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Obeid S, Guyomarc'h F. Atomic force microscopy of food assembly: Structural and mechanical insights at the nanoscale and potential opportunities from other fields. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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2
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Lansakara TI, Morris HS, Singh P, Kohen A, Tivanski AV. Rigid Double-Stranded DNA Linkers for Single Molecule Enzyme-Drug Interaction Measurements Using Molecular Recognition Force Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4174-4183. [PMID: 32233509 DOI: 10.1021/acs.langmuir.9b03495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-molecule studies can reveal the distribution of states and interactions between ligand-enzyme complexes not accessible for most studies that measure a large ensemble average response of many molecules. Furthermore, in some biological applications, the information regarding the outliers, not the average of measured properties, can be more important. The high spatial and force resolution provided by atomic force microscopy (AFM) under physiological conditions has been utilized in this study to quantify the force-distance relations of enzyme-drug interactions. Different immobilization techniques of the protein to a surface and the drug to AFM tip were quantitatively compared to improve the accuracy and precision of the measurement. Protein that is directly bound to the surface, forming a monolayer, was compared to enzyme molecules bound to the surface with rigid double-stranded (ds) DNA spacers. These surfaces immobilization techniques were studied with the drug bound directly to the AFM tip and drug bound via flexible poly(ethylene glycol) and rigid dsDNA linkers. The activity of the enzyme was found to be not significantly altered by immobilization methods relative to its activity in solution. The findings indicate that the approach for studying drug-enzyme interaction based on rigid dsDNA linker on the surface and either flexible or rigid linker on the tip affords straightforward, highly specific, reproducible, and accurate force measurements with a potential for single-molecule level studies. The method could facilitate in-depth examination of a broad spectrum of biological targets and potential drugs.
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Affiliation(s)
| | - Holly S Morris
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Alexei V Tivanski
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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Shan Y, Xu C, Wang M, Zhu Z, Wu FG, Shi Z, Cui Q, Arumugam GM. Bilinear Staphylococcus aureus detection based on suspension immunoassay. Talanta 2019; 192:154-159. [DOI: 10.1016/j.talanta.2018.09.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/06/2018] [Accepted: 09/09/2018] [Indexed: 12/23/2022]
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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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5
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Ultra-sensitive chemiluminescent detection of Staphylococcus aureus based on competitive binding of Staphylococcus protein A-modified magnetic beads to immunoglobulin G. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1769-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Kwak TJ, Lee JW, Yoon DS, Lee SW. Investigation of the Binding Force between Protein A and Immunoglobulin G Using Dielectrophoretic(DEP) Tweezers Inside a Microfluidic Chip. ACTA ACUST UNITED AC 2013. [DOI: 10.9718/jber.2013.34.3.123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ditzler LR, Sen A, Gannon MJ, Kohen A, Tivanski AV. Self-assembled enzymatic monolayer directly bound to a gold surface: activity and molecular recognition force spectroscopy studies. J Am Chem Soc 2011; 133:13284-7. [PMID: 21809877 PMCID: PMC4343314 DOI: 10.1021/ja205409v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli dihydrofolate reductase (ecDHFR) has one surface cysteine, C152, located opposite and distal to the active site. Here, we show that the enzyme spontaneously assembles on an ultraflat gold surface as a homogeneous, covalently bound monolayer. Surprisingly, the activity of the gold-immobilized ecDHFR as measured by radiographic analysis was found to be similar to that of the free enzyme in solution. Molecular recognition force spectroscopy was used to study the dissociation forces involved in the rupture of AFM probe-tethered methotrexate (MTX, a tight-binding inhibitor of DHFR) from the gold-immobilized enzyme. Treatment of the ecDHFR monolayer with free MTX diminished the interaction of the functionalized tip with the surface, suggesting that the interaction was indeed active-site specific. These findings demonstrate the viability of a simple and direct enzymatic surface-functionalization without the use of spacers, thus, opening the door to further applications in the area of biomacromolecular force spectroscopy.
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Affiliation(s)
| | | | - Michael J. Gannon
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52245
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52245
| | - Alexei V. Tivanski
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52245
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Wildling L, Unterauer B, Zhu R, Rupprecht A, Haselgrübler T, Rankl C, Ebner A, Vater D, Pollheimer P, Pohl EE, Hinterdorfer P, Gruber HJ. Linking of sensor molecules with amino groups to amino-functionalized AFM tips. Bioconjug Chem 2011; 22:1239-48. [PMID: 21542606 PMCID: PMC3115690 DOI: 10.1021/bc200099t] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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The measuring tip of an atomic force microscope (AFM) can be upgraded to a specific biosensor by attaching one or a few biomolecules to the apex of the tip. The biofunctionalized tip is then used to map cognate target molecules on a sample surface or to study biophysical parameters of interaction with the target molecules. The functionality of tip-bound sensor molecules is greatly enhanced if they are linked via a thin, flexible polymer chain. In a typical scheme of tip functionalization, reactive groups are first generated on the tip surface, a bifunctional cross-linker is then attached with one of its two reactive ends, and finally the probe molecule of interest is coupled to the free end of the cross-linker. Unfortunately, the most popular functional group generated on the tip surface is the amino group, while at the same time, the only useful coupling functions of many biomolecules (such as antibodies) are also NH2 groups. In the past, various tricks or detours were applied to minimize the undesired bivalent reaction of bifunctional linkers with adjacent NH2 groups on the tip surface. In the present study, an uncompromising solution to this problem was found with the help of a new cross-linker (“acetal-PEG-NHS”) which possesses one activated carboxyl group and one acetal-protected benzaldehyde function. The activated carboxyl ensures rapid unilateral attachment to the amino-functionalized tip, and only then is the terminal acetal group converted into the amino-reactive benzaldehyde function by mild treatment (1% citric acid, 1–10 min) which does not harm the AFM tip. As an exception, AFM tips with magnetic coating become demagnetized in 1% citric acid. This problem was solved by deprotecting the acetal group before coupling the PEG linker to the AFM tip. Bivalent binding of the corresponding linker (“aldehyde-PEG-NHS”) to adjacent NH2 groups on the tip was largely suppressed by high linker concentrations. In this way, magnetic AFM tips could be functionalized with an ethylene diamine derivative of ATP which showed specific interaction with mitochondrial uncoupling protein 1 (UCP1) that had been purified and reconstituted in a mica-supported planar lipid bilayer.
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Affiliation(s)
- Linda Wildling
- Institute of Biophysics, J. Kepler University, Altenberger Str. 69, A-4040 Linz, Austria
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Buck AW, Fowler VG, Yongsunthon R, Liu J, DiBartola AC, Que YA, Moreillon P, Lower SK. Bonds between fibronectin and fibronectin-binding proteins on Staphylococcus aureus and Lactococcus lactis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10764-10770. [PMID: 20218549 PMCID: PMC2893610 DOI: 10.1021/la100549u] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/02/2010] [Indexed: 05/28/2023]
Abstract
Bacterial cell-wall-associated fibronectin binding proteins A and B (FnBPA and FnBPB) form bonds with host fibronectin. This binding reaction is often the initial step in prosthetic device infections. Atomic force microscopy was used to evaluate binding interactions between a fibronectin-coated probe and laboratory-derived Staphylococcus aureus that are (i) defective in both FnBPA and FnBPB (fnbA fnbB double mutant, DU5883), (ii) capable of expressing only FnBPA (fnbA fnbB double mutant complemented with pFNBA4), or (iii) capable of expressing only FnBPB (fnbA fnbB double mutant complemented with pFNBB4). These experiments were repeated using Lactococcus lactis constructs expressing fnbA and fnbB genes from S. aureus. A distinct force signature was observed for those bacteria that expressed FnBPA or FnBPB. Analysis of this force signature with the biomechanical wormlike chain model suggests that parallel bonds form between fibronectin and FnBPs on a bacterium. The strength and covalence of bonds were evaluated via nonlinear regression of force profiles. Binding events were more frequent (p < 0.01) for S. aureus expressing FnBPA or FnBPB than for the S. aureus double mutant. The binding force, frequency, and profile were similar between the FnBPA and FnBPB expressing strains of S. aureus. The absence of both FnBPs from the surface of S. aureus removed its ability to form a detectable bond with fibronectin. By contrast, ectopic expression of FnBPA or FnBPB on the surface of L. lactis conferred fibronectin binding characteristics similar to those of S. aureus. These measurements demonstrate that fibronectin-binding adhesins FnBPA and FnBPB are necessary and sufficient for the binding of S. aureus to prosthetic devices that are coated with host fibronectin.
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Affiliation(s)
| | - Vance G. Fowler
- Duke University Medical Center, Durham, North Carolina
- Duke Clinical Research Institute, Durham, North Carolina
| | | | - Jie Liu
- The Ohio State University, Columbus, Ohio
| | | | - Yok-Ai Que
- Massachusetts General Hospital, Boston, Massachusetts
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Methods and estimations of uncertainties in single-molecule dynamic force spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:911-22. [DOI: 10.1007/s00249-009-0471-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 04/20/2009] [Accepted: 04/28/2009] [Indexed: 02/05/2023]
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12
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Dubrovin EV, Voloshin AG, Kraevsky SV, Ignatyuk TE, Abramchuk SS, Yaminsky IV, Ignatov SG. Atomic force microscopy investigation of phage infection of bacteria. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13068-13074. [PMID: 18850726 DOI: 10.1021/la8022612] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Atomic force microscopy (AFM) was used to study the process of infection of bacterial cells by bacteriophages, for which purpose experimental protocols were elaborated. Three types of bacteriophages were characterized with AFM and transmission electron microscopy (TEM). Bacteriophage interaction with cells was studied for three bacterial hosts: Gram-negative Escherichia coli 057 and Salmonella enteritidis 89 and Gram-positive Bacillus thuringiensis 393. Depending on the phase of lytic cycle, different cell surface changes are observed in AFM images of infected cells in comparison with intact cells: from phage adsorption on the cells and flagella to complete lysis of the cells, accompanied by the release of a large number of newly formed phages. Control experiments (cells without phages and cells with nonspecific phages) did not reveal any surface changes. Penetration of phages inside obligate aerobe Bacillus thuringiensis was shown to be oxygen-dependent and required aeration in laboratory conditions. Our results show great potential of using AFM for numerous fundamental and applied tasks connected with pathogen-host interaction.
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Affiliation(s)
- Evgeniy V Dubrovin
- Department of Physics of Polymers and Crystals, Faculty of Physics, Moscow State University, Moscow, Russian Federation.
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Coldren FM, Foteinopoulou K, Verbeeten WMH, Carroll DL, Laso M. Modeling the effect of cell-associated polymeric fluid layers on force spectroscopy measurements. Part II: experimental results and comparison with model predictions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:9588-9597. [PMID: 18666789 DOI: 10.1021/la800944q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this paper, experimentally obtained force curves on Staphylococcus aureus are compared with a previously developed model that incorporates hydrodynamic effects of extracellular polysaccharides together with the elastic response of the bacterium and cantilever. Force-displacement curves were predicted without any adjustable parameters. It is demonstrated that experimental results can be accurately described by our model, especially if viscoelastic effects of the extracellular polysaccharide layer are taken into account. Polysaccharide layer viscoelasticity was treated by means of a multimode Phan-Thien/Tanner (PTT) constitutive equation. Typical maximum relaxation times range from 0.2 to 2 s, whereas the corresponding zero-shear-rate viscosities are 6-9 Pa.s, based on published, steady-state rheological measurements on Staphylococcus aureus polysaccharide extracted from its native environment. The bacterial elastic constant is found to be in the range 0.02-0.4 N/m, corresponding to bacterial wall Young's moduli in the range of a few hundred MPa. Repeatability of measurements performed on different bacteria is found to be only fair, due to large individuum variability, whereas repetitions of measurements on the same bacterium showed high reproducibility. Improved force-indentation curve predictions are expected if transient rheological characterization of extracellular polysaccharides is available. More desirable however is the direct, in vivo rheological characterization of the extracellular polysaccharide. A model-based analysis of experimental force-indentation curves shows that appreciable further experimental improvements are still necessary to achieve this goal.
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Affiliation(s)
- Faith M Coldren
- Center for Nanotechnology and Molecular Materials, Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, USA
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Dittrich M, Luttge A. Microorganisms, mineral surfaces, and aquatic environments: learning from the past for future progress. GEOBIOLOGY 2008; 6:201-213. [PMID: 18459966 DOI: 10.1111/j.1472-4669.2008.00159.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The interactions between the geosphere and the biosphere are central questions in environmental and geological research. The relationship between bacteria and their environment is an important example of these interactions. By studying microbial communities in modern environments, it is possible to understand the underlying mechanisms that shape these environments and apply this knowledge to the rock record. Recently, new experimental and theoretical methods, ranging from nano- and biotechnology to mathematical and conceptual modelling, have come into play. Thus, new opportunities for interdisciplinary research in the field of geobiology have emerged. In this paper, we review aspects of state-of-the-art imaging and modelling techniques and propose a research concept linking the experimental and the theoretical approaches.
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Affiliation(s)
- M Dittrich
- Swiss Federal Institute of Aquatic Research, Eawag and Swiss Federal Institute of Technology, ETH, Seestrasse 79, 6047 Kastanienbaum, Switzerland.
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15
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Boujday S, Bantegnie A, Briand E, Marnet PG, Salmain M, Pradier CM. In-Depth Investigation of Protein Adsorption on Gold Surfaces: Correlating the Structure and Density to the Efficiency of the Sensing Layer. J Phys Chem B 2008; 112:6708-15. [DOI: 10.1021/jp711916g] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Souhir Boujday
- UPMC Univ Paris 6, UMR CNRS 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, CNRS, UMR 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, Laboratoire de Chimie et Biochimie des Complexes Moléculaires, UMR CNRS 7576, Ecole Nationale Supérieure de Chimie de Paris, F75005 Paris, France, and Agrocampus-Rennes, Département des sciences animales, UMR ENSAR/INRA, 35042 Rennes, France
| | - Aurore Bantegnie
- UPMC Univ Paris 6, UMR CNRS 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, CNRS, UMR 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, Laboratoire de Chimie et Biochimie des Complexes Moléculaires, UMR CNRS 7576, Ecole Nationale Supérieure de Chimie de Paris, F75005 Paris, France, and Agrocampus-Rennes, Département des sciences animales, UMR ENSAR/INRA, 35042 Rennes, France
| | - Elisabeth Briand
- UPMC Univ Paris 6, UMR CNRS 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, CNRS, UMR 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, Laboratoire de Chimie et Biochimie des Complexes Moléculaires, UMR CNRS 7576, Ecole Nationale Supérieure de Chimie de Paris, F75005 Paris, France, and Agrocampus-Rennes, Département des sciences animales, UMR ENSAR/INRA, 35042 Rennes, France
| | - Pierre-Guy Marnet
- UPMC Univ Paris 6, UMR CNRS 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, CNRS, UMR 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, Laboratoire de Chimie et Biochimie des Complexes Moléculaires, UMR CNRS 7576, Ecole Nationale Supérieure de Chimie de Paris, F75005 Paris, France, and Agrocampus-Rennes, Département des sciences animales, UMR ENSAR/INRA, 35042 Rennes, France
| | - Michèle Salmain
- UPMC Univ Paris 6, UMR CNRS 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, CNRS, UMR 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, Laboratoire de Chimie et Biochimie des Complexes Moléculaires, UMR CNRS 7576, Ecole Nationale Supérieure de Chimie de Paris, F75005 Paris, France, and Agrocampus-Rennes, Département des sciences animales, UMR ENSAR/INRA, 35042 Rennes, France
| | - Claire-Marie Pradier
- UPMC Univ Paris 6, UMR CNRS 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, CNRS, UMR 7609, Laboratoire de Réactivité de Surface, F75005 Paris, France, Laboratoire de Chimie et Biochimie des Complexes Moléculaires, UMR CNRS 7576, Ecole Nationale Supérieure de Chimie de Paris, F75005 Paris, France, and Agrocampus-Rennes, Département des sciences animales, UMR ENSAR/INRA, 35042 Rennes, France
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Gaboriaud F, Parcha BS, Gee ML, Holden JA, Strugnell RA. Spatially resolved force spectroscopy of bacterial surfaces using force-volume imaging. Colloids Surf B Biointerfaces 2008; 62:206-13. [DOI: 10.1016/j.colsurfb.2007.10.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 09/20/2007] [Accepted: 10/03/2007] [Indexed: 11/29/2022]
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Salomo M, Keyser UF, Struhalla M, Kremer F. Optical tweezers to study single Protein A/Immunoglobulin G interactions at varying conditions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:927-34. [DOI: 10.1007/s00249-008-0310-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 03/05/2008] [Accepted: 03/10/2008] [Indexed: 10/22/2022]
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Functionalization of Probe Tips and Supports for Single-Molecule Recognition Force Microscopy. Top Curr Chem (Cham) 2008; 285:29-76. [DOI: 10.1007/128_2007_24] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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