLondon WC1E 6JF (UK)
| | - Sam M Janes
- Lungs for Living Research Centre, Division of Medicine, University College LondonLondon WC1E 6JF (UK)
| | - Stefan Howorka
- Department of Chemistry, University College London, Institute of Structural and Molecular Biology, 20 Gordon StreetLondon WC1H OAJ (UK)
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14
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Burns JR, Al-Juffali N, Janes SM, Howorka S. Membrane-Spanning DNA Nanopores with Cytotoxic Effect. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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15
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Lamprecht C, Hinterdorfer P, Ebner A. Applications of biosensing atomic force microscopy in monitoring drug and nanoparticle delivery. Expert Opin Drug Deliv 2014; 11:1237-53. [PMID: 24809228 DOI: 10.1517/17425247.2014.917078] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The therapeutic effects of medicinal drugs not only depend on their properties, but also on effective transport to the target receptor. Here we highlight recent developments in this discipline and show applications of atomic force microscopy (AFM) that enable us to track the effects of drugs and the effectiveness of nanoparticle delivery at the single molecule level. AREAS COVERED Physiological AFM imaging enables visualization of topographical changes to cells as a result of drug exposure and allows observation of cellular responses that yield morphological changes. When we upgrade the regular measuring tip to a molecular biosensor, it enables investigation of functional changes at the molecular level via single molecule force spectroscopy. EXPERT OPINION Biosensing AFM techniques have generated powerful tools to monitor drug delivery in (living) cells. While technical developments in actual AFM methods have simplified measurements at relevant physiological conditions, understanding both the biological and technical background is still a crucial factor. However, due to its potential impact, we expect the number of application-based biosensing AFM techniques to further increase in the near future.
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Affiliation(s)
- Constanze Lamprecht
- University of Kiel, Institute of Materials Science Biocompatible Nanomaterials , Kaiserstr.2, 24143 Kiel , Germany
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16
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Pei H, Zuo X, Zhu D, Huang Q, Fan C. Functional DNA nanostructures for theranostic applications. Acc Chem Res 2014; 47:550-9. [PMID: 24380626 DOI: 10.1021/ar400195t] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, "art-like" DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. One of the major barricades for the biosensor design lies in the restricted target accessibility at the solid-water interface. DNA nanotechnology provides a convenient approach to well control the biomolecule-confined surface to increase the ability of molecular recognition at the biosensing interface. For example, tetrahedral DNA nanostructures with thiol modifications can be self-assembled at the gold surface with high reproducibility. Since DNA tetrahedra are highly rigid and well-defined structures with atomic precision and versatile functionality, they provide scaffolds for anchoring of a variety of biomolecular probes (DNA, aptamers, peptides, and proteins) for biosensing. Significantly, this DNA nanostructure-based biosensing platform greatly increases target accessibility and improves the sensitivity for various types of molecular targets (DNA, RNA, proteins, and small molecules) by several orders of magnitude. In an alternative approach, DNA nanostructures provide a framework for the development of dynamic nanosensors that can function inside the cell. DNA tetrahedra are found to be facilely cell permeable and can sense and image specific molecules in cells. More importantly, these DNA nanostructures can be efficient drug delivery nanocarriers. Since they are DNA molecules by themselves, they have shown excellent cellular biocompatibility with minimal cytotoxicity. As an example, DNA tetrahedra tailored with CpG oligonucleotide drugs have shown greatly improved immunostimulatory effects that makes them a highly promising nanomedicine. By taking them together, we believe these functionalized DNA nanostructures can be a type of intelligent theranostic nanodevice for simultaneous sensing, diagnosis, and therapy inside the cell.
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Affiliation(s)
- Hao Pei
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaolei Zuo
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dan Zhu
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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17
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Burns JR, Göpfrich K, Wood JW, Thacker VV, Stulz E, Keyser UF, Howorka S. Lipid-bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor. Angew Chem Int Ed Engl 2013; 52:12069-72. [PMID: 24014236 PMCID: PMC4016739 DOI: 10.1002/anie.201305765] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, University College London20 Gordon Street, London WC1H OAJ (UK)
| | - Kerstin Göpfrich
- Cavendish Laboratory, University of CambridgeCambridge CB3 0HE (UK)
| | - James W Wood
- School of Chemistry, University of SouthamptonSouthampton SO17 1BJ (UK)
| | - Vivek V Thacker
- Cavendish Laboratory, University of CambridgeCambridge CB3 0HE (UK)
| | - Eugen Stulz
- School of Chemistry, University of SouthamptonSouthampton SO17 1BJ (UK)
| | - Ulrich F Keyser
- Cavendish Laboratory, University of CambridgeCambridge CB3 0HE (UK)
| | - Stefan Howorka
- Department of Chemistry, University College London20 Gordon Street, London WC1H OAJ (UK)
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18
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Burns JR, Göpfrich K, Wood JW, Thacker VV, Stulz E, Keyser UF, Howorka S. Lipid-Bilayer-Spanning DNA Nanopores with a Bifunctional Porphyrin Anchor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305765] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Evtugyn G, Cherkina U, Porfireva A, Danzberger J, Ebner A, Hianik T. Electrochemical Aptasensor Based on ZnO Modified Gold Electrode. ELECTROANAL 2013. [DOI: 10.1002/elan.201300195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Howorka S. DNA nanoarchitectonics: assembled DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7344-7353. [PMID: 23373872 DOI: 10.1021/la3045785] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, England, United Kingdom.
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21
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Burns JR, Stulz E, Howorka S. Self-assembled DNA nanopores that span lipid bilayers. NANO LETTERS 2013; 13:2351-6. [PMID: 23611515 DOI: 10.1021/nl304147f] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA nanotechnology excels at rationally designing bottom-up structures that can functionally replicate naturally occurring proteins. Here we describe the design and generation of a stable DNA-based nanopore that structurally mimics the amphiphilic nature of protein pores and inserts into bilayers to support a steady transmembrane flow of ions. The pore carries an outer hydrophobic belt comprised of small chemical alkyl groups which mask the negatively charged oligonucleotide backbone. This modification overcomes the otherwise inherent energetic mismatch to the hydrophobic environment of the membrane. By merging the fields of nanopores and DNA nanotechnology, we expect that the small membrane-spanning DNA pore will help open up the design of entirely new molecular devices for a broad range of applications including sensing, electric circuits, catalysis, and research into nanofluidics and controlled transmembrane transport.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, England, United Kingdom
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22
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Lee Y, Kwon SH, Kim Y, Lee JB, Park JW. Mapping of Surface-Immobilized DNA with Force-Based Atomic Force Microscopy. Anal Chem 2013; 85:4045-50. [DOI: 10.1021/ac3037848] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoonhee Lee
- Department
of Chemistry, ‡School of Interdisciplinary Bioscience and Bioengineering, §Department of Physics, and ∥Division of
Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, San 31
Hyoja-dong, Pohang, 790-784, South Korea
| | - Sung Hong Kwon
- Department
of Chemistry, ‡School of Interdisciplinary Bioscience and Bioengineering, §Department of Physics, and ∥Division of
Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, San 31
Hyoja-dong, Pohang, 790-784, South Korea
| | - Youngkyu Kim
- Department
of Chemistry, ‡School of Interdisciplinary Bioscience and Bioengineering, §Department of Physics, and ∥Division of
Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, San 31
Hyoja-dong, Pohang, 790-784, South Korea
| | - Jong-Bong Lee
- Department
of Chemistry, ‡School of Interdisciplinary Bioscience and Bioengineering, §Department of Physics, and ∥Division of
Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, San 31
Hyoja-dong, Pohang, 790-784, South Korea
| | - Joon Won Park
- Department
of Chemistry, ‡School of Interdisciplinary Bioscience and Bioengineering, §Department of Physics, and ∥Division of
Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, San 31
Hyoja-dong, Pohang, 790-784, South Korea
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23
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Leitner M, Fantner GE, Fantner EJ, Ivanova K, Ivanov T, Rangelow I, Ebner A, Rangl M, Tang J, Hinterdorfer P. Increased imaging speed and force sensitivity for bio-applications with small cantilevers using a conventional AFM setup. Micron 2012; 43:1399-407. [PMID: 22721963 PMCID: PMC3430863 DOI: 10.1016/j.micron.2012.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 05/15/2012] [Accepted: 05/15/2012] [Indexed: 11/27/2022]
Abstract
In this study, we demonstrate the increased performance in speed and sensitivity achieved by the use of small AFM cantilevers on a standard AFM system. For this, small rectangular silicon oxynitride cantilevers were utilized to arrive at faster atomic force microscopy (AFM) imaging times and more sensitive molecular recognition force spectroscopy (MRFS) experiments. The cantilevers we used had lengths between 13 and 46 μm, a width of about 11 μm, and a thickness between 150 and 600 nm. They were coated with chromium and gold on the backside for a better laser reflection. We characterized these small cantilevers through their frequency spectrum and with electron microscopy. Due to their small size and high resonance frequency we were able to increase the imaging speed by a factor of 10 without any loss in resolution for images from several μm scansize down to the nanometer scale. This was shown on bacterial surface layers (s-layer) with tapping mode under aqueous, near physiological conditions and on nuclear membranes in contact mode in ambient environment. In addition, we showed that single molecular forces can be measured with an up to 5 times higher force sensitivity in comparison to conventional cantilevers with similar spring constants.
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Affiliation(s)
- Michael Leitner
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria
| | - Georg E. Fantner
- École Polytechnique Fédéral de Lausanne, Laboratoire de bio- et nano-instrumentation, CH-1015 Lausanne, Switzerland
| | - Ernest J. Fantner
- SCL-Sensortech, Tech Gate Vienna, Science and Technology Park, A-1220 Wien, Austria
| | - Katerina Ivanova
- SCL-Sensortech, Tech Gate Vienna, Science and Technology Park, A-1220 Wien, Austria
| | - Tzvetan Ivanov
- Fachgebiet für Mikro- und nanoelektronische Systeme, Fakultät für Elektrotechnik und Informationstechnik, TU Ilmenau, D-98693 Ilmenau, Germany
| | - Ivo Rangelow
- Fachgebiet für Mikro- und nanoelektronische Systeme, Fakultät für Elektrotechnik und Informationstechnik, TU Ilmenau, D-98693 Ilmenau, Germany
| | - Andreas Ebner
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria
| | - Martina Rangl
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria
| | - Jilin Tang
- Chinese Academy of Science, Chang Chun Institute of Applied Chemistry, 130021 Changchun, China
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria
- Center for Advanced Bioanalysis (CBL), A-4020 Linz, Austria
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24
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Han X, Qin M, Pan H, Cao Y, Wang W. A versatile "multiple fishhooks" approach for the study of ligand-receptor interactions using single-molecule atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10020-10025. [PMID: 22690829 DOI: 10.1021/la301903z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Despite the powerfulness of atomic force microscopy (AFM)-based single-molecule force spectroscopy in the study of ligand-receptor interactions, complicated cantilever functionalization and data interpretation have often been a great hurdle for its widespread application. Here, we present a much simplified experimental scheme by using a "multiple fishhooks" approach. In this strategy, multiple ligands are labeled on a single polymer chain, which forms complexes with receptors anchored on the substrate surface. Therefore, multiple single-bond rupture events can be captured in the same force-extension curves, similar to the widely used polyprotein approach. This method also allows nonsingle-molecule events and nonspecific interactions between cantilever and surface to be readily excluded from real data pool and greatly increases the quality and quantity of single-molecule data. The biggest advantage of our approach over the previously reported one is the choice of a naturally occurring polysaccharide, hyaluronan, the conformation of which in solution can be fine-tuned by pH, as the polymer backbone of the "multiple fishhooks" handle. Furthermore, our approach greatly simplifies the chemical synthesis of the polymer handle, allowing bioactive molecules to be easily one-step labeled on the handles in aqueous solution. We validate this strategy using the widely studied streptavidin-biotin system, and our single-molecule AFM results are in good agreement with previously reported ones. We anticipate that this novel strategy can be used as a versatile tool to study other complex and challenging ligand-receptor interactions.
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Affiliation(s)
- Xiaotian Han
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu, People's Republic of China
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25
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Schlapak R, Danzberger J, Armitage D, Morgan D, Ebner A, Hinterdorfer P, Pollheimer P, Gruber HJ, Schäffler F, Howorka S. Nanoscale DNA tetrahedra improve biomolecular recognition on patterned surfaces. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:89-97. [PMID: 22083943 DOI: 10.1002/smll.201101576] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Indexed: 05/31/2023]
Abstract
The bottom-up approach of DNA nano-biotechnology can create biomaterials with defined properties relevant for a wide range of applications. This report describes nanoscale DNA tetrahedra that are beneficial to the field of biosensing and the targeted immobilization of biochemical receptors on substrate surfaces. The DNA nanostructures act as immobilization agents that are able to present individual molecules at a defined nanoscale distance to the solvent thereby improving biomolecular recognition of analytes. The tetrahedral display devices are self-assembled from four oligonucleotides. Three of the four tetrahedron vertices are equipped with disulfide groups to enable oriented binding to gold surfaces. The fourth vertex at the top of the bound tetrahedron presents the biomolecular receptor to the solvent. In assays testing the molecular accessibility via DNA hybridization and protein capturing, tetrahedron-tethered receptors outperformed conventional immobilization approaches with regard to specificity and amount of captured polypeptide by a factor of up to seven. The bottom-up strategy of creating DNA tetrahedrons is also compatible with the top-down route of nanopatterning of inorganic substrates, as demonstrated by the specific coating of micro- to nanoscale gold squares amid surrounding blank or poly(ethylene glycol)-passivated glass surfaces. DNA tetrahedra can create biofunctionalized surfaces of rationally designed properties that are of relevance in analytical chemistry, cell biology, and single-molecule biophysics.
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Affiliation(s)
- Robert Schlapak
- Center for Advanced Bioanalysis, Upper Austrian Research, 4020 Linz, Austria
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