Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

A microphysiological system for handling graphene related materials under flow conditions

The field of nanotechnology has developed rapidly in recent decades due to its broad applications in many industrial and biomedical fields. Notably, 2D materials such as graphene-related materials (GRMs) have been extensively explored and, as such, their safety needs to be assessed. However, GRMs tend to deposit quickly, present low stability in aqueous solutions, and adsorb to plastic materials. Consequently, traditional approaches based on static assays facilitate their deposition and adsorption and fail to recreate human physiological conditions. Organ-on-a-chip (OOC) technology could, however, solve these drawbacks and lead to the development of microphysiological systems (MPSs) that mimic the microenvironment present in human tissues. In light of the above, in the present study a microfluidic system under flow conditions has been optimised to minimise graphene oxide (GO) and few-layer graphene (FLG) adsorption and deposition. For that purpose, a kidney-on-a-chip was developed and optimised to evaluate the effects of exposure to GO and FLG flakes at a sublethal dose under fluid flow conditions. In summary, MPSs are an innovative and precise tool for evaluating the effects of exposure to GRMs and other type of nanomaterials.

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.

Advancing piezoelectric 2D nanomaterials for applications in drug delivery systems and therapeutic approaches

Precision drug delivery and multimodal synergistic therapy are crucial in treating diverse ailments, such as cancer, tissue damage, and degenerative diseases. Electrodes that emit electric pulses have proven effective in enhancing molecule release and permeability in drug delivery systems. Moreover, the physiological electrical microenvironment plays a vital role in regulating biological functions and triggering action potentials in neural and muscular tissues. Due to their unique noncentrosymmetric structures, many 2D materials exhibit outstanding piezoelectric performance, generating positive and negative charges under mechanical forces. This ability facilitates precise drug targeting and ensures high stimulus responsiveness, thereby controlling cellular destinies. Additionally, the abundant active sites within piezoelectric 2D materials facilitate efficient catalysis through piezochemical coupling, offering multimodal synergistic therapeutic strategies. However, the full potential of piezoelectric 2D nanomaterials in drug delivery system design remains underexplored due to research gaps. In this context, the current applications of piezoelectric 2D materials in disease management are summarized in this review, and the development of drug delivery systems influenced by these materials is forecast.

Label-Free Imaging of DNA Interactions with 2D Materials

Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.

Two-dimensional nanomaterials induced nano-bio interfacial effects and biomedical applications in cancer treatment

Two-dimensional nanomaterials (2D NMs), characterized by a large number of atoms or molecules arranged in one dimension (typically thickness) while having tiny dimensions in the other two dimensions, have emerged as a pivotal class of materials with unique properties. Their flat and sheet-like structure imparts distinctive physical, chemical, and electronic attributes, which offers several advantages in biomedical applications, including enhanced surface area for efficient drug loading, surface-exposed atoms allowing precise chemical modifications, and the ability to form hierarchical multilayer structures for synergistic functionality. Exploring their nano-bio interfacial interactions with biological components holds significant importance in comprehensively and systematically guiding safe applications. However, the current lack of in-depth analysis and comprehensive understanding of interfacial effects on cancer treatment motivates our ongoing efforts in this field. This study provides a comprehensive survey of recent advances in utilizing 2D NMs for cancer treatment. It offers insights into the structural characteristics, synthesis methods, and surface modifications of diverse 2D NMs. The investigation further delves into the formation of nano-bio interfaces during their in vivo utilization. Notably, the study discusses a wide array of biomedical applications in cancer treatment. With their potential to revolutionize therapeutic strategies and outcomes, 2D NMs are poised at the forefront of cancer treatment, holding the promise of transformative advancements.

Impact of luminescent MoSe2 quantum dots on activity of trypsin under different pH environment

It is vital that a straightforward detection approach for trypsin should be developed as it is important diagnostic tool for a number of diseases. Herein, the impact of luminescent MoSe2 quantum dots on trypsin activity under different pH environment has been studied. Addition of trypsin to MoSe2 quantum dots enhanced the fluorescence of quantum dots whereas quantum dots resulted in quenching of fluorescence of trypsin. The quenching behavior at various pH and temperature was examined and revealed that the MoSe2-trypsin complex stabilized through the electrostatic interactions. The obtained negative values of zeta potential of the complex -0.11 mV, -0.30 mV and -0.59 mV for pH 6.0,7.6 and 9.0 respectively confirmed the stability of the complex. The separation between the donor and acceptor atoms in energy transfer mechanism was found to decrease (1.48 nm to 1.44 nm to 1.30 nm) with increasing value of pH. It was also evident that trypsin retained its enzyme activity in the trypsin-MoSe2 complex and under different pH environment. The Vant Hoff plot from quenching revealed 1 binding site for quantum dots by trypsin for all pH of buffer solution. The complex formation of trypsin-MoSe2 quantum dots was verified for the first time using fluorescence spectroscopy and it revealed that tryspin form complex with MoSe2 quantum dots through electrostatic interactions. Our results revealed that the MoSe2 quantum dots stabilized and sheltered the active sites of trypsin, which was likely the cause of the increased bioavailability of MoSe2 quantum dots in enzymes.

The Hybrid Nano-Biointerface between Proteins/Peptides and Two-Dimensional Nanomaterials

In typical protein-nanoparticle surface interactions, the biomolecule surface binding and consequent conformational changes are intermingled with each other and are pivotal to the multiple functional properties of the resulting hybrid bioengineered nanomaterial. In this review, we focus on the peculiar properties of the layer formed when biomolecules, especially proteins and peptides, face two-dimensional (2D) nanomaterials, to provide an overview of the state-of-the-art knowledge and the current challenges concerning the biomolecule coronas and, in general, the 2D nano-biointerface established when peptides and proteins interact with the nanosheet surface. Specifically, this review includes both experimental and simulation studies, including some recent machine learning results of a wide range of nanomaterial and peptide/protein systems.

Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA

The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.

Moderate binding of villin headpiece protein to C3N3 nanosheet reveals the suitable biocompatibility of this nanomaterial

Since its recent successful synthesis and due to its promising physical and chemical properties, the carbon nitrite nanomaterial, C3N3, has attracted considerable attention in various scientific areas. However, thus far, little effort has been devoted to investigating the structural influence of the direct interaction of this 2D nanomaterial and biomolecules, including proteins and biomembranes so as to understand the physical origin of its bio-effect, particularly from the molecular landscape. Such information is fundamental to correlate to the potential nanotoxicology of the C3N3 nanomaterial. In this work, we explored the potential structural influence of a C3N3 nanosheet on the prototypical globular protein, villin headpiece (HP35) using all-atom molecular dynamics (MD) simulations. We found that HP35 could maintain its native conformations upon adsorption onto the C3N3 nanosheet regardless of the diversity in the binding sites, implying the potential advantage of C3N3 in protecting the biomolecular structure. The adsorption was mediated primarily by vdW interactions. Moreover, once adsorbed on the C3N3 surface, HP35 remains relatively fixed on the nanostructure without a distinct lateral translation, which may aid in keeping the structural integrity of the protein. In addition, the porous topological structure of C3N3 and the special water layer present on the C3N3 holes conjointly contributed to the restricted motion of HP35 via the formation of a high free energy barrier and a steric hindrance to prevent the surface displacement. This work revealed for the first time the potential influence of the 2D C3N3 nanomaterial in the protein structure and provided the corresponding in-depth molecular-level mechanism, which is valuable for future applications of C3N3 in bionanomedicine.

Design of a Hierarchical Assembly at a Solid-Liquid Interface Using an Asymmetric Protein Needle

Design and control of processes for a hierarchical assembly of proteins remain challenging because it requires consideration of design principles with atomic-level accuracy. Previous studies have adopted symmetry-based strategies to minimize the complexity of protein-protein interactions and this has placed constraints on the structures of the resulting protein assemblies. In the present work, we used an anisotropic-shaped protein needle, gene product 5 (gp5) from bacteriophage T4 with a C-terminal hexahistidine-tag (His-tag) (gp5_CHis), to construct a hierarchical assembly with two distinct protein-protein interaction sites. High-speed atomic force microscopy (HS-AFM) measurements reveal that it forms unique tetrameric clusters through its N-terminal head on a mica surface. The clusters further self-assemble into a monolayer through the C-terminal His-tag. The HS-AFM images and displacement analyses show that the monolayer is a network-like structure rather than a crystalline lattice. Our results expand the toolbox for constructing hierarchical protein assemblies based on structural anisotropy.

Advances in Biologically Applicable Graphene-Based 2D Nanomaterials

Climate change and increasing contamination of the environment, due to anthropogenic activities, are accompanied with a growing negative impact on human life. Nowadays, humanity is threatened by the increasing incidence of difficult-to-treat cancer and various infectious diseases caused by resistant pathogens, but, on the other hand, ensuring sufficient safe food for balanced human nutrition is threatened by a growing infestation of agriculturally important plants, by various pathogens or by the deteriorating condition of agricultural land. One way to deal with all these undesirable facts is to try to develop technologies and sophisticated materials that could help overcome these negative effects/gloomy prospects. One possibility is to try to use nanotechnology and, within this broad field, to focus also on the study of two-dimensional carbon-based nanomaterials, which have excellent prospects to be used in various economic sectors. In this brief up-to-date overview, attention is paid to recent applications of graphene-based nanomaterials, i.e., graphene, graphene quantum dots, graphene oxide, graphene oxide quantum dots, and reduced graphene oxide. These materials and their various modifications and combinations with other compounds are discussed, regarding their biomedical and agro-ecological applications, i.e., as materials investigated for their antineoplastic and anti-invasive effects, for their effects against various plant pathogens, and as carriers of bioactive agents (drugs, pesticides, fertilizers) as well as materials suitable to be used in theranostics. The negative effects of graphene-based nanomaterials on living organisms, including their mode of action, are analyzed as well.