1
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Brunetti G, De Pastina A, Hegner M. Quantitative epitope analysis reveals drastic 63% reduced immuno-affinity and 60% enhanced transmissibility for SARS-CoV-2 variants. Nanoscale Adv 2021; 3:6903-6911. [PMID: 36132357 PMCID: PMC9419875 DOI: 10.1039/d1na00554e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/22/2021] [Indexed: 06/15/2023]
Abstract
SARS-CoV-2 is the cause of a global pandemic that has led to more than 4 million deaths, continues to spread and holds the world in a tight grip. The virus has developed substantial mutations that undermine the efficacy of current vaccines and monoclonal antibody therapies. Semi-quantitative immuno - and neutralization assays are unable to provide direct quantitative insights about the minute variations of emerging mutants. Here, we develop a quantitative assay that enables synchronous screening of emerging variant epitopes with single amino acid resolution. We report on specific label-free quantitative nanomechanical analysis of pseudovirus spike interaction with ACE2 receptors. Within minutes, we can characterize the B.1.1.7 variant transmissibility due to its 63% increased binding, and measure a 60% reduced efficacy of antibodies towards B.1.351 and P.1 variants. Our technology can assist vaccine development studies, with focus on comparing protection patterns and novel vaccine candidates and tracking of immunity over time.
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Affiliation(s)
- Giulio Brunetti
- Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin (TCD) D02 Dublin Ireland
| | - Annalisa De Pastina
- Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin (TCD) D02 Dublin Ireland
| | - Martin Hegner
- Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin (TCD) D02 Dublin Ireland
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2
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De Pastina A, Padovani F, Brunetti G, Rotella C, Niosi F, Usov V, Hegner M. Multimodal real-time frequency tracking of cantilever arrays in liquid environment for biodetection: Comprehensive setup and performance analysis. Rev Sci Instrum 2021; 92:065001. [PMID: 34243575 DOI: 10.1063/5.0047631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
We present a nanomechanical platform for real-time quantitative label-free detection of target biomolecules in a liquid environment with mass sensitivity down to few pg. Newly fabricated arrays of up to 18 cantilevers are integrated in a micromachined fluidic chamber, connected to software-controlled fluidic pumps for automated sample injections. We discuss two functionalization approaches to independently sensitize the interface of different cantilevers. A custom piezo-stack actuator and optical readout system enable the measurement of resonance frequencies up to 2 MHz. We implement a new measurement strategy based on a phase-locked loop (PLL), built via in-house developed software. The PLL allows us to track, within the same experiment, the evolution of resonance frequency over time of up to four modes for all the cantilevers in the array. With respect to the previous measurement technique, based on standard frequency sweep, the PLL enhances the estimated detection limit of the device by a factor of 7 (down to 2 pg in 5 min integration time) and the time resolution by more than threefold (below 15 s), being on par with commercial gold-standard techniques. The detection limit and noise of the new setup are investigated via Allan deviation and standard deviation analysis, considering different resonance modes and interface chemistries. As a proof-of-concept, we show the immobilization and label-free in situ detection of live bacterial cells (E. coli), demonstrating qualitative and quantitative agreement in the mechanical response of three different resonance modes.
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Affiliation(s)
- Annalisa De Pastina
- School of Physics, Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin (TCD), D02 Dublin, Ireland
| | - Francesco Padovani
- Institute of Functional Epigenetics, Helmholtz Zentrum München (HMGU), Neuherberg 85764, Germany
| | - Giulio Brunetti
- School of Physics, Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin (TCD), D02 Dublin, Ireland
| | - Chiara Rotella
- School of Physics, Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin (TCD), D02 Dublin, Ireland
| | - Fabio Niosi
- School of Physics, Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin (TCD), D02 Dublin, Ireland
| | - Victor Usov
- School of Physics, Trinity College Dublin (TCD), D02 Dublin, Ireland
| | - Martin Hegner
- School of Physics, Center for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin (TCD), D02 Dublin, Ireland
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3
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Brunetti G, Padovani F, De Pastina A, Rotella C, Monahan A, Hoffman SL, Jongo SA, Abdulla S, Corradin G, Pluschke G, Daubenberger C, Hegner M. Nanotechnological immunoassay for rapid label-free analysis of candidate malaria vaccines. Nanoscale 2021; 13:2338-2349. [PMID: 33438712 DOI: 10.1039/d0nr08083g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Malaria is a life-threatening epidemic disease with half of the world's population at risk. Although its incidence rate has fallen since 2010, this ratio dramatically stalled between 2014 and 2018. New fast and optimized tools in vaccine analysis and seroconversion testing are critically needed. We developed a clinical diagnostic device based on piezo-actuated nanoresonators that perform as quantitative in situ calibrated nano-bio sensors for specific detection of multiple target molecules in serum samples. The immunoassay successfully diagnoses humoral immune responses induced by malaria vaccine candidates and reveals the timeline and stage of the infection. We applied the newly developed strategy to a variety of different samples, from pure antibody/vaccine solutions, to blood samples from clinical trials on both naïve and pre-exposed malaria volunteers from sub-Saharan countries. Our nanomechanical assay provides a direct one-step label-free quantitative immunoassay that is on par with the gold-standard, multi-step enzyme-linked immunosorbent assay (ELISA). We achieve a limit of detection of few pg ml-1, or sub-pM concentrations. The 6 μl sample volume allows more than 50 experiments from one finger prick. Furthermore, we simultaneously detected multiple analytes by differential functionalization of multiple sensors in parallel. The inherent differential read-out with in situ controls reduces false positive results. Due to the faster turnaround time, the minimal volume required and the automatized handling system, this technique has great potential for miniaturization and routine diagnostics in pandemic emergencies.
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Affiliation(s)
- Giulio Brunetti
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin, Ireland.
| | - Francesco Padovani
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin, Ireland. and Institute of Functional Epigenetics, Helmholtz Zentrum München (HMGU), Neuherberg 85764, Germany
| | - Annalisa De Pastina
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin, Ireland.
| | - Chiara Rotella
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin, Ireland.
| | - Amy Monahan
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin, Ireland.
| | | | - Said A Jongo
- Bagamoyo Research and Training Centre, Ifakara Health Institute, Bagamoyo, Tanzania
| | - Salim Abdulla
- Bagamoyo Research and Training Centre, Ifakara Health Institute, Bagamoyo, Tanzania
| | | | - Gerd Pluschke
- Medical Parasitology and Infection Biology Department, Molecular Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland and University of Basel, Switzerland
| | - Claudia Daubenberger
- University of Basel, Switzerland and Medical Parasitology and Infection Biology Department, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland.
| | - Martin Hegner
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin, Ireland.
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4
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Duffy J, Padovani F, Brunetti G, Noy P, Certa U, Hegner M. Towards personalised rapid label free miRNA detection for cancer and liver injury diagnostics in cell lysates and blood based samples. Nanoscale 2018; 10:12797-12804. [PMID: 29947396 DOI: 10.1039/c8nr03604g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Advances in prevention, diagnosis and therapy are coupled to innovation and development of new medical tools, leading to improved patient prognosis. We developed an automatic biosensor platform that could provide a non-invasive, rapid and personalised diagnosis using nanomechanical cantilever sensors. miRNA are involved in gene expression and are extractable biomarkers for multiple diseases. We detected specific expression patterns of miRNA relevant to cancer and adverse drug effects directly in cell lysates or blood based samples using only a few microliters of sample within one hour. Specific miRNA hybridisation to the upper cantilever surface induces physical bending of the sensor which is detected by monitoring the position of a laser that reflects from the sensors surface. Internal reference sensors negate environmental and nonspecific effects. We showed that the sensitivity of label free cantilever nanomechanical sensing of miRNA surpasses that of surface plasmon resonance by more than three orders of magnitude. A cancer associated miRNA expression profile from cell lysates and one associated with hepatocytes derived from necrotic liver tissue in blood-based samples has been successfully detected. Our label free mechanical approach displays the capability to perform in relevant clinical samples while also obtaining comparable results to PCR based techniques. Without the need to individually extend, amplify or label each target allowing multitarget analysis from one sample.
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Affiliation(s)
- James Duffy
- Centre Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin 2, Ireland.
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5
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Zheng LQ, Wang X, Shao F, Hegner M, Zenobi R. Nanoscale Chemical Imaging of Reversible Photoisomerization of an Azobenzene-Thiol Self-Assembled Monolayer by Tip-Enhanced Raman Spectroscopy. Angew Chem Int Ed Engl 2017; 57:1025-1029. [DOI: 10.1002/anie.201710443] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/25/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Li-Qing Zheng
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
| | - Xing Wang
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
| | - Feng Shao
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
| | - Martin Hegner
- Center for Research on Adaptive Nanostructures and Nanodevices; School of Physics; Trinity College Dublin; Dublin 2 Ireland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
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6
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Zheng LQ, Wang X, Shao F, Hegner M, Zenobi R. Nanoscale Chemical Imaging of Reversible Photoisomerization of an Azobenzene-Thiol Self-Assembled Monolayer by Tip-Enhanced Raman Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Li-Qing Zheng
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
| | - Xing Wang
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
| | - Feng Shao
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
| | - Martin Hegner
- Center for Research on Adaptive Nanostructures and Nanodevices; School of Physics; Trinity College Dublin; Dublin 2 Ireland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology; ETH Zurich; 8093 Zurich Switzerland
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7
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Abstract
Clinical coagulation diagnostics often requires multiple tests. Coagulation times are a first indication of an abnormal coagulation process, such as a coagulation factor deficiency. To determine the specific deficient factor, additional immuno- and/or enzyme assays are necessary. Currently, every clinical laboratory has to normalize their assays (international normalized ratio, INR), and therefore, certain variability within the clinical analytics exists. We report a novel strategy for a quick, reliable and quantitative diagnosis of blood coagulation diseases (e.g. haemophilia) and for monitoring factor replacement and anticoagulant therapies (e.g. heparin treatment). We exploit nano-oscillations of microcantilevers for real-time measurements of the evolving blood plasma clot strength (viscosity). The sensors are oscillated at multiple high resonance mode numbers, in order to minimise the oscillation amplitude (a few nanometers), to provide direct internal control and to increase the quality factor. Along with the activated thromboplastin time (aPTT) and prothrombin time (PT) other parameters important for thrombosis diagnostics can be obtained, including the final clot strength and the fibrinolysis time. We demonstrate the dependence of the parameters on factor deficiencies and we diagnose a specific factor deficiency through an integrated and quantitative in situ immunoassay. This approach does not require continuous calibration since it delivers an absolute quantity (clot strength). The low sample volume required (a few μl) and the ability to measure different parameters within the same test (PT, aPTT and global coagulation assay) make the presented technique a versatile point-of-care device for clinical coagulation diagnostics.
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Affiliation(s)
- Francesco Padovani
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Ireland.
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8
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9
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Affiliation(s)
| | - James Duffy
- CRANN, School of Physics, Trinity College Dublin, Dublin 2, Ireland
| | - Martin Hegner
- CRANN, School of Physics, Trinity College Dublin, Dublin 2, Ireland
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10
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Katranidis A, Wruck F, Nierhaus KH, Büldt G, Hegner M. Following Translation and Folding of Individual Proteins by Single Ribosomes in Real-Time using Optical Tweezers. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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11
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Jadhav VS, Brüggemann D, Wruck F, Hegner M. Single-molecule mechanics of protein-labelled DNA handles. Beilstein J Nanotechnol 2016; 7:138-148. [PMID: 26925362 PMCID: PMC4734302 DOI: 10.3762/bjnano.7.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/18/2016] [Indexed: 05/07/2023]
Abstract
DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA-protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG)-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp) were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG) beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD) imaging control experiments revealed that quantum dot-streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein-DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular recognition in time-critical molecular motor studies.
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Affiliation(s)
- Vivek S Jadhav
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Dorothea Brüggemann
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
- Institute for Biophysics, University of Bremen, Bremen, Germany
| | - Florian Wruck
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
| | - Martin Hegner
- CRANN – The Naughton Institute, School of Physics, Trinity College Dublin, Dublin, Ireland
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12
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Winters S, Berner NC, Mishra R, Dümbgen KC, Backes C, Hegner M, Hirsch A, Duesberg GS. On-surface derivatisation of aromatic molecules on graphene: the importance of packing density. Chem Commun (Camb) 2015; 51:16778-81. [DOI: 10.1039/c5cc06433c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the production of high packing density molecular monolayers on graphene through a modified transfer process and demonstrate their increased stability during derivatisation.
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Affiliation(s)
- Sinéad Winters
- CRANN and School of Chemistry
- Trinity College
- Dublin
- Ireland
- Advanced Materials and BioEngineering Research (AMBER) Centre
| | - Nina C. Berner
- CRANN and School of Chemistry
- Trinity College
- Dublin
- Ireland
- Advanced Materials and BioEngineering Research (AMBER) Centre
| | - Rohit Mishra
- CRANN and School of Physics
- Trinity College
- Dublin
- Ireland
| | - Kim C. Dümbgen
- CRANN and School of Chemistry
- Trinity College
- Dublin
- Ireland
- Advanced Materials and BioEngineering Research (AMBER) Centre
| | - Claudia Backes
- Advanced Materials and BioEngineering Research (AMBER) Centre
- Trinity College
- Dublin
- Ireland
- CRANN and School of Physics
| | - Martin Hegner
- CRANN and School of Physics
- Trinity College
- Dublin
- Ireland
| | - Andreas Hirsch
- Institute of Organic Chemistry II
- University of Erlangen-Nürnberg
- 91054 Erlangen
- Germany
| | - Georg S. Duesberg
- CRANN and School of Chemistry
- Trinity College
- Dublin
- Ireland
- Advanced Materials and BioEngineering Research (AMBER) Centre
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13
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Abstract
A nanomechanical technique for rapid real time detection and monitoring of microorganism growth will significantly reduce costs and diagnosis times in industrial and clinical settings. Owing to their label free detection mechanism and unprecedented sensitivity to the mass and elastic modulus of biological structures, dynamically operated cantilever arrays provide an opportunity to rapidly detect and track the evolution of microbial growth. Here we report the monitoring of the growth of single Aspergillus niger spores via the multimode response of microcantilevers. The fungal hyphal structure affects the cantilevers' nanomechanical properties as it propagates along the sensor. We demonstrate, for the first time, the mapping of cellular events with great accuracy using a cantilever frequency response. Imaging of growth conditions on the cantilever, which is performed in parallel, allows for verification of these results. Theoretical comparison and finite element modelling confirm experimental findings and allow for determination of the hyphal elastic modulus.
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Affiliation(s)
- Niall Maloney
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), School of Physics, Trinity College Dublin, Dublin 2, Ireland.
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14
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Mishra R, Hegner M. Effect of non-specific species competition from total RNA on the static mode hybridization response of nanomechanical assays of oligonucleotides. Nanotechnology 2014; 25:225501. [PMID: 24807191 DOI: 10.1088/0957-4484/25/22/225501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We investigate here the nanomechanical response of microcantilever sensors in real-time for detecting a range of ultra-low concentrations of oligonucleotides in a complex background of total cellular RNA extracts from cell lines without labeling or amplification. Cantilever sensor arrays were functionalized with probe single stranded DNA (ssDNA) and reference ssDNA to obtain a differential signal. They were then exposed to complementary target ssDNA strands that were spiked in a fragmented total cellular RNA background in biologically relevant concentrations so as to provide clinically significant analysis. We present a model for prediction of the sensor behavior in competitive backgrounds with parameters that are indicators of the change in nanomechanical response with variation in the target and background concentration. For nanomechanical assays to compete with current technologies it is essential to comprehend such responses with eventual impact on areas like understanding non-coding RNA pharmacokinetics, nucleic acid biomarker assays and miRNA quantification for disease monitoring and diagnosis to mention a few. Additionally, we also achieved a femtomolar sensitivity limit for online oligonucleotide detection in a non-competitive environment with these sensors.
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Affiliation(s)
- Rohit Mishra
- Centre for Research on Adaptive Nanostructures and Nanodevices, School of Physics, Trinity College, Dublin 2, Ireland
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15
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Maloney N, Lukacs G, Ball SL, Hegner M. Device for filamentous fungi growth monitoring using the multimodal frequency response of cantilevers. Rev Sci Instrum 2014; 85:015003. [PMID: 24517802 DOI: 10.1063/1.4854655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Filamentous fungi cause opportunistic infections in hospital patients. A fast assay to detect viable spores is of great interest. We present a device that is capable of monitoring fungi growth in real time via the dynamic operation of cantilevers in an array. The ability to detect minute frequency shifts for higher order flexural resonance modes is demonstrated using hydrogel functionalised cantilevers. The use of higher order resonance modes sees the sensor dependent mass responsivity enhanced by a factor of 13 in comparison to measurements utilizing the fundamental resonance mode only. As a proof of principle measurement, Aspergillus niger growth is monitored using the first two flexural resonance modes. The detection of single spore growth within 10 h is reported for the first time. The ability to detect and monitor the growth of single spores, within a small time frame, is advantageous in both clinical and industrial settings.
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Affiliation(s)
- N Maloney
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland
| | - G Lukacs
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland
| | - S L Ball
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland
| | - M Hegner
- Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland
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16
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Katranidis A, Grange W, Schlesinger R, Hegner M, Bueldt G. Force Measurements of the Disruption of the Nascent Polypeptide Chain from the Ribosome by Optical Tweezers. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.2399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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17
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Haas P, Then P, Wild A, Grange W, Zorman S, Hegner M, Calame M, Aebi U, Flammer J, Hecht B. Fast quantitative single-molecule detection at ultralow concentrations. Anal Chem 2010; 82:6299-302. [PMID: 20568715 DOI: 10.1021/ac100779c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The applicability of single-molecule fluorescence assays in liquids is limited by diffusion to concentrations in the low picomolar range. Here, we demonstrate quantitative single-molecule detection at attomolar concentrations within 1 min by excitation and detection of fluorescence through a single-mode optical fiber in presence of turbulent flow. The combination of high detectability and short measurement times promises applications in ultrasensitive assays, sensors, and point-of-care medical diagnostics.
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Affiliation(s)
- Philippe Haas
- National Center of Competence for Research in Nanoscale Science (NCCR), Institute of Physics, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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18
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Abstract
Microfabricated cantilever sensors have attracted much interest in recent years as devices for the fast and reliable detection of small concentrations of molecules in air and solution. In addition to application of such sensors for gas and chemical-vapor sensing, for example as an artificial nose, they have also been employed to measure physical properties of tiny amounts of materials in miniaturized versions of conventional standard techniques such as calorimetry, thermogravimetry, weighing, photothermal spectroscopy, as well as for monitoring chemical reactions such as catalysis on small surfaces. In the past few years, the cantilever-sensor concept has been extended to biochemical applications and as an analytical device for measurements of biomaterials. Because of the label-free detection principle of cantilever sensors, their small size and scalability, this kind of device is advantageous for diagnostic applications and disease monitoring, as well as for genomics or proteomics purposes. The use of microcantilever arrays enables detection of several analytes simultaneously and solves the inherent problem of thermal drift often present when using single microcantilever sensors, as some of the cantilevers can be used as sensor cantilevers for detection, and other cantilevers serve as passivated reference cantilevers that do not exhibit affinity to the molecules to be detected.
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Affiliation(s)
- Bharat Bhushan
- Ohio State University, Nanoprobe Laboratory for Bio- and Nanotechnology and Biomimetics (NLB2), 201 W. 19th Avenue, 43210-1142 Columbus, OH USA
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19
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Braun T, Ghatkesar MK, Backmann N, Grange W, Boulanger P, Letellier L, Lang HP, Bietsch A, Gerber C, Hegner M. Quantitative time-resolved measurement of membrane protein-ligand interactions using microcantilever array sensors. Nat Nanotechnol 2009; 4:179-85. [PMID: 19265848 DOI: 10.1038/nnano.2008.398] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 12/03/2008] [Indexed: 05/17/2023]
Abstract
Membrane proteins are central to many biological processes, and the interactions between transmembrane protein receptors and their ligands are of fundamental importance in medical research. However, measuring and characterizing these interactions is challenging. Here we report that sensors based on arrays of resonating microcantilevers can measure such interactions under physiological conditions. A protein receptor--the FhuA receptor of Escherichia coli--is crystallized in liposomes, and the proteoliposomes then immobilized on the chemically activated gold-coated surface of the sensor by ink-jet spotting in a humid environment, thus keeping the receptors functional. Quantitative mass-binding measurements of the bacterial virus T5 at subpicomolar concentrations are performed. These experiments demonstrate the potential of resonating microcantilevers for the specific, label-free and time-resolved detection of membrane protein-ligand interactions in a micro-array format.
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Affiliation(s)
- Thomas Braun
- School of Physics and Centre for Research on Adaptive Nanostructures and Nanodevices, Naughton Institute, Trinity College Dublin, Dublin 2, Ireland
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Ghatkesar MK, Lang HP, Gerber C, Hegner M, Braun T. Comprehensive characterization of molecular interactions based on nanomechanics. PLoS One 2008; 3:e3610. [PMID: 18978938 PMCID: PMC2572191 DOI: 10.1371/journal.pone.0003610] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 10/08/2008] [Indexed: 11/18/2022] Open
Abstract
Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6) Da) adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da) to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions.
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Affiliation(s)
- Murali Krishna Ghatkesar
- National Center of Competence for Research in Nanoscience, Institute of Physics, University of Basel, Basel, Switzerland
- California Institute of Technology, Pasadena, California, United States of America
| | - Hans-Peter Lang
- National Center of Competence for Research in Nanoscience, Institute of Physics, University of Basel, Basel, Switzerland
| | - Christoph Gerber
- National Center of Competence for Research in Nanoscience, Institute of Physics, University of Basel, Basel, Switzerland
| | - Martin Hegner
- CRANN, SFI Nanoscience Institute, Trinity College, University of Dublin, Dublin, Ireland
- * E-mail: (MH); (TB)
| | - Thomas Braun
- National Center of Competence for Research in Nanoscience, Institute of Physics, University of Basel, Basel, Switzerland
- CRANN, SFI Nanoscience Institute, Trinity College, University of Dublin, Dublin, Ireland
- * E-mail: (MH); (TB)
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22
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Abstract
The translocation of single-stranded DNA (ssDNA) across membranes of two cells is a fundamental biological process occurring in both bacterial conjugation and Agrobacterium pathogenesis. Whereas bacterial conjugation spreads antibiotic resistance, Agrobacterium facilitates efficient interkingdom transfer of ssDNA from its cytoplasm to the host plant cell nucleus. These processes rely on the Type IV secretion system (T4SS), an active multiprotein channel spanning the bacterial inner and outer membranes. T4SSs export specific proteins, among them relaxases, which covalently bind to the 5' end of the translocated ssDNA and mediate ssDNA export. In Agrobacterium tumefaciens, another exported protein-VirE2-enhances ssDNA transfer efficiency 2000-fold. VirE2 binds cooperatively to the transferred ssDNA (T-DNA) and forms a compact helical structure, mediating T-DNA import into the host cell nucleus. We demonstrated-using single-molecule techniques-that by cooperatively binding to ssDNA, VirE2 proteins act as a powerful molecular machine. VirE2 actively pulls ssDNA and is capable of working against 50-pN loads without the need for external energy sources. Combining biochemical and cell biology data, we suggest that, in vivo, VirE2 binding to ssDNA allows an efficient import and pulling of ssDNA into the host. These findings provide a new insight into the ssDNA translocation mechanism from the recipient cell perspective. Efficient translocation only relies on the presence of ssDNA binding proteins in the recipient cell that compacts ssDNA upon binding. This facilitated transfer could hence be a more general ssDNA import mechanism also occurring in bacterial conjugation and DNA uptake processes.
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Affiliation(s)
- Wilfried Grange
- Centre for Research on Adaptive Nanostructures and Nanodevices, Trinity College Dublin, Dublin, Ireland
- National Centre of Competence in Research Nanoscale Science, Institute of Physics, Basel, Switzerland
| | - Myriam Duckely
- M. E. Müller Institute for Structural Biology, Basel, Switzerland
- Novartis AG, Basel, Switzerland
| | - Sudhir Husale
- National Centre of Competence in Research Nanoscale Science, Institute of Physics, Basel, Switzerland
- Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
| | - Susan Jacob
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andreas Engel
- M. E. Müller Institute for Structural Biology, Basel, Switzerland
| | - Martin Hegner
- Centre for Research on Adaptive Nanostructures and Nanodevices, Trinity College Dublin, Dublin, Ireland
- National Centre of Competence in Research Nanoscale Science, Institute of Physics, Basel, Switzerland
- * To whom correspondence should be addressed. E-mail:
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23
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Huber F, Lang HP, Hegner M, Despont M, Drechsler U, Gerber C. Analyzing refractive index changes and differential bending in microcantilever arrays. Rev Sci Instrum 2008; 79:086110. [PMID: 19044391 DOI: 10.1063/1.2969912] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new microcantilever array design is investigated comprising eight flexible microcantilevers introducing two solid bars, enabling to subtract contributions from differences in refractive index in an optical laser read out system. Changes in the refractive index do not contribute undesirably to bending signals at picomolar to micromolar DNA or protein concentrations. However, measurements of samples with high salt concentrations or serum are affected, requiring corrections for refractive index artifacts. Moreover, to obtain a deeper understanding of molecular stress formation, the differential curvature of cantilevers is analyzed by positioning the laser spots along the surface of the levers during pH experiments.
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Affiliation(s)
- François Huber
- NCCR Nanoscale Science, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
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Grange W, Haas P, Wild A, Lieb MA, Calame M, Hegner M, Hecht B. Detection of transient events in the presence of background noise. J Phys Chem B 2008; 112:7140-4. [PMID: 18476735 DOI: 10.1021/jp7114862] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a method to detect and count transient burstlike signals in the presence of a significant stationary noise. To discriminate a transient signal from the background noise, an optimum threshold is determined using an iterative algorithm that yields the probability distribution of the background noise. Knowledge of the probability distribution of the noise then allows the determination of the number of transient events with a quantifiable error (wrong-positives). We apply the method, which does not rely on the choice of free parameters, to the detection and counting of transient single-molecule fluorescence events in the presence of a strong background noise. The method will be of importance in various ultra sensing applications.
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Affiliation(s)
- Wilfried Grange
- Centre for Research on Adaptive Nanostructures and Nanodevices, Trinity College Dublin, College Green, Dublin 2, Ireland.
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25
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Abstract
The interaction of cationic surfactants with single dsDNA molecules has been studied using force-measuring optical tweezers. For hydrophobic chains of length 12 and greater, pulling experiments show characteristic features (e.g. hysteresis between the pulling and relaxation curves, force-plateau along the force curves), typical of a condensed phase (compaction of a long DNA into a micron-sized particle). Depending on the length of the hydrophobic chain of the surfactant, we observe different mechanical behaviours of the complex (DNA-surfactants), which provide evidence for different binding modes. Taken together, our measurements suggest that short-chain surfactants, which do not induce any condensation, could lie down on the DNA surface and directly interact with the DNA grooves through hydrophobic–hydrophobic interactions. In contrast, long-chain surfactants could have their aliphatic tails pointing away from the DNA surface, which could promote inter-molecular interactions between hydrophobic chains and subsequently favour DNA condensation.
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Affiliation(s)
- Sudhir Husale
- Rowland Institute at Harvard, Harvard University, 100 Edwin H Land Blvd., Cambridge MA 02142, USA
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26
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Braun T, Ghatkesar MK, Barwich V, Backmann N, Huber F, Grange W, Nugaeva N, Lang HP, Ramseyer JP, Gerber C, Hegner M. Digital processing of multi-mode nano-mechanical cantilever data. ACTA ACUST UNITED AC 2007. [DOI: 10.1088/1742-6596/61/1/069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Lang HP, Ramseyer JP, Grange W, Braun T, Schmid D, Hunziker P, Jung C, Hegner M, Gerber C. An Artificial Nose Based on Microcantilever Array Sensors. ACTA ACUST UNITED AC 2007. [DOI: 10.1088/1742-6596/61/1/133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Huber F, Backmann N, Grange W, Hegner M, Gerber C, Lang HP. Analyzing Gene Expression Using Combined Nanomechanical Cantilever Sensors. ACTA ACUST UNITED AC 2007. [DOI: 10.1088/1742-6596/61/1/090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Nugaeva N, Gfeller KY, Backmann N, Düggelin M, Lang HP, Güntherodt HJ, Hegner M. An antibody-sensitized microfabricated cantilever for the growth detection of Aspergillus niger spores. Microsc Microanal 2007; 13:13-7. [PMID: 17234032 DOI: 10.1017/s1431927607070067] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2006] [Accepted: 09/18/2006] [Indexed: 05/13/2023]
Abstract
We demonstrate a new sensitive biosensor for detection of vital fungal spores of Aspergillus niger. The biosensor is based on silicon microfabricated cantilever arrays operated in dynamic mode. The change in resonance frequency of the sensor is a function of mass binding to the cantilever surface. For specific A. niger spore immobilization on the cantilever, each cantilever was individually coated with anti-Aspergillus niger polyclonal antibodies. We demonstrate the detection of single A. niger spores and their subsequent growth on the functionalized cantilever surface by online measurements of resonance frequency shifts. The new biosensor operating in humid air allows quantitative and qualitative detection of A. niger spores as well as detection of vital, functional spores in situ within approximately 4 h. The detection limit of the sensor is 103 CFU mL-1. Mass sensitivity of the cantilever sensor is approximately 53 pg Hz-1.
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Affiliation(s)
- Natalia Nugaeva
- Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
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30
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Dorrestijn M, Bietsch A, Açikalin T, Raman A, Hegner M, Meyer E, Gerber C. Chladni figures revisited based on nanomechanics. Phys Rev Lett 2007; 98:026102. [PMID: 17358621 DOI: 10.1103/physrevlett.98.026102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Indexed: 05/14/2023]
Abstract
Chladni patterns based on nanomechanics in the microfluidic environment are presented. In contrast with the macroscopic observations in the gaseous environment, nanoparticles are found to move to the nodes, whereas micron-sized particles move to the antinodes of the vibrating interface. This opens the door to size-based sorting of particles in microfluidic systems, and to highly parallel and controlled assembly of biosensors and nanoelectronic circuits.
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Affiliation(s)
- M Dorrestijn
- National Center of Competence in Research on Nanoscale Science, Institute of Physics, University of Basel, Basel, Switzerland
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31
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Watari M, Galbraith J, Lang HP, Sousa M, Hegner M, Gerber C, Horton MA, McKendry RA. Investigating the Molecular Mechanisms of In-Plane Mechanochemistry on Cantilever Arrays. J Am Chem Soc 2006; 129:601-9. [PMID: 17227023 DOI: 10.1021/ja065222x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Free-standing cantilevers, which directly translate specific biochemical reactions into micromechanical motion, have recently attracted much attention as label-free biosensors and micro/nano robotic devices. To exploit this mechanochemical sensing technology, it is essential to develop a fundamental understanding of the origins of surface stress. Here we report a detailed study into the molecular basis of stress generation in aqueous environments focusing on the pH titration of model mercaptohexadecanoic acid self-assembled monolayers (SAMs), using in situ reference cantilevers coated with nonionizable hexadecanethiol SAMs. Semiautomated data analysis and a statistical model were developed to quantify cyclic deprotonation/protonation reactions on multiple arrays. In-plane force titrations were found to have the sensitivity to detect ionic hydrogen bond formation between protonated and nonprotonated carboxylic acid groups in the proximity of the surface pK1/2, which generated a mean tensile differential surface stress of +1.2 +/- 0.3 mN/m at pH 6.0, corresponding to 1 pN attractive force between two adjacent MHA molecules. Conversely, the magnitude of compressive differential surface stress was found to increase progressively with pH >/= 7.0, reaching a maximum of -14.5 +/- 0.5 mN/m at pH 9.0, attributed to enhanced electrostatic repulsion between deprotonated carboxylic acid groups. However, striking differences were observed in the micromechanical responses to different ionic strength and ion species present in the aqueous environment, highlighting the critical role of counter- and co-ions on surface stress. Our findings provide fundamental insights into the molecular mechanisms of in-plane mechanochemistry, which may be exploited for biosensing and nanoactuation applications.
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Affiliation(s)
- Moyu Watari
- London Centre for Nanotechnology and Department of Medicine, University College London, 5 University Street, London WC1E 6JJ, UK
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32
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Zhang J, Lang HP, Huber F, Bietsch A, Grange W, Certa U, McKendry R, Güntherodt HJ, Hegner M, Gerber C. Rapid and label-free nanomechanical detection of biomarker transcripts in human RNA. Nat Nanotechnol 2006; 1:214-220. [PMID: 18654189 DOI: 10.1038/nnano.2006.134] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 10/30/2006] [Indexed: 05/26/2023]
Abstract
The availability of entire genome sequences has triggered the development of microarrays for clinical diagnostics that measure the expression levels of specific genes. Methods that involve labelling can achieve picomolar detection sensitivity, but they are costly, labour-intensive and time-consuming. Moreover, target amplification or biochemical labelling can influence the original signal. We have improved the biosensitivity of label-free cantilever-array sensors by orders of magnitude to detect mRNA biomarker candidates in total cellular RNA. Differential gene expression of the gene 1-8U, a potential marker for cancer progression or viral infections, has been observed in a complex background. The measurements provide results within minutes at the picomolar level without target amplification, and are sensitive to base mismatches. This qualifies the technology as a rapid method to validate biomarkers that reveal disease risk, disease progression or therapy response. We foresee cantilever arrays being used as a tool to evaluate treatment response efficacy for personalized medical diagnostics.
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Affiliation(s)
- J Zhang
- NCCR Nanoscale Science, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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33
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Huber F, Hegner M, Gerber C, Güntherodt HJ, Lang HP. Label free analysis of transcription factors using microcantilever arrays. Biosens Bioelectron 2006; 21:1599-605. [PMID: 16137876 DOI: 10.1016/j.bios.2005.07.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 07/20/2005] [Accepted: 07/22/2005] [Indexed: 10/25/2022]
Abstract
We report the measurement of protein interaction with double-stranded DNA oligonucleotides using cantilever microarray technology. We investigated two different DNA-binding proteins, the transcription factors SP1 and NF-kappaB, using cantilever arrays as they allow label-free measurement of different biomolecular interactions in parallel. Double-stranded DNA oligonucleotides containing a specific binding site for a transcription factor were sensitized on gold-coated cantilevers. The binding of the transcription factor creates a surface stress, resulting in a bending of the cantilevers. Both transcription factors could be detected independently at concentrations of 80-100 nM. A concentration dependence of the bending signal was measured using concentrations from 100 to 400 nM of NF-kappaB. The experiments show that the recognition sequence of one transcription factor can serve as a reference for the other, highlighting the sequence specificity of transcription factor binding.
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34
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Braun T, Backmann N, Vögtli M, Bietsch A, Engel A, Lang HP, Gerber C, Hegner M. Conformational change of bacteriorhodopsin quantitatively monitored by microcantilever sensors. Biophys J 2006; 90:2970-7. [PMID: 16443650 PMCID: PMC1414560 DOI: 10.1529/biophysj.105.072934] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriorhodopsin proteoliposomes were used as a model system to explore the applicability of micromechanical cantilever arrays to detect conformational changes in membrane protein patches. The three main results of our study concern: 1), reliable functionalization of micromechanical cantilever arrays with proteoliposomes using ink jet spotting; 2), successful detection of the prosthetic retinal removal (bleaching) from the bacteriorhodopsin protein by measuring the induced nanomechanical surface stress change; and 3), the quantitative response thereof, which depends linearly on the amount of removed retinal. Our results show this technique to be a potential tool to measure membrane protein-based receptor-ligand interactions and conformational changes.
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Affiliation(s)
- Thomas Braun
- National Center of Competence for Research in Nanoscale Science, Institute of Physics, and Maurice E. Müller Institute, Biozentrum, University of Basel, 4056 Basel, Switzerland
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35
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Nugaeva N, Gfeller KY, Backmann N, Lang HP, Düggelin M, Hegner M. Micromechanical cantilever array sensors for selective fungal immobilization and fast growth detection. Biosens Bioelectron 2005; 21:849-56. [PMID: 16257652 DOI: 10.1016/j.bios.2005.02.004] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 02/04/2005] [Accepted: 02/04/2005] [Indexed: 11/22/2022]
Abstract
We demonstrate the use of micromechanical cantilever arrays for selective immobilization and fast quantitative detection of vital fungal spores. Micro-fabricated uncoated as well as gold-coated silicon cantilevers were functionalized with concanavalin A, fibronectin or immunoglobulin G. In our experiments two major morphological fungal forms were used--the mycelial form Aspergillus niger and the unicellular yeast form Saccharomyces cerevisiae, as models to explore a new method for growth detection of eukaryotic organisms using cantilever arrays. We exploited the specific biomolecular interactions of surface grafted proteins with the molecular structures on the fungal cell surface. It was found that these proteins have different affinities and efficiencies to bind the spores. Maximum spore immobilization, germination and mycelium growth was observed on the immunoglobulin G functionalized cantilever surfaces. We show that spore immobilization and germination of the mycelial fungus A. niger and yeast S. cerevisiae led to shifts in resonance frequency within a few hours as measured by dynamically operated cantilever arrays, whereas conventional techniques would require several days. The biosensor could detect the target fungi in a range of 10(3) - 10(6) CFUml(-1). The measured shift is proportional to the mass of single fungal spores and can be used to evaluate spore contamination levels. Applications lie in the field of medical and agricultural diagnostics, food- and water-quality monitoring.
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Affiliation(s)
- Natalia Nugaeva
- Institute of Physics, University of Basel, Klingelbergstrasse 82, Switzerland
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36
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Backmann N, Zahnd C, Huber F, Bietsch A, Plückthun A, Lang HP, Güntherodt HJ, Hegner M, Gerber C. A label-free immunosensor array using single-chain antibody fragments. Proc Natl Acad Sci U S A 2005; 102:14587-92. [PMID: 16192357 PMCID: PMC1253559 DOI: 10.1073/pnas.0504917102] [Citation(s) in RCA: 232] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 09/01/2005] [Indexed: 11/18/2022] Open
Abstract
We report a microcantilever-based immunosensor operated in static deflection mode with a performance comparable with surface plasmon resonance, using single-chain Fv (scFv) antibody fragments as receptor molecules. As a model system scFv fragments with specificity to two different antigens were applied. We introduced a cysteine residue at the C terminus of each scFv construct to allow covalent attachment to gold-coated sensor interfaces in directed orientation. Application of an array enabled simultaneous deflection measurements of sensing and reference cantilevers. The differential deflection signal revealed specific antigen binding and was proportional to the antigen concentration in solution. Using small, oriented scFv fragments as receptor molecules we increased the sensitivity of microcantilevers to approximately 1 nM.
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Affiliation(s)
- Natalija Backmann
- National Center of Competence in Research for Nanoscience, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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37
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Braun T, Barwich V, Ghatkesar MK, Bredekamp AH, Gerber C, Hegner M, Lang HP. Micromechanical mass sensors for biomolecular detection in a physiological environment. Phys Rev E Stat Nonlin Soft Matter Phys 2005; 72:031907. [PMID: 16241482 DOI: 10.1103/physreve.72.031907] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/19/2005] [Indexed: 05/05/2023]
Abstract
Micromechanical cantilever arrays are used to measure time-resolved adsorption of tiny masses based on protein-ligand interactions. Here, streptavidin-biotin interactions are investigated in a physiological environment. A measurement method is introduced using higher flexural modes of a silicon cantilever in order to enhance the sensitivity of mass detection. Modeling the cantilever vibration in liquid allows the measurement of absolute mass changes. We show time-resolved mass adsorption of final 7+/-0.7 ng biotinylated latex beads. The sensitivity obtained is about 2.5 pg/Hz measuring at a center frequency of 750 kHz.
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Affiliation(s)
- Thomas Braun
- National Center of Competence for Research in Nanoscience, Institute of Physics, University of Basel, 4056 Basel, Switzerland
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38
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Gfeller KY, Nugaeva N, Hegner M. Micromechanical oscillators as rapid biosensor for the detection of active growth of Escherichia coli. Biosens Bioelectron 2005; 21:528-33. [PMID: 16076445 DOI: 10.1016/j.bios.2004.11.018] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 11/19/2004] [Accepted: 11/23/2004] [Indexed: 11/18/2022]
Abstract
A rapid biosensor for the detection of bacterial growth was developed using micromechanical oscillators coated by common nutritive layers. The change in resonance frequency as a function of the increasing mass on a cantilever array forms the basis of the detection scheme. The sensor is able to detect active growth of Escherichia coli cells within 1 h which is significantly faster than any conventional plating method which requires at least 24 h. The growth of E. coli was confirmed by scanning electron microscopy. This new sensing method for the detection of active bacterial growth allows future applications in, e.g., rapid antibiotic susceptibility testing by adding antibiotics to the nutritive layer.
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Affiliation(s)
- Karin Y Gfeller
- Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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39
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Shahgaldian P, Pieles U, Hegner M. Enantioselective recognition of phenylalanine by a chiral amphiphilic macrocycle at the air-water interface: a copper-mediated mechanism. Langmuir 2005; 21:6503-7. [PMID: 15982059 DOI: 10.1021/la0503101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The synthesis of a new chiral amphiphilic calix[4]resorcinarene, tetrakis(N-methylprolyl)tetraundecylcalix[4]resorcinarene (L-RA-Pro), bearing four L-prolyl moieties at the macrocyclic upper rim and four undecyl chains at the lower rim is described. This synthesis has been carried out via a Mannich-type reaction of L-proline and formaldehyde. It has been shown by means of Langmuir balance technique that L-RA-Pro self-assemble as well-defined monomolecular layers at the air-water interface. The effect of various cations on the stability of these monolayers has been studied. The experiments reveal that while there is a slight stabilization effect of K+, Cd2+, Co2+, Mg2+, and Ni2+, there is a high decrease in the collapse pressure in the presence of Cu(II) cation, showing that monolayers of L-RA-Pro, formed at the air-water interface, have a certain selectivity for copper(II) ions with regard to other cations tested. This supramolecular complex exhibits enantioselective recognition properties vs phenylalanine; the mechanism of this interaction is discussed.
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Affiliation(s)
- Patrick Shahgaldian
- Abteilung Chemie/Nano-Technologie, Fachhochschule beider Basel, Gründenstrasse 40, CH-4132 Muttenz, Switzerland.
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40
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Abstract
A rapid biosensor for the detection of bacterial growth was developed using micromechanical oscillators coated in common nutritive layers. The change in resonance frequency as a function of the increasing mass on a cantilever array forms the basis of the detection scheme. The calculated mass sensitivity according to the mechanical properties of the cantilever sensor is approximately 50 pg/Hz; this mass corresponds to an approximate sensitivity of approximately 100 Escherichia coli cells. The sensor is able to detect active growth of E. coli cells within 1 h. The starting number of E. coli cells initially attached to the sensor cantilever was, on average, approximately 1,000 cells. Furthermore, this method allows the detection of selective growth of E. coli within only 2 h by adding antibiotics to the nutritive layers. The growth of E. coli was confirmed by scanning electron microscopy. This new sensing method for the detection of selective bacterial growth allows future applications in, e.g., rapid antibiotic susceptibility testing.
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Affiliation(s)
- Karin Y Gfeller
- Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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Schoenauer R, Bertoncini P, Machaidze G, Aebi U, Perriard JC, Hegner M, Agarkova I. Myomesin is a molecular spring with adaptable elasticity. J Mol Biol 2005; 349:367-79. [PMID: 15890201 DOI: 10.1016/j.jmb.2005.03.055] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 03/11/2005] [Accepted: 03/21/2005] [Indexed: 11/19/2022]
Abstract
The M-band is a transverse structure in the center of the sarcomere, which is thought to stabilize the thick filament lattice. It was shown recently that the constitutive vertebrate M-band component myomesin can form antiparallel dimers, which might cross-link the neighboring thick filaments. Myomesin consists mainly of immunoglobulin-like (Ig) and fibronectin type III (Fn) domains, while several muscle types express the EH-myomesin splice isoform, generated by the inclusion of the unique EH-segment of about 100 amino acid residues (aa) in the center of the molecule. Here we use atomic force microscopy (AFM), transmission electron microscopy (TEM) and circular dichroism (CD) spectroscopy for the biophysical characterization of myomesin. The AFM identifies the "mechanical fingerprints" of the modules constituting the myomesin molecule. Stretching of homomeric polyproteins, constructed of Ig and Fn domains of human myomesin, produces a typical saw-tooth pattern in the force-extension curve. The domains readily refold after relaxation. In contrast, stretching of a heterogeneous polyprotein, containing several repeats of the My6-EH fragment reveals a long initial plateau corresponding to the sum of EH-segment contour lengths, followed by several My6 unfolding peaks. According to this, the EH-segment is characterized as an entropic chain with a persistence length of about 0.3nm. In TEM pictures, the EH-domain appears as a gap in the molecule, indicating a random coil conformation similar to the PEVK region of titin. CD spectroscopy measurements support this result, demonstrating a mostly non-folded conformation for the EH-segment. We suggest that similarly to titin, myomesin is a molecular spring, whose elasticity is modulated by alternative splicing. The Ig and Fn domains might function as reversible "shock absorbers" by sequential unfolding in the case of extremely high or long sustained stretching forces. These complex visco-elastic properties of myomesin might be crucial for the stability of the sarcomere.
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Affiliation(s)
- Roman Schoenauer
- Institute of Cell Biology, ETH Zürich-Hönggerberg, CH-8093 Zürich, Switzerland
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Bertoncini P, Schoenauer R, Agarkova I, Hegner M, Perriard JC, Güntherodt HJ. Study of the mechanical properties of myomesin proteins using dynamic force spectroscopy. J Mol Biol 2005; 348:1127-37. [PMID: 15854649 DOI: 10.1016/j.jmb.2005.03.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 03/13/2005] [Accepted: 03/14/2005] [Indexed: 11/22/2022]
Abstract
Myomesin is the most prominent structural component of the sarcomeric M-Band that is expressed in mammalian heart and skeletal muscles. Like titin, this protein is an intracellular member of the Ig-fibronectin superfamily, which has a flexible filamentous structure and which is largely composed of two types of domain that are similar to immunoglobulin (Ig)-like and fibronectin type III (FNIII) domains. Several myomesin isoforms have been identified, and their expression patterns are highly regulated both spatially and temporally. Particularly, alternative splicing in the central part of the molecule gives rise to an isoform, EH (embryonic heart)-myomesin, containing a serine and proline-rich insertion with no well-defined secondary structure, the EH segment. EH-myomesin represents the major myomesin isoform at embryonic stages of mammalian heart and is rapidly down-regulated around birth, but it is re-expressed in the heart of patients suffering from dilated cardio-myopathy. Here, in order to facilitate a better understanding of the physiological, and possibly pathological, functions of myomesin proteins, we explore the mechanical stability, elasticity and force-driven structural changes of human myomesin's sub-molecular segments using single-molecule force spectroscopy and protein engineering. We find that human myomesin molecules are composed of modules (Ig and FNIII), that are designed to withstand force and we demonstrate that the human cardiac EH segment functions like an additional elastic stretch in the middle part of the EH-myomesin and behaves like a random coil. Consequently myomesin isoforms (proteins with or without the EH segment) have different elastic properties, the EH-myomesin being the more compliant one. These findings imply that the compliance of the M-band increases with the amount of EH-myomesin it contains. So, we provide the evidence that not only titin but also other sarcomeric proteins have complicated visco-elastic properties depending on the contractile parameters in different muscle types.
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Affiliation(s)
- P Bertoncini
- Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
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Hegner M. The Basel NanoBio-Network. Chimia (Aarau) 2004. [DOI: 10.2533/000942904777677164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Affiliation(s)
- Martin Hegner
- NCCR Nanoscale Science, Department of Physics, University of Basel, Switzerland
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Bietsch A, Hegner M, Lang HP, Gerber C. Inkjet deposition of alkanethiolate monolayers and DNA oligonucleotides on gold: evaluation of spot uniformity by wet etching. Langmuir 2004; 20:5119-22. [PMID: 15984277 DOI: 10.1021/la049621m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Inkjet printing allows localized, contact-free deposition of liquids onto arbitrary substrates. In this article we demonstrate the fast formation of high-quality self-assembled monolayers (SAMs) on gold surfaces. Using a selective etch process, we verify the uniformity of the deposited spots. A direct comparison with microcontact-printed SAMs on Au revealed similar resist quality as inkjet-deposited alkanethiolate SAMs. Likewise, inkjet printing of thiol-functionalized and non-thiolated single-stranded DNA oligomers formed molecular layers protecting Au from etchants. For all compounds used, we achieved etched patterns that were homogeneous and free of defects. These results indicate that an inkjet is a convenient tool for surface functionalization and the direct writing of molecular films and resists.
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Affiliation(s)
- Alexander Bietsch
- National Competence Centre in Research for Nanoscience, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
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Schwarzenbach MS, Reimann P, Thommen V, Hegner M, Mumenthaler M, Schwob J, Güntherodt HJ. Topological structure and chemical composition of inner surfaces of borosilicate vials. PDA J Pharm Sci Technol 2004; 58:169-75. [PMID: 15233256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The use of atomic force microscopy (AFM) and x-ray photoelectron spectroscopy (XPS) is described to characterize the inner surfaces of pharmaceutical vials. The two type I borosilicate glasses included in this study slightly differ in their amounts of alkaline oxides. The topography and chemistry of the inner surfaces of vials are predominantly caused by the forming process. A structural and chemical modification of the inner surface of vials was also observed when exposing the surface to different pH conditions and special treatment like washing and sterilization, which are routine operation steps during galenical manufacturing.
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Hegner M, Grange W, Bertoncini P. Measurement of Single Molecular Interactions by Dynamic Force Microscopy. Atomic Force Microscopy 2003; 242:369-81. [PMID: 14578536 DOI: 10.1385/1-59259-647-9:369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin Hegner
- NCCR Nanoscale Science, Department of Physics, University of Basel, Switzerland
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Hegner M, Grange W. Mechanics and imaging of single DNA molecules. J Muscle Res Cell Motil 2003; 23:367-75. [PMID: 12785091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
We review recent experiments that have revealed mechanical properties of single DNA molecules using advanced manipulation and force sensing techniques(scanning force microscopy (SFM), optical or magnetic tweezers, microneedles). From such measurements, intrinsic relevant parameters (persistence length, stretch modulus) as well as their dependence on external parameters (non-physiological conditions, coating with binding agents or proteins) are obtained on a single-molecule level. In addition, imaging of DNA molecules using SFM is presented.
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Affiliation(s)
- M Hegner
- Institute of Physics, NCCR Nanoscale Science, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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