Construction and modeling of concatemeric DNA multilayers on a planar surface as monitored by QCM-D and SPR

Current Opportunities and Challenges in Biopolymer Thin Film Analysis—Determination of Film Thickness

Polymer thin films with thickness below 100 nm are a fascinating class of 2D materials with commercial and research applications in many branches ranging from coatings to photoresists and insulating materials, to mention just a few uses. Biopolymers have extended the scope of polymer thin films with unique materials such as cellulose, cellulose nanocrystals, cellulose nanofibrils with tunable water uptake, crystallinity and optical properties. The key information needed in thin biopolymer film use and research is film thickness. It is often challenging to determine precisely and hence several techniques and their combinations are used. Additional challenges with hydrophilic biopolymers such as cellulose are the presence of humidity and the soft and often heterogenous structure of the films. This minireview summarizes currently used methods and techniques for biopolymer thin film thickness analysis and outlines challenges for accurate and reproducible characterization. Cellulose is chosen as the representative biopolymer.

Changes of Viscoelastic Properties of Aptamer-Based Sensing Layers Following Interaction with Listeria innocua

A multiharmonic quartz crystal microbalance (QCM) has been applied to study the viscoelastic properties of the aptamer-based sensing layers at the surface of a QCM transducer covered by neutravidin following interaction with bacteria Listeria innocua. Addition of bacteria in the concentration range 5 × 103-106 CFU/mL resulted in a decrease of resonant frequency and in an increase of dissipation. The frequency decrease has been lower than one would expect considering the dimension of the bacteria. This can be caused by lower penetration depth of the acoustics wave (approximately 120 nm) in comparison with the thickness of the bacterial layer (approximately 500 nm). Addition of E. coli at the surface of neutravidin as well as aptamer layers did not result in significant changes in frequency and dissipation. Using the Kelvin-Voight model the analysis of the viscoelastic properties of the sensing layers was performed and several parameters such as penetration depth, Γ, viscosity coefficient, η, and shear modulus, μ, were determined following various modifications of QCM transducer. The penetration depth decreased following adsorption of the neutravidin layer, which is evidence of the formation of a rigid protein structure. This value did not change significantly following adsorption of aptamers and Listeria innocua. Viscosity coefficient was higher for the neutravidin layer in comparison with the naked QCM transducer in a buffer. However, a further increase of viscosity coefficient took place following attachment of aptamers suggesting their softer structure. The interaction of Listeria innocua with the aptamer layer resulted in slight decrease of viscosity coefficient. The shearing modulus increased for the neutravidin layer and decreased following aptamer adsorption, while a slight increase of µ was observed after the addition of Listeria innocua.

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

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.

Sensor Based on Aptamer Folding to Detect Low-Molecular Weight Analytes

Aptamers have emerged as promising biorecognition elements in the development of biosensors. The present work focuses on the application of quartz crystal microbalance with dissipation monitoring (QCM-D) for the enantioselective detection of a low molecular weight target molecule (less than 200 Da) by aptamer-based sensors. While QCM-D is a powerful technique for label-free, real-time characterization and quantification of molecular interactions at interfaces, the detection of small molecules interacting with immobilized receptors still remains a challenge. In the present study, we take advantage of the aptamer conformational changes upon the target binding that induces displacement of water acoustically coupled to the sensing layer. As a consequence, this phenomenon leads to a significant enhancement of the detection signal. The methodology is exemplified with the enantioselective recognition of a low molecular weight model compound, L-tyrosinamide (L-Tym). QCM-D monitoring of L-Tym interaction with the aptamer monolayer leads to an appreciable signal that can be further exploited for analytical purposes or thermodynamics studies. Furthermore, in situ combination of QCM-D with spectroscopic ellipsometry unambiguously demonstrates that the conformational change induces a nanometric decrease of the aptamer monolayer thickness. Since QCM-D is sensitive to the whole mass of the sensing layer including water that is acoustically coupled, a decrease in thickness of the highly hydrated aptamer layer induces a sizable release of water that can be easily detected by QCM-D.

Viscoelastic properties of electrochemically deposited protein/metal complexes

The interfacial gelation of proteins at metallic surfaces was investigated with an electrochemical quartz crystal microbalance (QCM). When Cr electrodes were corroded in proteinaceous solutions, it was found that gels will form at the Cr surfaces if molybdate ions are also present in the solution. Gelation is reversible and can also be controlled with the electrochemical potential at the electrode. Further, a method was developed to characterize the viscoelastic properties of thin films in liquid media using the QCM as a high-frequency rheometer. By measuring the frequency and dissipation at multiple harmonics of the resonance frequency, the viscoelastic phase angle, density-modulus product, and areal mass of a film can be determined. The method was applied to characterize the protein films, demonstrating that they have a phase angle near 55° and a density-modulus product of ≈10(7) Pa·g/cm(3). Data imply that the gels are composed of a weakly cross-linked proteinaceous network with properties similar to albumin solutions with concentrations in the range of ≈40 wt %.

The effect of nanoparticle location and shape on thermal transitions observed in hydrated layer-by-layer assemblies

Nanoparticles can have a profound effect on thermal transitions observed in polymer nanocomposites. Many layer-by-layer (LbL) assemblies contain nanoparticles for added functionality, but the resulting effects of nanoparticles on an LbL film's thermal properties are not known. Previously, we have shown that a nanoparticle-free LbL film containing strong polyelectrolytes, poly(diallyldimethylammonium chloride)/poly(styrene sulfonate) (PDAC/PSS), exhibited a single reversible thermal transition much like a glass-melt transition. In the work presented here, nanoparticles of either spherical (SiO2) or platelet (Laponite clay) shape are inserted at varying vertical locations throughout PDAC/PSS LbL films. Temperature-controlled quartz crystal microbalance (QCM-D) and modulated differential scanning calorimetry (MDSC) are applied, for which QCM-D proved to be more sensitive to the transition. All Laponite-containing films possess two thermal transitions. During growth, Laponite-containing films exhibit steady increases in dissipation, which is proposed to arise from mechanically decoupled regions separated by the Laponite nanoparticles. For SiO2-containing films, three transitions are detectable only when the SiO2 nanoparticles are placed in the middle of the film; no transitions are observed for SiO2 placed at the bottom or top, perhaps because of a weakening of the transition. The lowest transition is close in value to that of neat PDAC/PSS LbL films, and was assigned to a "bulk" response. The higher transition(s) is attributed to polymer chains in an interfacial region near the nanoparticle. We propose that nanoparticles restrict segmental mobility, thus elevating the transition temperature in the interfacial region.

Sensing conformational changes in DNA upon ligand binding using QCM-D. Polyamine condensation and Rad51 extension of DNA layers

Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59-184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59 bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film deformation allows comparative studies of two or more analytes using the same DNA layer as demonstrated here by spermine and spermidine.