Single-molecule detection of proteins and toxins in food using atomic force microscopy

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Characterization of the effect of chromium salts on tropocollagen molecules and molecular aggregates

Though the capability of chromium treatment to improve the stability and mechanical properties of collagen fibrils is well-known, the influence of different chromium salts on collagen molecules (tropocollagen) is not well characterized. In this study, the effect of Cr³⁺ treatment on the conformation and hydrodynamic properties of collagen was studied using atomic force microscopy (AFM) and dynamic light scattering (DLS). Statistical analysis of contours of adsorbed tropocollagen molecules using the two-dimensional worm-like chain model revealed a reduction of the persistence length (i.e., the increase of flexibility) from ≈72 nm in water to ≈56-57 nm in chromium (III) salt solutions. DLS studies demonstrated an increase of the hydrodynamic radius from ≈140 nm in water to ≈190 nm in chromium (III) salt solutions, which is associated with protein aggregation. The kinetics of collagen aggregation was shown to be ionic strength dependent. Collagen molecules treated with three different chromium (III) salts demonstrated similar properties such as flexibility, aggregation kinetics, and susceptibility to enzymatic cleavage. The observed effects are explained by a model that considers the formation of chromium-associated intra- and intermolecular crosslinks. The obtained results provide novel insights into the effect of chromium salts on the conformation and properties of tropocollagen molecules.

Highly sensitively detection of amine vapors released during shrimp spoilage by fluorescent molecules locked in covalent organic frameworks

The fluorescent sensors allow sensitive detection of amine vapors for assessing the safety and quality of seafood products. However, high diffusion resistance and insufficient recognition sites usually limit the sensitivity of the sensors. Here, we employed an emulsion-confined assembly strategy to uniform encapsulate fluorescent molecules perylene diimide (PDI) molecules into covalent organic frameworks (COFs) to achieve ultrasensitive detection of amine vapors. The detection mechanism is based on the photoinduced electron transfer from amine to the excited PDI. This method exhibits a broad linear detection range from 8 ppb to 800 ppm and the limit of detection reaches as low as 1.2 ppb. The real-time detection of the amine vapors produced during shrimp spoilage is successfully achieved with excellent performance. This provides a versatile method for the on-demand synthesis of functional materials with high fluorescence properties for the development of chemical sensors via encapsulating different fluorescent molecules into COFs.

An aptamer-assisted biological nanopore biosensor for ultra-sensitive detection of ochratoxin A with a portable single-molecule measuring instrument

Biological nanopore-based single-molecule detection technology has shown ultrahigh sensitivity to various target analyte. But the detection scope of interesting targets is limited due to the lack of effective signal conversion strategies. In addition, conventional nanopore detection instruments are cumbersome, resulting nanopore detection can only be performed in laboratory. Herein, a customizable nanopore current amplifier is constructed to lower the cost and increase the portability of the nanopore instrument, and then an immobilized aptamer-based signal conversion strategy is proposed for α-hemolysin (α-HL) nanopore to detect small molecules (ochratoxin A, OTA). The presence of OTA in sample would trigger the release of probe single-strand DNA (ssDNA) from magnetic beads, which could subsequently cause current blockage in nanopore. The results show that the signal frequency of probe ssDNA has a linear relationship with the OTA concentration in the range of 2 × 10¹～2 × 10³ pmol/L. Compared to other methods, our sensing system has achieved an ultra-sensitive detection of OTA with the detection limit as low as 1.697 pmol/L. This strategy could broaden the scope of nanopore detection and have the potential for rapid and in-situ detection of other food contaminants in the future.

Plant-Based: A Perspective on Nutritional and Technological Issues. Are We Ready for "Precision Processing"?

The rapid evolution of consumers' preference despite being still rooted in taste is rapidly combining with an exponential growth of environmental awareness. Both are forcing innovation into the food industry sector. Today, it is common in the scientific literature to find awareness of nutrition and sustainability, functionality and freshness, taste, and pollution; the most relevant and recognized trends are evolving with unprecedent speed toward a new paradigm. The perfect storm of fast-growing population, together with an exploding level of environmental pollution, is combining with the request for functional foods with more defined health properties and is strongly pushing the food sector to new defined innovation objectives to keep and develop the economic role of most loved brands around the world. The most debated conundrum is how to provide healthy food for all human beings, without further affecting our Mother Earth. Innovation in food raw materials as well as innovation in food processing seems to be the magic solution to provide twice with half, that is, to double the food production combined with declining resources. One of the fastest growing segments in the food industry is the plant-based segment. The status of the available options in food processing applied to plant-based food will be discussed, with a special focus on novel physical processing technologies and atomic force microscopy as possible complementary weapons in science-based definition of a sustainable nutrition approach. A call for a new paradigm such as "precision processing" should be adopted to drive the evolution of the whole food system.

Single molecule detection; from microscopy to sensors

Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.

Ultrasound enhanced the binding ability of chitinase onto chitin: From an AFM insight

In order to evaluate the effect of ultrasound to chitinase from a molecular level, atomic force microscopy (AFM) was employed to investigate the interaction force of chitinase binding onto chitin surface. In the measurement of force-distance curve, a series of pull-off events were discovered using the immobilized AFM tips with chitinase either treated by ultrasound or not, whereas no interaction peak was observed by the AFM tips without chitinase, indicating that the obtained adhesion forces were coming from the binding functions between chitinase and chitin. Through the analysis of these force curves, at the loading velocity of 0.3 μm/s, the maximum binding force of the chitinase treated by ultrasound for 20 min onto chitin was measured to be 105.33 ± 23.51 pN, while the untreated onto chitin was 71.05 ± 12.73 pN, suggesting the stronger binding force between ultrasonic treated chitinase and chitin substrate. Therefore, AFM has provided a useful method to directly and quantitatively characterize the interactions between chitinase and chitin, and successfully proved that ultrasound could activate chitinase by enhancing the binding ability of chitinase onto chitin.