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Saftics A, Kurunczi S, Peter B, Szekacs I, Ramsden JJ, Horvath R. Data evaluation for surface-sensitive label-free methods to obtain real-time kinetic and structural information of thin films: A practical review with related software packages. Adv Colloid Interface Sci 2021; 294:102431. [PMID: 34330074 DOI: 10.1016/j.cis.2021.102431] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 02/07/2023]
Abstract
Interfacial layers are important in a wide range of applications in biomedicine, biosensing, analytical chemistry and the maritime industries. Given the growing number of applications, analysis of such layers and understanding their behavior is becoming crucial. Label-free surface sensitive methods are excellent for monitoring the formation kinetics, structure and its evolution of thin layers, even at the nanoscale. In this paper, we review existing and commercially available label-free techniques and demonstrate how the experimentally obtained data can be utilized to extract kinetic and structural information during and after formation, and any subsequent adsorption/desorption processes. We outline techniques, some traditional and some novel, based on the principles of optical and mechanical transduction. Our special focus is the current possibilities of combining label-free methods, which is a powerful approach to extend the range of detected and deduced parameters. We summarize the most important theoretical considerations for obtaining reliable information from measurements taking place in liquid environments and, hence, with layers in a hydrated state. A thorough treamtmaent of the various kinetic and structural quantities obtained from evaluation of the raw label-free data are provided. Such quantities include layer thickness, refractive index, optical anisotropy (and molecular orientation derived therefrom), degree of hydration, viscoelasticity, as well as association and dissociation rate constants and occupied area of subsequently adsorbed species. To demonstrate the effect of variations in model conditions on the observed data, simulations of kinetic curves at various model settings are also included. Based on our own extensive experience with optical waveguide lightmode spectroscopy (OWLS) and the quartz crystal microbalance (QCM), we have developed dedicated software packages for data analysis, which are made available to the scientific community alongside this paper.
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Orgovan N, Patko D, Hos C, Kurunczi S, Szabó B, Ramsden JJ, Horvath R. Sample handling in surface sensitive chemical and biological sensing: a practical review of basic fluidics and analyte transport. Adv Colloid Interface Sci 2014; 211:1-16. [PMID: 24846752 DOI: 10.1016/j.cis.2014.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
Abstract
This paper gives an overview of the advantages and associated caveats of the most common sample handling methods in surface-sensitive chemical and biological sensing. We summarize the basic theoretical and practical considerations one faces when designing and assembling the fluidic part of the sensor devices. The influence of analyte size, the use of closed and flow-through cuvettes, the importance of flow rate, tubing length and diameter, bubble traps, pressure-driven pumping, cuvette dead volumes, and sample injection systems are all discussed. Typical application areas of particular arrangements are also highlighted, such as the monitoring of cellular adhesion, biomolecule adsorption-desorption and ligand-receptor affinity binding. Our work is a practical review in the sense that for every sample handling arrangement considered we present our own experimental data and critically review our experience with the given arrangement. In the experimental part we focus on sample handling in optical waveguide lightmode spectroscopy (OWLS) measurements, but the present study is equally applicable for other biosensing technologies in which an analyte in solution is captured at a surface and its presence is monitored. Explicit attention is given to features that are expected to play an increasingly decisive role in determining the reliability of (bio)chemical sensing measurements, such as analyte transport to the sensor surface; the distorting influence of dead volumes in the fluidic system; and the appropriate sample handling of cell suspensions (e.g. their quasi-simultaneous deposition). At the appropriate places, biological aspects closely related to fluidics (e.g. cellular mechanotransduction, competitive adsorption, blood flow in veins) are also discussed, particularly with regard to their models used in biosensing.
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Huang F, Xu P, Liang H. Using dual-polarization interferometry to study surface-initiated DNA hybridization chain reactions in real time. Biosens Bioelectron 2014; 51:317-23. [DOI: 10.1016/j.bios.2013.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
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Rawlings RA, Krishnan V, Walter NG. Viral RNAi suppressor reversibly binds siRNA to outcompete Dicer and RISC via multiple turnover. J Mol Biol 2011; 408:262-76. [PMID: 21354178 DOI: 10.1016/j.jmb.2011.02.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 02/02/2011] [Accepted: 02/16/2011] [Indexed: 01/13/2023]
Abstract
RNA interference is a conserved gene regulatory mechanism employed by most eukaryotes as a key component of their innate immune response to viruses and retrotransposons. During viral infection, the RNase-III-type endonuclease Dicer cleaves viral double-stranded RNA into small interfering RNAs (siRNAs) 21-24 nucleotides in length and helps load them into the RNA-induced silencing complex (RISC) to guide the cleavage of complementary viral RNA. As a countermeasure, many viruses have evolved viral RNA silencing suppressors (RSS) that tightly, and presumably quantitatively, bind siRNAs to thwart RNA-interference-mediated degradation. Viral RSS proteins also act across kingdoms as potential immunosuppressors in gene therapeutic applications. Here we report fluorescence quenching and electrophoretic mobility shift assays that probe siRNA binding by the dimeric RSS p19 from Carnation Italian Ringspot Virus, as well as by human Dicer and RISC assembly complexes. We find that the siRNA:p19 interaction is readily reversible, characterized by rapid binding [(1.69 ± 0.07) × 10(8) M(-)(1) s(-1)] and marked dissociation (k(off)=0.062 ± 0.002 s(-1)). We also observe that p19 efficiently competes with recombinant Dicer and inhibits the formation of RISC-related assembly complexes found in human cell extract. Computational modeling based on these results provides evidence for the transient formation of a ternary complex between siRNA, human Dicer, and p19. An expanded model of RNA silencing indicates that multiple turnover by reversible binding of siRNAs potentiates the efficiency of the suppressor protein. Our predictive model is expected to be applicable to the dosing of p19 as a silencing suppressor in viral gene therapy.
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Affiliation(s)
- Renata A Rawlings
- Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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Abstract
AbstractSemiconductor quantum dots of cadmium sulfide, CdS, are approximately the size of proteins and are photoluminescent in the red, yellow, or green, depending on surface preparation. This photoluminescence is very sensitive to the Nature and amount of adsorbates. We have found that DNAs with intrinsic curvature adsorb more strongly to the surface of 47 Å CdS quantum dots, as judged by concentration-dependent changes in photoluminescence. The binding constants we obtain are similar to those found for nonspecific protein-DNA interactions. The surface groups of the CdS substrate also influence DNA adsorption. Thus these protein-sized colloidal particles can be used in chemical sensing applications for curved or kinked DNA; DNA with unusual structures is thought to influence biological function such as transcription.
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Zhang J, Li H, Chen W, Cao P, Wang M. Preparation of extracellular domain 3 of human VEGF receptor-2 and the monitoring of its real-time binding to VEGF by biosensors. Biotechnol Prog 2010; 25:1703-8. [PMID: 19731341 DOI: 10.1002/btpr.252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) plays an important role in stimulating the proliferation of endothelial cells and improving the permeability of blood vessels, which is involved in tumor angiogenesis, a process that is essential for tumor growth and metastasis. In this study, we describe a method for high yield of recombinant extracellular domain 3 (KDR3) of human VEGFR-2 in an Escherichia coli system with further purification by cation exchange chromatography and immobilized metal affinity chromatography (IMAC). The biological activity of recombinant KDR3 was performed by sequestering VEGF in HUVEC proliferation assay. The real-time binding of human VEGF to immobilized KDR3 was monitored by a label-free biosensor, Optical waveguide lightmode spectroscopy (OWLS). Under the given experimental conditions, the association rate constant k(a) was 4.2 x 10(3) M(-1) s(-1) and the dissociation rate k(d) was 5.1 x 10(-3) s(-1). The dissociation constant K(D) was then calculated to be 1.2 x 10(-6) M. The obtained values will serve as baseline parameters for the design of improved versions of recombinant soluble VEGF receptors and the evaluation of developed anti-KDR antibodies. In addition, such a scenario established by the use of OWLS will potentiate the kinetic study of ligand/receptor and antigen/antibody. The receptor discussed here, which block VEGF binding to cell membrane KDR, have potential clinical application in the treatment of cancer and other diseases where pathological angiogenesis is involved.
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Affiliation(s)
- Juan Zhang
- School of Life Science & Technology, China Pharmaceutical University, Nanjing 210009, PR China
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Shanshiashvili LV, Suknidze NC, Machaidze GG, Mikeladze DG, Ramsden JJ. Adhesion and clustering of charge isomers of myelin basic protein at model myelin membranes. Arch Biochem Biophys 2003; 419:170-7. [PMID: 14592460 DOI: 10.1016/j.abb.2003.09.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The association of myelin basic protein charge isomers with the lipid part of the myelin membrane was investigated at the microscopic (molecular) level in a model membrane system, using optical waveguide lightmode spectrometry to determine with high precision the kinetics of association and dissociation to planar phospholipid membranes under controlled hydrodynamic conditions and over a range of protein concentrations. Detailed analysis of the data revealed a rich and intricate behaviour and clearly showed that the membrane protein affinity is characterized by at least four independent parameters: (i) the association rate coefficient characterizing the protein-membrane interaction energy as the protein approaches the fluid-membrane interface; (ii) the protein-membrane adhesion, i.e., the probability that it will remain at the membrane after arrival; (iii) the protein conformation at the membrane; and (iv) the protein's tendency to cluster at the membrane. Some of these parameters varied in characteristic ways as the bulk solution concentration of the protein was varied, giving further clues to the detailed molecular comportment of the protein. The parameters and their characteristic variations with bulk concentration were markedly different for the different isomers. Implications of these results for neurological disorders involving demyelination, such as multiple sclerosis, are discussed.
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Affiliation(s)
- L V Shanshiashvili
- I.S. Beritashvili Institute of Physiology, Georgian Academy of Sciences, Tbilisi, Georgia
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Yang F, Ouporov IV, Fernandes C, Motriuk D, Thomasson KA. Brownian Dynamics Simulating the Ionic-Strength Dependence of the Nonspecific Association of 434 Cro Repressor Binding B-DNA. J Phys Chem B 2001. [DOI: 10.1021/jp012122z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fan Yang
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202-9024, Lansing Community College, P.O. Box 40010, Lansing, Michigan 48901-7210, and Division of Physical Science, Casper College, Casper, Wyoming 82601
| | - Igor V. Ouporov
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202-9024, Lansing Community College, P.O. Box 40010, Lansing, Michigan 48901-7210, and Division of Physical Science, Casper College, Casper, Wyoming 82601
| | - Coretta Fernandes
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202-9024, Lansing Community College, P.O. Box 40010, Lansing, Michigan 48901-7210, and Division of Physical Science, Casper College, Casper, Wyoming 82601
| | - Dagmara Motriuk
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202-9024, Lansing Community College, P.O. Box 40010, Lansing, Michigan 48901-7210, and Division of Physical Science, Casper College, Casper, Wyoming 82601
| | - Kathryn A. Thomasson
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202-9024, Lansing Community College, P.O. Box 40010, Lansing, Michigan 48901-7210, and Division of Physical Science, Casper College, Casper, Wyoming 82601
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Hall D. Use of optical biosensors for the study of mechanistically concerted surface adsorption processes. Anal Biochem 2001; 288:109-25. [PMID: 11152582 DOI: 10.1006/abio.2000.4851] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advent of commercial optical biosensors, such as the BIAcore from Pharmacia and IAsys from Affinity Sensors, has made available to the biochemist a powerful means to examine and characterize the interaction of biological macromolecules with a binding surface. By analysis of the kinetic and equilibrium aspects of the observed experimental adsorption isotherms, rate and affinity constants can be determined. This Review focuses on pertinent aspects of the technology and its use for the performance and quantitative characterization of some various types of mechanistically concerted adsorption behavior.
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Affiliation(s)
- D Hall
- Section on Physical Biochemistry, National Institute of Diabetes, Digestive, and Kidney Disease, Bethesda, Maryland, 20892, USA.
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Thomasson KA, Ouporov IV, Baumgartner T, Czlapinski J, Kaldor T, Northrup SH. Free Energy of Nonspecific Binding of Cro Repressor Protein to DNA. J Phys Chem B 1997. [DOI: 10.1021/jp971924k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathryn A. Thomasson
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58203-9024, and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505
| | - Igor V. Ouporov
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58203-9024, and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505
| | - Tamara Baumgartner
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58203-9024, and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505
| | - Jennifer Czlapinski
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58203-9024, and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505
| | - Thea Kaldor
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58203-9024, and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505
| | - Scott H. Northrup
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58203-9024, and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505
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Mahtab R, Rogers JP, Singleton CP, Murphy CJ. Preferential Adsorption of a “Kinked” DNA to a Neutral Curved Surface: Comparisons to and Implications for Nonspecific DNA−Protein Interactions. J Am Chem Soc 1996. [DOI: 10.1021/ja961602e] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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