Monitoring DNA binding to Escherichia coli lactose repressor using quartz crystal microbalance with dissipation

Probing the Interaction Mechanism of Sodium Oleate and Dodecyl Amine with Quartz Surfaces in the Presence of Ca2+ Ions by AFM Force Measurement

Quartz is a key raw material in high-tech fields (such as photovoltaics and semiconductor microelectronics), and the most efficient extraction method of quartz is mineral flotation. Quartz activation plays a crucial role in mineral flotation. However, the mechanism underlying the process remains unclear, and the role of additional metal ions is controversial. In this study, the interaction forces between the quartz surface, the dodecylamine (DDA) cation/sodium oleate (NaOL) anion mixed collectors, and Ca2+ were analyzed using atomic force microscopy in order to systematically explore the activation process of quartz flotation. The results confirmed that the activation process was initialized from NaOL, which was adsorbed on the surface of a calcium-covered quartz surface. The existence of DDA inhibited the binding of Ca2+ to NaOL so that more Ca2+ was adsorbed on the quartz surface to provide the adsorption site for NaOL. Moreover, the best adsorption condition of Ca2+ + NaOL + DDA mixed solution was analyzed by quartz crystal microbalance with dissipation, and it demonstrated that the most stable chemisorption environment on the quartz surface was at pH 11.0. In these circumstances, Ca2+ could first adsorb in a point-like manner on the quartz surface, which was then adsorbed with a mixture of NaOL and DDA. This result showed that, at a specific pH, Ca2+ could encourage the coadsorption of cationic/anionic mixed collectors on quartz. This work provides an important new understanding of the intermolecular interactions that take place during complex mineral flotation processes between chemical additives and mineral surfaces. The methodology used in this study can be easily adapted to different interfacial processes, including water treatment, membrane technology, bioengineering, and oil production.

Detecting DNA Loops Using Tethered Particle Motion

The range of motion of a micron-sized bead tethered by a single polymer provides a dynamic readout of the effective length of the polymer. The excursions of the bead may reflect the intrinsic flexibility and/or topology of the polymer as well as changes due to the action activity of ligands that bind the polymer. This is a simple yet powerful experimental approach to investigate such interactions between DNA and proteins as demonstrated by experiments with the lac repressor. This protein forms a stable, tetrameric oligomer with two binding sites and can produce a loop of DNA between recognition sites separated along the length of a DNA molecule.

Facile ultrathin film of silver nanoparticles for bacteria sensing

Silver nanoparticles (AgNPs) exhibit excellent anti-microbial and bactericidal properties. Due to bacterial abhorrence for AgNPs, it is difficult to develop a label-free, sensitive and low-cost bacteria sensor using them. In the present article, we report that an ultrathin and uniform Langmuir-Schaefer (LS) film of AgNPs can be employed for bacteria sensing effectively as compared to that of non-uniform and randomly distributed AgNPs in spin coated film. The uniformly distributed AgNPs in the LS film offer a relatively larger contact surface for bacteria as compared to that of spin coated film. Due to higher contact surface, adsorption of the bacteria on LS film is strongly preferable as compared to that of spin coated film leading to an enhanced sensing performance of the LS film than that of spin coated film. Soil bacteria was grown by the standard protocol and were utilized as model system for bacteria sensing application. The soil bacteria sensing was done by monitoring the piezoresponse and dissipation parameters using a quartz crystal microbalance, simultaneously. Our study indicates that the LS film of AgNPs not only facilitates the adsorption of the soil bacteria but also kills them.

Two-Step Adsorption of a Switchable Tertiary Amine Surfactant Measured Using a Quartz Crystal Microbalance with Dissipation

The adsorption of a switchable cationic surfactant, N, N, N'-trimethyl- N'-tallow-1,3-diaminopropane (DTTM, Duomeen TTM), at the silica/aqueous solution interface is characterized using a quartz crystal microbalance with dissipation (QCM-D). The adsorption isotherms reveal that changes in the solution pH or salinity affect surfactant adsorption in competing ways. In particular, the combination of the degree of protonation of the surfactant and electrostatic interactions is responsible for surfactant adsorption. The kinetics of adsorption is carefully measured using the real-time measurement of a QCM-D, allowing us to fit the experimental data with analytical models. At pH values of 3 and 5, where the DTTM is protonated, DTTM exhibits two-step adsorption. This is representative of a fast step in which the surfactant molecules are adsorbed with head-groups orientated toward the surface, followed by a slower second step corresponding to formation of interfacial surfactant aggregates on the silica surface.

Quartz Crystal Microbalance With Dissipation Monitoring: A Powerful Method to Predict the in vivo Behavior of Bioengineered Surfaces

The Quartz Crystal Microbalance with dissipation monitoring (QCM-D) is a tool to measure mass and viscosity in processes occurring at or near surfaces, or within thin films. QCM-D is able to detect extremely small chemical, mechanical, and electrical changes taking place on the sensor surface and to convert them into electrical signals which can be investigated to study dynamic process. Surface nanotopography and chemical composition are of pivotal importance in biomedical applications since interactions of medical devices with the physiological environment are mediated by surface features. This review is intended to provide readers with an up-to-date summary of QCM-D applications in the study of cell behavior and to discuss the future trends for the use of QCM-D as a high-throughput method to study cell/surface interactions overcoming the current challenges in the design of biomedical devices.

QCM-D study of nanoparticle interactions

Quartz crystal microbalance with dissipation monitoring (QCM-D) has been proven to be a powerful research tool to investigate in situ interactions between nanoparticles and different functionalized surfaces in liquids. QCM-D can also be used to quantitatively determine adsorption kinetics of polymers, DNA and proteins from solutions on various substrate surfaces while providing insights into conformations of adsorbed molecules. This review aims to provide a comprehensive overview on various important applications of QCM-D, focusing on deposition of nanoparticles and attachment-detachment of nanoparticles on model membranes in complex fluid systems. We will first describe the working principle of QCM-D and DLVO theory pertinent to understanding nanoparticle deposition phenomena. The interactions between different nanoparticles and functionalized surfaces for different application areas are then critically reviewed. Finally, the potential applications of QCM-D in other important fields are proposed and knowledge gaps are identified.

Kinetic characterization of the retinoic X receptor binding to specific and unspecific DNA oligoduplexes with a quartz crystal microbalance

Quartz Crystal Microbalance (QCM) biosensor technology was used to study the interaction of the DNA-binding domain (DBD) of the transcription factor RXRα with immobilized specific (DR1) and unspecific (DR1neg) DNA oligoduplexes. We identify the QCM sensor frequency at the susceptance minimum (fBmin) as a better measuring parameter, and we show that fBmin is proportional to the mass adsorbed at the sensor surface and is not influenced by interferences coming from viscoelastic variations of the adsorbed layers or buffers. This parameter was used to study the binding of RXRα to DNA and to calculate the association and dissociation kinetic constants of RXRαDBD-DR1 interaction. We show that RXRαDBD binds to DNA both as a monomer and as a homodimer, and that the mechanism of binding is salt dependent and occurs in two steps. The QCM biosensor data reveal that a high ionic strength buffer prevents the unspecific interactions and at a lower ionic strength the dissociation of RXRαDBD-DR1 occurs in two phases.

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.