Molecular Recognition by Silicon Nanowire Field-Effect Transistor and Single-Molecule Force Spectroscopy

Silicon nanowire (SiNW) field-effect transistors (FETs) have been developed as very sensitive and label-free biomolecular sensors. The detection principle operating in a SiNW biosensor is indirect. The biomolecules are detected by measuring the changes in the current through the transistor. Those changes are produced by the electrical field created by the biomolecule. Here, we have combined nanolithography, chemical functionalization, electrical measurements and molecular recognition methods to correlate the current measured by the SiNW transistor with the presence of specific molecular recognition events on the surface of the SiNW. Oxidation scanning probe lithography (o-SPL) was applied to fabricate sub-12 nm SiNW field-effect transistors. The devices were applied to detect very small concentrations of proteins (500 pM). Atomic force microscopy (AFM) single-molecule force spectroscopy (SMFS) experiments allowed the identification of the protein adsorption sites on the surface of the nanowire. We detected specific interactions between the biotin-functionalized AFM tip and individual avidin molecules adsorbed to the SiNW. The measurements confirmed that electrical current changes measured by the device were associated with the deposition of avidin molecules.

Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays

The non-covalent biological bonds that constitute protein–protein or protein–ligand interactions play crucial roles in many cellular functions, including mitosis, motility, and cell–cell adhesion. The effect of external force ($$F$$ F ) on the unbinding rate ($${k}_{\text{off}}\left(F\right)$$ k off F ) of macromolecular interactions is a crucial parameter to understanding the mechanisms behind these functions. Optical tweezer-based single-molecule force spectroscopy is frequently used to obtain quantitative force-dependent dissociation data on slip, catch, and ideal bonds. However, analyses of this data using dissociation time or dissociation force histograms often quantitatively compare bonds without fully characterizing their underlying biophysical properties. Additionally, the results of histogram-based analyses can depend on the rate at which force was applied during the experiment and the experiment’s sensitivity. Here, we present an analytically derived cumulative distribution function-like approach to analyzing force-dependent dissociation force spectroscopy data. We demonstrate the benefits and limitations of the technique using stochastic simulations of various bond types. We show that it can be used to obtain the detachment rate and force sensitivity of biological macromolecular bonds from force spectroscopy experiments by explicitly accounting for loading rate and noisy data. We also discuss the implications of our results on using optical tweezers to collect force-dependent dissociation data.

Evidenced Cucurbit[n]uril-based Host-Guest Interactions by Single-Molecule Force Spectroscopy

In this work, enhanced guest pairs interactions in the cavity of cucurbit[8]uril (CB[8]) are quantitatively determined by Single-molecule force spectroscopy (SMFS). Significantly, light-driven dynamic conformational change of guest pairs leads...

IMPROVING THE EFFICIENCY OF THE CONTACT FORCE METHOD OF THE ATOMIC FORCE SPECTROSCOPY

Предложена методика, оптимизирующая метод контактной силовой спектроскопии. С помощью макроязыка, интегрированного в программное обеспечение NOVA установки сканирующего зондового микроскопа Solver P47, был разработан алгоритм, позволяющий анализировать силовые кривые, не покидая его основного интерфейса. Апробация метода выполнена на образцах синтезированного полимера, поскольку одним из важнейших механических свойств, определяющим их спектр областей применения, является упругость. В работе получены локальные значения модуля Юнга на поверхности полимера методом контактной силовой спектроскопии с применением скрипта YUNG, разработанного с помощью макроязыка, интегрированного в программу управления сканирующего зондового микроскопа. Показано, что применение скрипта YUNG позволяет оптимизировать метод контактной силовой спектроскопии по поиску показателя степени γ, выбору модели для расчета силы взаимодействия для дальнейшего определения локального модуля Юнга. We propose a technique that optimizing the method of contact force spectroscopy. With the help of a macro language integrated into the NOVA software of the Solver P47 scanning probe microscope, an algorithm was developed that allows analyzing force curves without leaving its main interface. The approbation of the method was done on samples of synthesized polymer, since one of the most important mechanical properties determining their range of applications is elasticity. In this paper, local values of the Young's modulus on the polymer surface are obtained by the method of contact force spectroscopy using the YUNG script developed using a macro language integrated into the control program of a scanning probe microscope. It is shown that the use of the YUNG script makes it possible to optimize the method of contact force spectroscopy by searching for the exponent γ, choosing a model for calculating the interaction force for further determination of the local Young modulus.