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Khmelinskaia A, Schwille P, Franquelim HG. Binding and Characterization of DNA Origami Nanostructures on Lipid Membranes. Methods Mol Biol 2023; 2639:231-255. [PMID: 37166721 DOI: 10.1007/978-1-0716-3028-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA origami is an extremely versatile nanoengineering tool with widespread applicability in various fields of research, including membrane physiology and biophysics. The possibility to easily modify DNA strands with lipophilic moieties enabled the recent development of a variety of membrane-active DNA origami devices. Biological membranes, as the core barriers of the cells, display vital structural and functional roles. Therefore, lipid bilayers are widely popular targets of DNA origami nanotechnology for synthetic biology and biomedical applications. In this chapter, we summarize the typical experimental methods used to investigate the interaction of DNA origami with synthetic membrane models. Herein, we present detailed protocols for the production of lipid model membranes and characterization of membrane-targeted DNA origami nanostructures using different microscopy approaches.
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Affiliation(s)
- Alena Khmelinskaia
- Max Planck Institute of Biochemistry, Munich, Germany
- Institute of Protein Design, University of Washington, Seattle, WA, USA
- Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | | | - Henri G Franquelim
- Max Planck Institute of Biochemistry, Munich, Germany.
- Interfaculty Centre for Bioactive Matter (b-ACTmatter), Leipzig University, Leipzig, Germany.
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Pellequer JL, Parot P, Navajas D, Kumar S, Svetličić V, Scheuring S, Hu J, Li B, Engler A, Sousa S, Lekka M, Szymoński M, Schillers H, Odorico M, Lafont F, Janel S, Rico F. Fifteen years of Servitude et Grandeur
to the application of a biophysical technique in medicine: The tale of AFMBioMed. J Mol Recognit 2018; 32:e2773. [DOI: 10.1002/jmr.2773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | - Daniel Navajas
- Institute for Bioengineering of Catalonia and CIBER de Enfermedades Respiratorias; Universitat de Barcelona; Barcelona Spain
| | - Sanjay Kumar
- Departments of Bioengineering and Chemical & Biomolecular Engineering; University of California, Berkeley; Berkeley California USA
| | | | - Simon Scheuring
- Department of Anesthesiology, Department of Physiology and Biophysics; Weill Cornell Medicine; New York City New York USA
| | - Jun Hu
- Shanghai Advanced Research Institute; Chinese Academy of Sciences; Shanghai China
- Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai China
| | - Bin Li
- Shanghai Advanced Research Institute; Chinese Academy of Sciences; Shanghai China
- Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai China
| | - Adam Engler
- Department of Bioengineering; University of California San Diego; La Jolla California USA
| | - Susana Sousa
- i3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- INEB-Instituto de Engenharia Biomédica; Universidade do Porto; Porto Portugal
- ISEP-Instituto Superior de Engenharia; Politécnico do Porto; Portugal
| | - Małgorzata Lekka
- Institute of Nuclear Physics Polish Academy of Sciences; Kraków Poland
| | - Marek Szymoński
- Center for Nanometer-scale Science and Advanced Materials, NANOSAM, Faculty of Physics, Astronomy and Applied Computer Science; Jagiellonian University; Kraków Poland
| | | | - Michael Odorico
- Institut de Chimie Séparative de Marcoule (ICSM), CEA, CNRS, ENSCM, Univ Montpellier, Marcoule; Montpellier France
| | - Frank Lafont
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Univ Lille; Lille France
| | - Sebastien Janel
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Univ Lille; Lille France
| | - Felix Rico
- LAI, U1067, Aix-Marseille Univ, CNRS, INSERM; Marseille France
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Gao Q, Liu H, Ding Q, Du J, Liu C, Yang W, Shen P, Yang C. A red-emitting indolium fluorescence probe for membranes - flavonoids interactions. LUMINESCENCE 2018; 33:582-587. [PMID: 29405584 DOI: 10.1002/bio.3449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/03/2017] [Indexed: 12/12/2022]
Abstract
The red-emitting indolium derivative compound (E)-2-(4-(diphenylamino)styryl)-1,3,3-trimethyl-3H-indol-1-ium iodide (H3) was demonstrated as a sensitive membrane fluorescence probe. The probe located at the interface of liposomes when mixed showed much fluorescence enhancement by inhibiting the twisted intramolecular charge transfer state. After ultrasonic treatment, it penetrated into lipid bilayers with the emissions leveling off and a rather large encapsulation efficiency (71.4%) in liposomes. The ζ-potential and particle size measurement confirmed that the charged indolium group was embedded deeply into lipid bilayers. The probe was then used to monitor the affinities of antioxidant flavonoids for membranes. It was verified that quercetin easily interacted with liposomes and dissociated the probe from the internal lipid within 60 s under the condition of simply mixing. The assessment of binding affinities of six flavonoids and the coincident results with their antioxidation activities indicated that it was a promising membrane probe for the study of drug bio-affinities.
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Affiliation(s)
- Qingyun Gao
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
| | - Han Liu
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
| | - Qiongjie Ding
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
| | - Jinya Du
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
| | - Chunlin Liu
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
| | - Wei Yang
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
| | - Ping Shen
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
| | - Changying Yang
- College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, P. R. China
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Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy. SENSORS 2015; 15:30683-92. [PMID: 26690165 PMCID: PMC4721743 DOI: 10.3390/s151229823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 11/30/2022]
Abstract
Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction.
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Manna S, Senapati S, Lindsay S, Zhang P. A three-arm scaffold carrying affinity molecules for multiplex recognition imaging by atomic force microscopy: the synthesis, attachment to silicon tips, and detection of proteins. J Am Chem Soc 2015; 137:7415-23. [PMID: 25996033 DOI: 10.1021/jacs.5b03079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have developed a multiplex imaging method for detection of proteins using atomic force microscopy (AFM), which we call multiplex recognition imaging (mRI). AFM has been harnessed to identify protein using a tip functionalized with an affinity molecule at a single molecule level. However, many events in biochemistry require identification of colocated factors simultaneously, and this is not possible with only one type of affinity molecule on an AFM tip. To enable AFM detection of multiple analytes, we designed a recognition head made from conjugating two different affinity molecules to a three-arm linker. When it is attached to an AFM tip, the recognition head would allow the affinity molecules to function in concert. In the present study, we synthesized two recognition heads: one was composed of two nucleic acid aptamers, and the other one composed of an aptamer and a cyclic peptide. They were attached to AFM tips through a catalyst-free click reaction. Our imaging results show that each affinity unit in the recognition head can recognize its respective cognate in an AFM scanning process independently and specifically. The AFM method was sensitive, only requiring 2 to 3 μL of protein solution with a concentration of ∼2 ng/mL for the detection with our current setup. When a mixed sample was deposited on a surface, the ratio of proteins could be determined by counting numbers of the analytes. Thus, this mRI approach has the potential to be used as a label-free system for detection of low-abundance protein biomarkers.
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Affiliation(s)
- Saikat Manna
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Subhadip Senapati
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Stuart Lindsay
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Peiming Zhang
- †Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
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Charge regulation and energy dissipation while compressing and sliding a cross-linked chitosan hydrogel layer. J Colloid Interface Sci 2015; 443:162-9. [DOI: 10.1016/j.jcis.2014.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/01/2014] [Indexed: 11/18/2022]
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Zhang M, Wang B, Xu B. Measurements of single molecular affinity interactions between carbohydrate-binding modules and crystalline cellulose fibrils. Phys Chem Chem Phys 2013; 15:6508-15. [PMID: 23532050 DOI: 10.1039/c3cp51072g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Combining atomic force microscopy (AFM) recognition imaging and single molecule dynamic force spectroscopy (SMDFS), we studied the single molecule affinity interactions between the carbohydrate-binding module (CBM) and plant cell wall cellulose using the CBM3a (from Clostridium thermocellum) and CBM2a (from Cellvibrio japonicus) functionalized AFM tips. The binding efficiencies of the CBMs to the cellulose were determined by the binding areas on the crystalline cellulose fibrils surface using the recognition imaging. Several dynamic and kinetic parameters, such as the reconstructed free energy change, energy barrier and bond lifetime constant, were also obtained based on the measured single molecule unbinding forces, which are used to illuminate the affinity of the CBMs binding to the natural and single cellulose surface from a totally different aspect. It was found that CBM3a has a little higher binding efficiency and affinity than CBM2a to both natural and extracted cellulose surfaces and both the CBMs have higher affinities to the natural cell wall cellulose compared to the extracted single cellulose. The in-depth understanding of the binding mechanisms of the CBM-cellulose interactions of this study may pave the way for more efficient plant cell wall degradation and eventually facilitate biofuel production.
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Affiliation(s)
- Mengmeng Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, GA 30602, USA
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Salvatore P, Zeng D, Karlsen KK, Chi Q, Wengel J, Ulstrup J. Electrochemistry of single metalloprotein and DNA-based molecules at Au(111) electrode surfaces. Chemphyschem 2013; 14:2101-11. [PMID: 23788363 DOI: 10.1002/cphc.201300299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 11/10/2022]
Abstract
We have briefly overviewed recent efforts in the electrochemistry of single transition metal complex, redox metalloprotein, and redox-marked oligonucleotide (ON) molecules. We have particularly studied self-assembled molecular monolayers (SAMs) of several 5'-C6-SH single- (ss) and double-strand (ds) ONs immobilized on Au(111) electrode surfaces via Au-S bond formation, using a combination of nucleic acid chemistry, electrochemistry and electrochemically controlled scanning tunnelling microscopy (in situ STM). Ds ONs stabilized by multiply charged cations and locked nucleic acid (LNA) monomers have been primary targets, with a view on stabilizing the ds-ONs and improving voltammetric signals of intercalating electrochemical redox probes. Voltammetric signals of the intercalator anthraquinone monosulfonate (AQMS) at ds-DNA/Au(111) surfaces diluted by mercaptohexanol are significantly sharpened and more robust in the presence than in the absence of [Co(NH3)6](3+). AQMS also displays robust Faradaic voltammetric signals specific to the ds form on binding to similar LNA/Au(111) surfaces, but this signal only evolves after successive voltammetric scanning into negative potential ranges. Triply charged spermidine (Spd) invokes itself a strong voltammetric signal, which is specific to the ds form and fully matched sequences. This signal is of non-Faradaic, capacitive origin but appears in the same potential range as the Faradaic AQMS signal. In situ STM shows that molecular scale structures of the size of Spd-stabilized ds-ONs are densely packed over the Au(111) surface in potential ranges around the capacitive peak potential.
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Affiliation(s)
- Princia Salvatore
- Department of Chemistry, Kemitorvet, Building 207, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Nanoscale mechanical properties of lipid bilayers and their relevance in biomembrane organization and function. Micron 2012; 43:1212-23. [DOI: 10.1016/j.micron.2012.03.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 03/19/2012] [Accepted: 03/20/2012] [Indexed: 12/27/2022]
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Zapotoczny S, Biedroń R, Marcinkiewicz J, Nowakowska M. Atomic force microscopy-based molecular studies on the recognition of immunogenic chlorinated ovalbumin by macrophage receptors. J Mol Recognit 2012; 25:82-8. [PMID: 22290769 DOI: 10.1002/jmr.2160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This report presents simple and reliable approach developed to study the specific recognition events between chlorinated ovalbumin (OVA) and macrophages using atomic force microscopy (AFM). Thanks to the elimination of nonspecific adhesion, the interactions of the native and chlorinated OVA with a membrane of macrophages could be quantified using exclusively the so-called adhesion frequency (AF). The proposed system not only enabled the application of AFM-based force measurements for such poorly defined ligand-receptor pairs but also significantly improved both the acquisition and the processing of the data. The proteins were immobilized on the gold-coated AFM tips from the aqueous solutions containing charged thiol adsorbates. Such surface dilution of the proteins ensured the presence of single or just a few macromolecules at the tip-surface contact. The formation of negatively charged monolayer on the tip dramatically limited its nonspecific interactions with the macrophage surface. In such systems, AF was used as a measure of the recognition events even if the interaction forces varied significantly for sets of measurements. The system with the native OVA, a weak immunogen, showed only negligible AF compared with 85% measured for the immunogenic chlorinated OVA. The AF values varied with the tip-macrophage contact time and loading velocity. Blocking of the receptors by the chlorinated OVA was also confirmed. The developed approach can be also used to study other ligand-receptor interactions in poorly defined biological systems with intrinsically broad distribution of the rupture forces, thus opening new fields for AFM-based recognition on molecular level.
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Affiliation(s)
- Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland.
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Hao X, Zhang J, Christensen HEM, Wang H, Ulstrup J. Electrochemical Single-Molecule AFM of the Redox Metalloenzyme Copper Nitrite Reductase in Action. Chemphyschem 2012; 13:2919-24. [DOI: 10.1002/cphc.201200220] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Indexed: 11/11/2022]
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Abstract
The atomic force microscope (AFM) is a high-resolution scanning-probe instrument which has become an important tool for cellular and molecular biophysics in recent years, but lacks the time resolution and functional specificities offered by fluorescence microscopic techniques. The advantages of both methods may be exploited by combining and synchronizing them. In this paper, the biological applications of AFM, fluorescence, and their combinations are briefly reviewed, and the assembly and utilization of a spatially and temporally synchronized AFM and total internal reflection fluorescence microscope are described. The application of the method is demonstrated on a fluorescently labeled cell culture.
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Affiliation(s)
- Miklós S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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Effects of resveratrol on membrane biophysical properties: relevance for its pharmacological effects. Chem Phys Lipids 2010; 163:747-54. [PMID: 20691168 DOI: 10.1016/j.chemphyslip.2010.07.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 07/05/2010] [Accepted: 07/22/2010] [Indexed: 01/05/2023]
Abstract
The current study gathers a range of spectrophotometric and spectrofluorimetric techniques to systematically monitor the effects of resveratrol (trans-3,5,4'-trihydrostilbene) on the biophysical properties of membrane model systems consisting of unilamellar liposomes of phosphatidylcholine (DPPC) with the ultimate goal of relating these effects with some of the well documented pharmacological properties of this compound, and clarifying some controversial results reported on the literature. Physiological conditions have been pursued, such as a buffered pH control with adjusted ionic strength similar to the blood plasma conditions (pH 7.4, I=0.1M) and the study at different membrane physical states (gel phase and fluid phase) for the assessment of resveratrol-membrane: aqueous partition coefficient by derivative spectroscopy. Results obtained by fluorescence quenching and anisotropy studies indicate that resveratrol has a membrane fluidizing effect and is able to permeate the membrane even in the gel phase. These results mirror the well described antioxidant effect of resveratrol, since antioxidants have to reach peroxidised rigid membranes and increase membrane fluidity in order to interact more efficiently with lipid radicals in the disordered lipid bilayer. Location of resveratrol pointed also to a membrane distribution that is favourable for scavenging the lipid radicals and was elucidated using probes positioned at different membrane depths suggesting that this compound penetrates into the acyl membrane region but also positions its polar hydroxyl group near the headgroup region of the membrane.
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Han SW, Mieda S, Nakamura C, Kihara T, Nakamura N, Miyake J. Successive detection of insulin-like growth factor-II bound to receptors on a living cell surface using an AFM. J Mol Recognit 2009; 24:17-22. [DOI: 10.1002/jmr.994] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Yan C, Yersin A, Afrin R, Sekiguchi H, Ikai A. Single molecular dynamic interactions between glycophorin A and lectin as probed by atomic force microscopy. Biophys Chem 2009; 144:72-7. [DOI: 10.1016/j.bpc.2009.06.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 06/25/2009] [Accepted: 06/25/2009] [Indexed: 12/01/2022]
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Specific molecular recognition and nonspecific contributions to bacterial interaction forces. Appl Environ Microbiol 2008; 74:2559-64. [PMID: 18344352 DOI: 10.1128/aem.02839-07] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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