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Sample preparation method to improve the efficiency of high-throughput single-molecule force spectroscopy. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-00097-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Abstract
Inefficient sample preparation methods hinder the performance of high-throughput single-molecule force spectroscopy (H-SMFS) for viscous damping among reactants and unstable linkage. Here, we demonstrated a sample preparation method for H-SMFS systems to achieve a higher ratio of effective target molecules per sample cell by gas-phase silanization and reactant hydrophobization. Digital holographic centrifugal force microscopy (DH-CFM) was used to verify its performance. The experimental result indicated that the DNA stretching success ratio was improved from 0.89% to 13.5%. This enhanced efficiency preparation method has potential application for force-based DNA stretching experiments and other modifying procedures.
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Pleshakova TO, Bukharina NS, Archakov AI, Ivanov YD. Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization. Int J Mol Sci 2018; 19:E1142. [PMID: 29642632 PMCID: PMC5979402 DOI: 10.3390/ijms19041142] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed.
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Affiliation(s)
| | - Natalia S Bukharina
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
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Li C, Ding Y, Soliman M, Lorenzo J, Dhasmana N, Chantharasupawong P, Ievlev AV, Gesquiere AJ, Tetard L, Thomas J. Probing Ternary Solvent Effect in High V(oc) Polymer Solar Cells Using Advanced AFM Techniques. ACS APPLIED MATERIALS & INTERFACES 2016; 8:4730-4738. [PMID: 26807919 DOI: 10.1021/acsami.5b12260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This work describes a simple method to develop a high V(oc) low band gap PSCs. In addition, two new atomic force microscopy (AFM)-based nanoscale characterization techniques to study the surface morphology and physical properties of the structured active layer are introduced. With the help of ternary solvent processing of the active layer and C60 buffer layer, a bulk heterojunction PSC with V(oc) more than 0.9 V and conversion efficiency 7.5% is developed. In order to understand the fundamental properties of the materials ruling the performance of the PSCs tested, AFM-based nanoscale characterization techniques including Pulsed-Force-Mode AFM (PFM-AFM) and Mode-Synthesizing AFM (MSAFM) are introduced. Interestingly, MSAFM exhibits high sensitivity for direct visualization of the donor-acceptor phases in the active layer of the PSCs. Finally, conductive-AFM (cAFM) studies reveal local variations in conductivity in the donor and acceptor phases as well as a significant increase in photocurrent in the PTB7:ICBA sample obtained with the ternary solvent processing.
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Affiliation(s)
- Chao Li
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- Department of Material Science and Engineering, University of Central Florida , Orlando, Florida 32816, United States
| | - Yi Ding
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- Department of Material Science and Engineering, University of Central Florida , Orlando, Florida 32816, United States
| | - Mikhael Soliman
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- Department of Material Science and Engineering, University of Central Florida , Orlando, Florida 32816, United States
| | - Josie Lorenzo
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- CREOL, College of Optics and Photonics, University of Central Florida , Orlando, Florida 32816, United States
| | - Nitesh Dhasmana
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- CREOL, College of Optics and Photonics, University of Central Florida , Orlando, Florida 32816, United States
| | - Panit Chantharasupawong
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- CREOL, College of Optics and Photonics, University of Central Florida , Orlando, Florida 32816, United States
| | - Anton V Ievlev
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory , 1 Bethel Valley Rd., Oak Ridge, Tennessee 37831, United States
| | - Andre J Gesquiere
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- Department of Material Science and Engineering, University of Central Florida , Orlando, Florida 32816, United States
- Department of Chemistry, University of Central Florida , Orlando, Florida 32816, United States
- CREOL, College of Optics and Photonics, University of Central Florida , Orlando, Florida 32816, United States
| | - Laurene Tetard
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- Department of Material Science and Engineering, University of Central Florida , Orlando, Florida 32816, United States
| | - Jayan Thomas
- NanoScience Technology Center, University of Central Florida , Orlando, Florida 32826, United States
- Department of Material Science and Engineering, University of Central Florida , Orlando, Florida 32816, United States
- CREOL, College of Optics and Photonics, University of Central Florida , Orlando, Florida 32816, United States
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Deen J, Sempels W, De Dier R, Vermant J, Dedecker P, Hofkens J, Neely RK. Combing of genomic DNA from droplets containing picograms of material. ACS NANO 2015; 9:809-816. [PMID: 25561163 PMCID: PMC4344373 DOI: 10.1021/nn5063497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 05/30/2023]
Abstract
Deposition of linear DNA molecules is a critical step in many single-molecule genomic approaches including DNA mapping, fiber-FISH, and several emerging sequencing technologies. In the ideal situation, the DNA that is deposited for these experiments is absolutely linear and uniformly stretched, thereby enabling accurate distance measurements. However, this is rarely the case, and furthermore, current approaches for the capture and linearization of DNA on a surface tend to require complex surface preparation and large amounts of starting material to achieve genomic-scale mapping. This makes them technically demanding and prevents their application in emerging fields of genomics, such as single-cell based analyses. Here we describe a simple and extremely efficient approach to the deposition and linearization of genomic DNA molecules. We employ droplets containing as little as tens of picograms of material and simply drag them, using a pipet tip, over a polymer-coated coverslip. In this report we highlight one particular polymer, Zeonex, which is remarkably efficient at capturing DNA. We characterize the method of DNA capture on the Zeonex surface and find that the use of droplets greatly facilitates the efficient deposition of DNA. This is the result of a circulating flow in the droplet that maintains a high DNA concentration at the interface of the surface/solution. Overall, our approach provides an accessible route to the study of genomic structural variation from samples containing no more than a handful of cells.
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Affiliation(s)
- Jochem Deen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Wouter Sempels
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Raf De Dier
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
| | - Jan Vermant
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
- Department of Materials, ETH Zürich, Vladimir Prelog Weg 5, CH 8093 Zürich, Switzerland
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Robert K. Neely
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Sang S, Zhao Y, Zhang W, Li P, Hu J, Li G. Surface stress-based biosensors. Biosens Bioelectron 2013; 51:124-35. [PMID: 23948243 DOI: 10.1016/j.bios.2013.07.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/27/2013] [Accepted: 07/12/2013] [Indexed: 01/13/2023]
Abstract
Surface stress-based biosensors, as one kind of label-free biosensors, have attracted lots of attention in the process of information gathering and measurement for the biological, chemical and medical application with the development of technology and society. This kind of biosensors offers many advantages such as short response time (less than milliseconds) and a typical sensitivity at nanogram, picoliter, femtojoule and attomolar level. Furthermore, it simplifies sample preparation and testing procedures. In this work, progress made towards the use of surface stress-based biosensors for achieving better performance is critically reviewed, including our recent achievement, the optimally circular membrane-based biosensors and biosensor array. The further scientific and technological challenges in this field are also summarized. Critical remark and future steps towards the ultimate surface stress-based biosensors are addressed.
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Affiliation(s)
- Shengbo Sang
- MicroNano System Research Center, Taiyuan University of Technology, Taiyuan, Shanxi 030024, People's Republic of China; Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education, Taiyuan University of Technology, Taiyuan, Shanxi 030024, People's Republic of China
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Barattin R, Voyer N. Chemical modifications of AFM tips for the study of molecular recognition events. Chem Commun (Camb) 2008:1513-32. [DOI: 10.1039/b614328h] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Roiter Y, Minko S. Adsorption of Polyelectrolyte versus Surface Charge: in Situ Single-Molecule Atomic Force Microscopy Experiments on Similarly, Oppositely, and Heterogeneously Charged Surfaces. J Phys Chem B 2007; 111:8597-604. [PMID: 17555343 DOI: 10.1021/jp070518q] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have studied the effect of the pH and surface charge of mica on the adsorption of the positively charged weak polyelectrolyte (PE) poly(2-vinylpyridine) (P2VP) using atomic force microscopy (AFM) single-molecule experiments. These AFM experiments were performed in situ directly under aqueous media. If the mica's surface and the PE are oppositely charged (pH > 3), the PE forms a flat adsorbed layer of two-dimensionally (2D) equilibrated self-avoiding random walk coils. The adsorbed layer's structure remains almost unchanged if the pH is decreased to pH 3 (the mica's surface is weakly charged). At pH 2 (the mica surface is decorated by spots of different electrical charges), the polyelectrolyte chains take the form of a 2D compressed coil. In this pH range, at an increased P2VP concentration in solution, the PE segments preferentially adsorb onto the top of previously adsorbed segments, rather than onto an unoccupied surface. We explain this behavior as being caused by the heterogeneous character of the charged surface and the competitive adsorption of hydronium ions. The further increase of polymer concentration results in a complete coverage of the mica substrate and the charge overcompensation by P2VP chains adsorbed on the similarly charged substrate, due to van der Waals forces.
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Affiliation(s)
- Yuri Roiter
- Clarkson University, Department of Chemistry and Biomolecular Science, 8 Clarkson Avenue, Potsdam, New York 13699-5810, USA
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Han SP, Yoda S, Kwak KJ, Suga K, Fujihira M. Interpretation of DNA adsorption on silanized surfaces by measuring interaction forces at various pHs using atomic force microscopy. Ultramicroscopy 2005. [DOI: 10.1016/j.ultramic.2005.06.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hards A, Zhou C, Seitz M, Bräuchle C, Zumbusch A. Simultaneous AFM Manipulation and Fluorescence Imaging of Single DNA Strands. Chemphyschem 2005; 6:534-40. [PMID: 15799480 DOI: 10.1002/cphc.200400515] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report combined atomic force and far-field fluorescence microscopic experiments which allow the simultaneous atomic force manipulation and optical observation of individual dye-labeled DNA molecules. A detailed understanding of the binding properties of DNA to different transparent surfaces is prerequisite for these investigations. Atomic force spectroscopy and fluorescence microscopy of single DNA strands yielded detailed insight into two different types of DNA binding onto transparent polylysine-coated and silanized glass surfaces. We subsequently demonstrate how the different binding can be exploited to perform two types of nanomanipulation experiments: On polylysine, strong electrostatic interactions over the whole length of the DNA strand enable the writing of micrometer-sized patterns. By contrast, the strong pointwise attachment of DNA to silanized surfaces allows horizontal stretching of single DNA strands to lengths exceeding 1.6 times the contour length of the DNA strand. With this new approach it is possible to directly observe the rupture of the strongly bonded DNA strand.
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Affiliation(s)
- Andrew Hards
- Department Chemie und Biochemie, Center for Nanoscience (CeNS), Ludwig-Maximilians Universität München, Butenandtstr. 11, 81377 München, Germany
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Kwak KJ, Sato F, Kudo H, Yoda S, Fujihira M. Topographic effects on adhesive force mapping of stretched DNA molecules by pulsed-force-mode atomic force microscopy. Ultramicroscopy 2004; 100:179-86. [PMID: 15231308 DOI: 10.1016/j.ultramic.2003.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2003] [Revised: 11/16/2003] [Accepted: 11/24/2003] [Indexed: 11/29/2022]
Abstract
Adhesive interaction between a tip and a sample surface was examined on a microscopic scale by pulsed-force-mode atomic force microscopy (PFM-AFM). The signal measured by monitoring pull-off force is influenced by various factors such as topography, elasticity, electrostatic charges, and adsorbed water on surfaces. Here, we focus on the topographic effects on the adhesive interaction. To clarify the topographic influence, the adhesive force measurement of a stretched DNA molecule with a smaller radius of curvature than that of a tip was carried out at low relative humidity (RH) with an alkanethiol-modified tip. The experimental conditions such as low RH and the use of the alkanethiol-modified tip were required to minimise the influence of water capillary force on hydrated DNA strands. The hydrophobic modification of a substrate surface was also important to minimise the adsorbed water effect. The DNA molecules were stretched on the substrate surfaces by an immobilisation process called a dynamic molecular combing method. The two-component vapour-phase surface modification with an alkylsilane mixed with a silane derivative containing an amino end group enhanced the DNA adsorption due to the electrostatic interaction. The experimental results for the topographic effects on the adhesive force mapping were reproducible.
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Affiliation(s)
- K J Kwak
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Kudo H, Okamoto Y, Kwak KJ, Fujihira M. Observation of removal of an Fmoc protecting group by scanning tunneling microscopy. Ultramicroscopy 2004; 100:353-8. [PMID: 15231329 DOI: 10.1016/j.ultramic.2003.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2003] [Revised: 11/16/2003] [Accepted: 11/24/2003] [Indexed: 11/17/2022]
Abstract
We demonstrate here by imaging successive surface reactions in self-assembled monolayers (SAMs) on Au(111) at molecular scale with a scanning tunneling microscope (STM): (i) SAM matrices formation with 1-octanethiol on Au(111) in ethanol, (ii) insertion of N-Fmoc-aminooctanethiol into the SAM matrices in ethanol, and (iii) removal of the Fmoc protecting group with tris(2-aminoethyl)amine (TAEA). The total reaction is formation of SAMs containing a small amount of NH2 terminated molecules in the CH3 terminated SAM matrices. After the reaction of the protecting group with TAEA, STM imaging revealed the decrease in heights of the inserted molecules on average. We attributed this observation to removal of the protecting group by taking account of a convolution of electronic and topographic contributions to observed STM heights. Apparent areas of the terminal groups, however, became larger on removal. The increase in the areas was attributed to water adsorption to the NH2 terminal group under air.
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Affiliation(s)
- H Kudo
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Atomic force microscope equipped with confocal laser scanning microscope for the spectroscopic measurement of the contact area in liquid. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.01.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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