Characterization of DNA-Hv1 histone interactions; discrimination of DNA size and shape

Hybrid Sensor Device for Simultaneous Surface Plasmon Resonance and Surface Acoustic Wave Measurements

Surface plasmon resonance (SPR) and Love wave (LW) surface acoustic wave (SAW) sensors have been established as reliable biosensing technologies for label-free, real-time monitoring of biomolecular interactions. This work reports the development of a combined SPR/LW-SAW platform to facilitate simultaneous optical and acoustic measurements for the investigation of biomolecules binding on a single surface. The system’s output provides recordings of two acoustic parameters, phase and amplitude of a Love wave, synchronized with SPR readings. We present the design and manufacturing of a novel experimental set-up employing, in addition to the SPR/LW-SAW device, a 3D-printed plastic holder combined with a PDMS microfluidic cell so that the platform can be used in a flow-through mode. The system was evaluated in a systematic study of the optical and acoustic responses for different surface perturbations, i.e., rigid mass loading (Au deposition), pure viscous loading (glycerol and sucrose solutions) and protein adsorption (BSA). Our results provide the theoretical and experimental basis for future application of the combined system to other biochemical and biophysical studies.

Quantitative and discriminative analysis of nucleic acid samples using luminometric nonspecific nanoparticle methods

Homogeneous simple assays utilizing luminescence quenching and time-resolved luminescence resonance energy transfer (TR-LRET) were developed for the quantification of nucleic acids without sequence information. Nucleic acids prevent the adsorption of a protein to europium nanoparticles which is detected as a luminescence quenching of europium nanoparticles with a soluble quencher or as a decrease of TR-LRET from europium nanoparticles to the acceptor dye. Contrary to the existing methods based on fluorescent dye binding to nucleic acids, equal sensitivities for both single- (ssDNA) and double-stranded DNA (dsDNA) were measured and a detection limit of 60 pg was calculated for the quenching assay. The average coefficient of variation was 5% for the quenching assay and 8% for the TR-LRET assay. The TR-LRET assay was also combined with a nucleic acid dye selective to dsDNA in a single tube assay to measure the total concentration of DNA and the ratio of ssDNA and dsDNA in the mixture. To our knowledge, such a multiplexed assay is not accomplished with commercially available assays.

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.

Imaging and analyzing the elasticity of vascular smooth muscle cells by atomic force acoustic microscope

Vascular smooth muscle cells (VSMCs) play an important role in the good performance of the vasculature. To study the surface, intracellular structure and elasticity of VSMCs, atomic force acoustic microscope (AFAM) was used for imaging VSMCs from A7r5 rat aorta arteries. The topography images of VSMCs were obtained in contact mode and the acoustic images were obtained by AFAM in sample vibration mode. Then, the force curve measurement derived using Young's modulus of the interested areas was used for evaluating elasticity properties. The acoustic images were found in higher resolution with more information than the topography images. The force curves showed the difference in Young's modulus of the different parts of VSMC. These findings demonstrate that AFAM is useful for displaying the surface, structure and elasticity property of VSMCs clearly, with short scanning time, negligible harm or damage to cell and nanometer-level resolution.

Convergence of dip-pen nanolithography and acoustic biosensors towards a rapid-analysis multi-sample microsystem

The present work demonstrates for the first time patterning of a ready-to-use biosensor with several different biomolecules using Dip-Pen Nanolithography (DPN) for the development of a procedure towards more rapid and efficient multi-sample detection. The biosensor platform used is based on a Surface Acoustic Wave (SAW) device integrated with a parallel-channel microfluidic module, termed as "microfluidics-on-SAW" ("μF-on-SAW"), for reproducible multi-sample analysis. Lipids with different functionalized head groups were patterned at distinct, microfluidic-formed rectangular domains with sharp edges all located on the same sensor surface; pattern quality was verified using a fluorescent microscope. The functionality of the head groups, the efficiency of the patterning method, and the suitability of DPN for the surface modification of the acoustic device were subsequently examined through acoustic experiments. The μF-on-SAW configuration was used to detect specific binding between the pre-patterned functionalized lipids with their corresponding biomolecules. The achievement of an improved sensitivity (5-fold compared to previous acoustic configurations) and reduced preparation time by at least 2 h clearly indicates the suitability of DPN as a direct patterning method for ready-to-use acoustic sensor devices like the μF-on-SAW towards integrated, rapid-analysis, multi-sample biosensing microsystem development.

Acoustic characterization of nanoswitch structures: application to the DNA Holliday Junction

A novel biophysical approach in combination with an acoustic device is demonstrated as a sensitive, rapid, and label-free technique for characterizing various structures of the DNA Holliday Junction (J1) nanoswitch. We were successful in discriminating the "closed" from the "open" state, as well as confirming that the digestion of the J1 junction resulted in the two, anticipated, rod-shaped, 20 bp long fragments. Furthermore, we propose a possible structure for the ∼10 nm long (DNA58) component participating in the J1 assembly. This work reveals the potential of acoustic devices as a powerful tool for molecular conformation studies.