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32 Dual Polarization Interferometry: A Real-Time Optical Technique for Measuring (Bio)molecular Orientation, Structure and Function at the Solid/Liquid Interface Graham H. Cross,1 Neville J. Freeman2 and Marcus J. Swann2 1 Department of Physics, Durham University, Durham, UK and 2 Farfield Scientific Ltd., Crewe, UK 1 INTRODUCTION Here we look at one such technique, dual polar- ization interferometry (DPI). This optical, surface analytical technique provides a multiparametric The challenging task of understanding and mea- measurement of molecules at a surface to give suring the function of proteins and other biological information on molecular dimension (layer thick- molecules in all their structural and environmental complexity is one that has spawned a myriad of ness) and packing (layer refractive index (RI), den- different techniques in the field of biological sci- sity) and surface loading and stoichiometry (mass). ences. These span those providing exquisite detail This combines the analytical nature of neutron in terms of molecular structure of a static system, reflection with the real-time, bench-top accessibil- such as X-ray crystallography or neutron reflec- ity associated with biosensors and can be used to tion, to those providing dynamic measurements of provide a link between a molecule’s structure and protein function such as protein–protein interac- its function. tion kinetics measured by some of the biosens- This chapter puts DPI in the context of other ing techniques covered in this handbook. Such multiparametric optical techniques, outlines the measurements provide pieces of a jigsaw puz- principles behind the technology and its imple- zle which need to be combined with others to mentation together with some simple examples provide a full picture. Of course, the function to provide validation of the measurement. The of any (bio)molecule is critically dependent on basic experimental and data analysis methods are its environment, structure, and molecular arrange- covered together with examples of areas of appli- ment. As such the ability to provide information cation of the technology specifically where struc- linking these different areas is of fundamental tural information complements more conventional interest. “mass” dependent measurement. Handbook of Biosensors and Biochips. Edited by Robert S. Marks, David C. Cullen, Isao Karube, Christopher R. Lowe and Howard H. Weetall. 2007 John Wiley & Sons, Ltd. ISBN 978-0-470-01905-4. 2 TRANSDUCER TECHNOLOGIES FOR BIOSENSORS The growth, metabolism, and replication of ligands and small molecules can provide informa- cells, the basic building blocks of life, depend tion about the specific nature of the interactions. very heavily on proteins. Proteins, while expressed For example, determining how the layer structure within the cells themselves, perform a vast range of an oriented immobilized protein changes on of functions of both an intracellular and intercellu- binding its partner can indicate the location on the lar nature. The profile of expressed proteins within protein at which the binding site resides. a cell depends upon the metabolic status of the cell, Indeed for protein–small molecule complexes, its age, and its local environment. Understanding interactions can be dominated by structural or con- the role that proteins play in the status of the cell formational changes. This is particularly relevant is crucial to the understanding of the diseased state to the pharmaceutical industry. Small molecules and is therefore of great importance within medical may interact in a range of ways with a protein, and pharmaceutical studies of disease. dependent on the nature and number of the bind- In order to understand the complex nature of ing sites. Determining a structural signature for a protein function and the many different roles small molecule binding can differentiate between a protein may have, real-time measurements of different modes of interaction. These may include proteins and their behavior is required. molecules binding to the same site with differ- The structure of a protein is determined by its ent degrees of specificity, whether they promote primary, secondary, and tertiary structures, the lat- a specific conformational change or not and those ter two being noncovalent in nature and a range of binding to unrelated sites. The behavior of proteins at interfaces (e.g., sur- interactions contribute to the final structure such faces) is of particular relevance. The first aspect as hydrogen bonding, electrostatic interactions, of this, is that many biologically important pro- and dispersion forces. These interactions occur cesses are interfacial in nature, with for example, between adjacent amino acid groups and may be the interaction of molecules at membrane surfaces mediated or altered by solvation, the ionic strength whether above, within, or across the membrane of the solution, and a range of other environmental bilayer. Lipid layers and vesicles can be immo- factors such as pH or temperature. Measurement of bilized and quantified and their interactions then the dimensions of a protein layer as a function of probed through both mass and structural changes. these variables can probe these factors, and a par- The second aspect relates to the many of the ticular protein’s sensitivity. The dynamic nature ways we use proteins, many of which require of the secondary and tertiary structures of pro- us either to immobilize them or to prevent them teins enables them to undergo structural changes from being immobilized at a surface. So follow- in response to stimuli which are often related to ing the structural evolution during the construction their functional roles. Structurally distinct regions of a protein surface to be used for example, as within a protein are often associated with specific a diagnostic test can help understand the factors functions and these structures may be conserved to influencing the functioning or otherwise of the undertake similar functions across a range of dif- proteins within the immobilized assembly. Alter- ferent proteins. Finally, these individual peptides natively, the detailed characterization of a surface often interact with other peptides to perform spe- and its interaction with proteins can be a valuable cific functions or to provide structural integrity and tool to understand the mechanisms of biofouling this final structure of the protein is known as the or protein resistant surfaces. quaternary structure. The shape of the protein, especially its exter- nal surface often provides pockets or clefts, which 2 TECHNOLOGY offer specific binding sites for small molecules or 2.1 Overview of Optical Techniques other proteins. Interaction with these sites is often described as “specific binding” and is associated Spectroscopic ellipsometry is the most familiar with the activation or regulation of the activity of method by which the optogeometrical proper- the protein. ties of thin films may be deduced.1,2 This tech- Probing the dimensional aspects of these inter- nique analyzes the state of polarization of light actions with other proteins, peptides, and other reflecting from multilayer reflective samples and DUAL POLARIZATION INTERFEROMETRY 3 uses the laws of electromagnetism (formulated with a view to what the expected mass change as Maxwell’s equations applied to reflection and should have been and there are too many poten- refraction at the layer interfaces) to resolve the tial contributions from other factors to make this a layer thicknesses and RIs of the layers. The anal- viable approach in general. Most instances can be ysis requires the experimenter to choose a specific attributed to effects such as binding-promoted sur- structural model from which the corresponding factant adsorption/desorption or ion motion due to expected data may be calculated and to which pI changes of the protein or related immobilization the observed data may be compared via an error matrix effects. In short, a single measurement by minimization process. There is, alongside this, an evanescent wave techniques cannot be interpreted increasing interest in optical-guided wave tech- for layer structure with any confidence without niques that are able to determine the average thick- some additional information. ness and density of ultrathin layers that bind to an With low noise instrumentation, evanescent optical waveguide surface.3–6 wave techniques have the capability to resolve In any optical waveguide structure, the light layer dimensional changes at the sub-angstrom field is not wholly confined within the physical level and RI increments of 10−6. boundaries of the guiding medium but, rather, Here we describe methods that use an addi- decays exponentially away from the boundaries. tional independent evanescent wave measurement This part of the optical field is known as the to remove these ambiguities (dual mode evanes- evanescent (vanishing) field. If a layer is added cent wave spectroscopy (DMEWS)). With dual to or removed from the original waveguide sur- mode evanescent wave methods, the capability face or an existing layer changes its thickness or inherent in spectroscopic ellipsometry is shared density the position of the boundary at which the by the guided wave techniques, the layer model light begins this exponential decay is altered. Such assumptions are similar but the methods of data changes alter the speed of propagation (“phase analysis are distinctly different. While in ellipsom- velocity”) of the whole field. Here, the measured etry the data is analyzed using
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