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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: 18] [Impact Index Per Article: 6.0] [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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Label-free Pb2+ detection on the layer-by-layer platform using real-time dual polarization interferometry. Talanta 2019; 202:336-341. [DOI: 10.1016/j.talanta.2019.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/20/2019] [Accepted: 05/02/2019] [Indexed: 11/17/2022]
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Zhou X, Yao D, He M, Xiao S, Liang H. Optimizing the Toehold Strategy of On-Chip Nucleic Acid Hybridization Probe for the Discrimination of Single Nucleotide Polymorphism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14811-14816. [PMID: 30110553 DOI: 10.1021/acs.langmuir.8b02134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The synthetic DNA hybridization probe has proved its importance in biology and biotechnology. In this study, taking advantage of a novel analytical technique called dual polarization interferometry (DPI), the influence of the toehold strategy of on-chip DNA hybridization probe on the discrimination of single nucleotide polymorphism (SNP) was investigated. Through adjusting the toehold length, the toehold strategies of on-chip toehold exchange probe were thoroughly optimized. For the "6/5" probe, an optimal discrimination factor of 78% against the spurious target was achieved. Moreover, the ability of the on-chip probe in SNP discrimination was significantly enhanced compared to its pure solution counterpart. This simple and rapid detection method for SNP discrimination based on the on-chip toehold exchange probe will show great potential in disease diagnosis.
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Affiliation(s)
- Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Miao He
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China
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Junius N, Oksanen E, Terrien M, Berzin C, Ferrer JL, Budayova-Spano M. A crystallization apparatus for temperature-controlled flow-cell dialysis with real-time visualization. J Appl Crystallogr 2016; 49:806-813. [PMID: 27275137 PMCID: PMC4886980 DOI: 10.1107/s1600576716004635] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
Many instrumentation developments in crystallization have concentrated on massive parallelization assays and reduction of sample volume per experiment to find initial crystallization conditions. Yet improving the size and diffraction quality of the crystals for diffraction studies often requires decoupling of crystal nucleation and growth. This in turn requires the control of variables such as precipitant and protein concentration, equilibration rate, and temperature, which are all difficult parameters to control in the existing setups. The success of the temperature-controlled batch method, originally developed to grow very large crystals for neutron crystallography, demonstrated that the rational optimization of crystal growth has potential in structural biology. A temperature-controlled dialysis button has been developed for our previous device, and a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature-precipitant concentration phase diagrams has been constructed. The presented approach differs from the current paradigm, since it involves serial instead of parallel experiments, exploring multiple crystallization conditions with the same protein sample. The sample is not consumed in the experiment and the conditions can be changed in a reversible fashion, using dialysis with a flowing precipitant reservoir as well as precise temperature control. The control software allows visualization of the crystals, as well as control of the temperature and composition of the crystallization solution. The rational crystallization optimization strategies presented here allow tailoring of crystal size, morphology and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.
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Affiliation(s)
- Niels Junius
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Esko Oksanen
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Christophe Berzin
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Jean-Luc Ferrer
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Monika Budayova-Spano
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
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Zheng Y, Hu T, Chen C, Yang F, Yang X. An anti-fouling aptasensor for detection of thrombin by dual polarization interferometry. Chem Commun (Camb) 2016; 51:5645-8. [PMID: 25714792 DOI: 10.1039/c4cc10337h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An anti-fouling surface was designed to effectively resist nonspecific protein adsorption using dual polarization interferometry, based on which the aptasensor for detection of thrombin was fabricated according to the specific interaction between thrombin and its 15-mer aptamer.
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Affiliation(s)
- Yu Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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Li K, Duan M, Wang H, Xiong Y, Zhang J, Jing B. Investigation of adsorption dynamics of demulsifier on asphaltene by dual polarization interferometry measurement. Colloid Polym Sci 2015. [DOI: 10.1007/s00396-015-3724-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Grøftehauge MK, Hajizadeh NR, Swann MJ, Pohl E. Protein-ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:36-44. [PMID: 25615858 PMCID: PMC4304684 DOI: 10.1107/s1399004714016617] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 07/17/2014] [Indexed: 11/10/2022]
Abstract
Over the last decades, a wide range of biophysical techniques investigating protein-ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.
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Affiliation(s)
| | - Nelly R. Hajizadeh
- Chemistry Department, Durham University, South Road, Durham DH1 3LE, England
| | - Marcus J. Swann
- Farfield, Biolin Scientific, 62 Wellington Road South, Stockport, Cheshire SK1 3SU, England
| | - Ehmke Pohl
- Chemistry Department and School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, England
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Li K, Duan M, Wang H, Zhang J, Jing B. Investigation on the adsorption behavior of polyacrylamide on resin by dual polarization interferometry. RSC Adv 2015. [DOI: 10.1039/c5ra00291e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The real-time adsorption data of polyacrylamide on resin were investigated by dual polarization interferometry, two adsorption types were obtained.
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Affiliation(s)
- Keyi Li
- College of Chemistry and Chemical Engineering
- Southwest Petroleum University
- China
| | - Ming Duan
- College of Chemistry and Chemical Engineering
- Southwest Petroleum University
- China
- Oil & Gas Field Applied Chemistry Key Laboratory of Sichuan Province
- Chengdu 610500
| | - Hu Wang
- Oil & Gas Field Applied Chemistry Key Laboratory of Sichuan Province
- Chengdu 610500
- China
| | - Jian Zhang
- State Key Laboratory of Offshore Oil Exploitation
- China
| | - Bo Jing
- State Key Laboratory of Offshore Oil Exploitation
- China
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Escorihuela J, González-Martínez MÁ, López-Paz JL, Puchades R, Maquieira Á, Gimenez-Romero D. Dual-Polarization Interferometry: A Novel Technique To Light up the Nanomolecular World. Chem Rev 2014; 115:265-94. [DOI: 10.1021/cr5002063] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jorge Escorihuela
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - Miguel Ángel González-Martínez
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - José Luis López-Paz
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - Rosa Puchades
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - Ángel Maquieira
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - David Gimenez-Romero
- Physical
Chemistry Department, Faculty of Chemistry, Universitat de València, Avenida Dr. Moliner 50, 46100 Burjassot, València, Spain
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Zheng Y, Yang C, Yang F, Yang X. Real-time study of interactions between cytosine-cytosine pairs in DNA oligonucleotides and silver ions using dual polarization interferometry. Anal Chem 2014; 86:3849-55. [PMID: 24611666 DOI: 10.1021/ac403992r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The real-time conformational changes of cytosine (C)-rich ssDNA oligonucleotides upon binding with silver ions (Ag(+)) were studied using dual polarization interferometry (DPI). Upon the addition of Ag(+), Ag(+) selectively bound to cytosine-cytosine mismatches and formed C-Ag(+)-C complexes, inducing change of the structure of the C-rich ssDNA from random coil conformation to duplex conformation, whereas the control ssDNA without cytosine-cytosine mismatches had no such signal, which was consistent with circular dichroism (CD) characterization. The conformational change of DNA was reflected on the changes of the mass, thickness, and density values resolved by DPI. The calibration curves showed that as the concentration of Ag(+) increased from 10 nM to 8 μM, the thickness and mass values increased linearly while the density values decreased linearly. Other metal ions such as K(+), Ca(2+), Na(+), Mg(2+), Zn(2+), Mn(2+), Ni(2+), and Pb(2+) did not interfere with the interaction between Ag(+) and C-rich ssDNA, indicating that this method had a good selectivity. The practical application of this biosensor was also investigated in real samples such as drinking water. Besides, cysteine could specifically capture Ag(+) from C-Ag(+)-C complexes and transformed the structure of the C-rich DNA back from rigid double-stranded conformation to random coil conformation, which allowed cysteine to be detected selectively as well. It is expected that this biosensing strategy may be utilized to study the interaction of DNA with other molecules.
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Affiliation(s)
- Yu Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
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Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
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