1
|
Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
Collapse
Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| |
Collapse
|
2
|
Incaviglia I, Frutiger A, Blickenstorfer Y, Treindl F, Ammirati G, Lüchtefeld I, Dreier B, Plückthun A, Vörös J, Reichmuth AM. An Approach for the Real-Time Quantification of Cytosolic Protein-Protein Interactions in Living Cells. ACS Sens 2021; 6:1572-1582. [PMID: 33759497 DOI: 10.1021/acssensors.0c02480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In recent years, cell-based assays have been frequently used in molecular interaction analysis. Cell-based assays complement traditional biochemical and biophysical methods, as they allow for molecular interaction analysis, mode of action studies, and even drug screening processes to be performed under physiologically relevant conditions. In most cellular assays, biomolecules are usually labeled to achieve specificity. In order to overcome some of the drawbacks associated with label-based assays, we have recently introduced "cell-based molography" as a biosensor for the analysis of specific molecular interactions involving native membrane receptors in living cells. Here, we expand this assay to cytosolic protein-protein interactions. First, we created a biomimetic membrane receptor by tethering one cytosolic interaction partner to the plasma membrane. The artificial construct is then coherently arranged into a two-dimensional pattern within the cytosol of living cells. Thanks to the molographic sensor, the specific interactions between the coherently arranged protein and its endogenous interaction partners become visible in real time without the use of a fluorescent label. This method turns out to be an important extension of cell-based molography because it expands the range of interactions that can be analyzed by molography to those in the cytosol of living cells.
Collapse
Affiliation(s)
- Ilaria Incaviglia
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Yves Blickenstorfer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Fridolin Treindl
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Giulia Ammirati
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Ines Lüchtefeld
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Janos Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas M Reichmuth
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| |
Collapse
|
3
|
Reichmuth AM, Kübrich K, Blickenstorfer Y, Frutiger A, Momotenko D, Gatterdam V, Treindl F, Fattinger C, Vörös J. Investigating Complex Samples with Molograms of Low-Affinity Binders. ACS Sens 2021; 6:1067-1076. [PMID: 33629586 DOI: 10.1021/acssensors.0c02346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In vitro diagnostics relies on the quantification of minute amounts of a specific biomolecule, called biomarker, from a biological sample. The majority of clinically relevant biomarkers for conditions beyond infectious diseases are detected by means of binding assays, where target biomarkers bind to a solid phase and are detected by biochemical or physical means. Nonspecifically bound biomolecules, the main source of variation in such assays, need to be washed away in a laborious process, restricting the development of widespread point-of-care diagnostics. Here, we show that a diffractometric assay provides a new, label-free possibility to investigate complex samples, such as blood plasma. A coherently arranged sub-micron pattern, that is, a peptide mologram, is created to demonstrate the insensitivity of this diffractometric assay to the unwanted masking effect of nonspecific interactions. In addition, using an array of low-affinity binders, we also demonstrate the feasibility of molecular profiling of blood plasma in real time and show that individual patients can be differentiated based on the binding kinetics of circulating proteins.
Collapse
Affiliation(s)
- Andreas M. Reichmuth
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Katharina Kübrich
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Yves Blickenstorfer
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Volker Gatterdam
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Fridolin Treindl
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Christof Fattinger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| |
Collapse
|
4
|
Frutiger A, Fattinger C, Vörös J. Ultra-Stable Molecular Sensors by Sub-Micron Referencing and Why They Should Be Interrogated by Optical Diffraction-Part I. The Concept of a Spatial Affinity Lock-in Amplifier. SENSORS (BASEL, SWITZERLAND) 2021; 21:E469. [PMID: 33440783 PMCID: PMC7827303 DOI: 10.3390/s21020469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022]
Abstract
Label-free optical biosensors, such as surface plasmon resonance, are sensitive and well-established for the characterization of molecular interactions. Yet, these sensors require stabilization and constant conditions even with the use of reference channels. In this paper, we use tools from signal processing to show why these sensors are so cross-sensitive and how to overcome their drawbacks. In particular, we conceptualize the spatial affinity lock-in as a universal design principle for sensitive molecular sensors even in the complete absence of stabilization. The spatial affinity lock-in is analogous to the well-established time-domain lock-in. Instead of a time-domain signal, it modulates the binding signal at a high spatial frequency to separate it from the low spatial frequency environmental noise in Fourier space. In addition, direct sampling of the locked-in sensor's response in Fourier space enabled by diffraction has advantages over sampling in real space as done by surface plasmon resonance sensors using the distributed reference principle. This paper and part II hint at the potential of spatially locked-in diffractometric biosensors to surpass state-of-the-art temperature-stabilized refractometric biosensors. Even simple, miniaturized and non-stabilized sensors might achieve the performance of bulky lab instruments. This may enable new applications in label-free analysis of molecular binding and point-of-care diagnostics.
Collapse
Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, University and ETH Zürich, 8092 Zürich, Switzerland;
| | - Christof Fattinger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute of Biomedical Engineering, University and ETH Zürich, 8092 Zürich, Switzerland;
| |
Collapse
|
5
|
Frutiger A, Gatterdam K, Blickenstorfer Y, Reichmuth AM, Fattinger C, Vörös J. Ultra Stable Molecular Sensors by Submicron Referencing and Why They Should Be Interrogated by Optical Diffraction-Part II. Experimental Demonstration. SENSORS (BASEL, SWITZERLAND) 2020; 21:E9. [PMID: 33375003 PMCID: PMC7792590 DOI: 10.3390/s21010009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Label-free optical biosensors are an invaluable tool for molecular interaction analysis. Over the past 30 years, refractometric biosensors and, in particular, surface plasmon resonance have matured to the de facto standard of this field despite a significant cross reactivity to environmental and experimental noise sources. In this paper, we demonstrate that sensors that apply the spatial affinity lock-in principle (part I) and perform readout by diffraction overcome the drawbacks of established refractometric biosensors. We show this with a direct comparison of the cover refractive index jump sensitivity as well as the surface mass resolution of an unstabilized diffractometric biosensor with a state-of-the-art Biacore 8k. A combined refractometric diffractometric biosensor demonstrates that a refractometric sensor requires a much higher measurement precision than the diffractometric to achieve the same resolution. In a conceptual and quantitative discussion, we elucidate the physical reasons behind and define the figure of merit of diffractometric biosensors. Because low-precision unstabilized diffractometric devices achieve the same resolution as bulky stabilized refractometric sensors, we believe that label-free optical sensors might soon move beyond the drug discovery lab as miniaturized, mass-produced environmental/medical sensors. In fact, combined with the right surface chemistry and recognition element, they might even bring the senses of smell/taste to our smart devices.
Collapse
Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, University and ETH Zürich, 8092 Zürich, Switzerland; (A.F.); (Y.B.); (A.M.R.)
| | - Karl Gatterdam
- Institute of Structural Biology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany;
| | - Yves Blickenstorfer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, University and ETH Zürich, 8092 Zürich, Switzerland; (A.F.); (Y.B.); (A.M.R.)
| | - Andreas Michael Reichmuth
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, University and ETH Zürich, 8092 Zürich, Switzerland; (A.F.); (Y.B.); (A.M.R.)
| | - Christof Fattinger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, University and ETH Zürich, 8092 Zürich, Switzerland; (A.F.); (Y.B.); (A.M.R.)
| |
Collapse
|