Nanobody click chemistry for convenient site-specific fluorescent labelling, single step immunocytochemistry and delivery into living cells by photoporation and live cell imaging

A live mammalian cells electroporation array for on-chip immunofluorescence

The detection of intracellular proteins in vitro is commonly realized with immunofluorescence techniques, through which antibodies or markers are delivered into fixed cells and recognize specific proteins. Many innovative techniques, however, avoid cells fixation by chemical compounds and, among the others, electroporation is widely used. Here we demonstrate that in situ electroporation on thin film SiO2 capacitive microelectrodes can be realized with high efficiency to deliver fluorescent markers and antibodies into mammalian cell lines and primary neuronal cells to detect intracellular proteins, like actin. The results presented in this work open the way to the use of this technique for the detection of potentially any target protein, even through subsequent electroporations.

Leveraging immunoliposomes as nanocarriers against SARS-CoV-2 and its emerging variants

The global COVID-19 pandemic arising from SARS-CoV-2 has impacted many lives, gaining interest worldwide ever since it was first identified in December 2019. Till 2023, 752 million cumulative cases and 6.8 million deaths were documented globally. COVID-19 has been rapidly evolving, affecting virus transmissibility and properties and contributing to increased disease severity. The Omicron is the most circulating variant of concern. Although success in its treatment has indicated progress in tackling the virus, limitations in delivering the current antiviral agents in battling emerging variants remain remarkable. With the latest advancements in nanotechnology for controlling infectious diseases, liposomes have the potential to counteract SARS-CoV-2 because of their ability to employ different targeting strategies, incorporating monoclonal antibodies for the active and passive targeting of infected patients. This review will present a concise summary of the possible strategies for utilizing immunoliposomes to improve current treatment against the occurrence of SARS-CoV-2 and its variants.

Photothermal Nanomaterial-Mediated Photoporation

ConspectusDelivering biological effector molecules in cultured cells is of fundamental importance to any study or application in which the modulation of gene expression is required. Examples range from generating engineered cell lines for studying gene function to the engineering of cells for cell-based therapies such as CAR-T cells and gene-corrected stem cells for regenerative medicine. It remains a great challenge, however, to deliver biological effector molecules across the cell membrane with minimal adverse effects on cell viability and functionality. While viral vectors have been frequently used to introduce foreign nucleic acids into cells, their use is associated with safety concerns such as immunogenicity, high manufacturing cost, and limited cargo capacity.For photoporation, depending on the laser energy, membrane permeabilization happens either by local heating or by laser-induced water vapor nanobubbles (VNB). In our first study on this topic, we demonstrated that the physical force exerted by suddenly formed VNB leads to more efficient intracellular delivery as compared to mere heating. Next, we explored the use of different photothermal nanomaterials, finding that graphene quantum dots display enhanced thermal stability compared to the more traditionally used gold nanoparticles, hence providing the possibility to increase the delivery efficiency by repeated laser activation. To enable its use for the production of engineered therapeutic cells, it would be better if contact with cells with nondegradable nanoparticles is avoided as it poses toxicity and regulatory concerns. Therefore, we recently demonstrated that photoporation can be performed with biodegradable polydopamine nanoparticles as well. Alternatively, we demonstrated that nanoparticle contact can be avoided by embedding the photothermal nanoparticles in a substrate made from biocompatible electrospun nanofibers. With this variety of photoporation approaches, over the years we demonstrated the successful delivery of a broad variety of biologics (mRNA, siRNA, Cas9 ribonucleoproteins, nanobodies, etc.) in many different cell types, including hard-to-transfect cells such as T cells, embryonic stem cells, neurons, and macrophages.In this Account, we will first start with a brief introduction of the general concept and a historical development of photoporation. In the next two sections, we will extensively discuss the various types of photothermal nanomaterials which have been used for photoporation. We discriminate two types of photothermal nanomaterials: single nanostructures and composite nanostructures. The first one includes examples such as gold nanoparticles, graphene quantum dots, and polydopamine nanoparticles. The second type includes polymeric films and nanofibers containing photothermal nanoparticles as well as composite nanoscale biolistic nanostructures. A thorough discussion will be given for each type of photothermal nanomaterial, from its synthesis and characterization to its application in photoporation, with its advantages and disadvantages. In the final section, we will provide an overall discussion and elaborate on future perspectives.

Cytoplasmic Expression of Nanobodies with Formylglycine Generating Enzyme Tag and Conversion to a Bio-Orthogonal Aldehyde Group

Nanobodies (Nbs) can be successfully retrieved following phage, bacterial, yeast, or ribosome display of immune, synthetic, or naïve libraries. However, after panning, multiple individual Nb clones need to be screened and assessed for solubility, antigen specificity, affinity, and potential biological function. Therefore, it is highly desirable to have a convenient expression strategy to obtain sufficient protein for in-depth characterization of the Nbs. The presence of a purification and detection tag, as well as a chemically reactive group to enable simple generation of Nb derivatives, would be of great help in this regard. Here, we provide a general protocol for high yield cytoplasmic expression and purification of formylglycine generating enzyme (FGE)-tagged Nbs. The cysteine within the FGE tag is easily converted to formylglycine by passing the FGE-tag containing Nb over a continuous-flow bio-catalysis system. The aldehyde group within the formylglycine side chain at the C-terminal end of the Nb is suitably located for subsequent bio-orthogonal reactions to fluorescent dyes, biotin, polyethylene glycol, or chromatography resins. We also include methods for production of high yield recombinant FGE, as well as conditions for its immobilization on Sepharose to produce the continuous-flow bio-catalysis system.

Site-Specific Fluorescent Labeling, Single-Step Immunocytochemistry, and Delivery of Nanobodies into Living Cells

The smallest natural antibody fragments currently available are single-domain antibodies obtained from camelid species and sharks (variable new antigen receptors). These molecules consist of a single amino acid chain of ~120 amino acids that adopts a typical immunoglobulin fold. Single-domain antibodies (nanobodies) are monovalent and can be isolated from immunized animals, from naïve libraries, or from synthetic libraries. Importantly, their complete DNA sequences are readily obtained by default, which greatly facilitates their rapid manipulation for various applications. Here, a PCR-based protocol for inserting a sortase A recognition sequence at the carboxy-terminus of a nanobody is described. Subsequently, a sortase A-catalyzed biochemical reaction results in tagging of the nanobody with a short carboxy-terminal amino acid sequence that carries a non-canonical residue (propargyl glycine). This allows click chemistry to be performed with an azido-derivatized fluorophore, with the ensuing fluorescent nanobody being covalently and site-specifically labeled. The labeled nanobody can be used directly for immunocytochemistry, omitting the classical secondary antibody step. Also described are methods for delivery of fluorescent nanobodies into the cytoplasm of mammalian cells by photoporation, a very low-toxicity approach involving laser light and graphene quantum dots. The combined protocol embodies a novel route for studying protein function in living cells at high resolution.

Gold labelling of a green fluorescent protein (GFP)-tag inside cells using recombinant nanobodies conjugated to 2.4 nm thiolate-coated gold nanoparticles

Advances in microscopy technology have prompted efforts to improve the reagents required to recognize specific molecules within the intracellular environment. For high-resolution electron microscopy, conjugation of selective binders originating from the immune response arsenal to gold nanoparticles (AuNPs) as contrasting agents is the method of choice to obtain labeling tools. However, conjugation of the minimal sized 15 kDa nanobody (Nb) to AuNPs remains challenging in comparison to the conjugation of 150 kDa IgG to AuNPs. Herein, effective Nb-AuNP assemblies are built using the selective and almost irreversible non-covalent associations between two peptide sequences deriving from a p53 heterotetramer domain variant. The 15 kDa GFP-binding Nb is fused to one dimerizing motif to obtain a recombinant Nb dimer with improved avidity for GFP while the other complementing dimerizing motif is equipped with thiols and grafted to a 2.4 nm substituted thiobenzoate-coordinated AuNP via thiolate exchange. After pegylation, the modified AuNPs are able to non-covalently anchor Nb dimers and the subsequent complexes demonstrate the ability to form immunogold label GFP-protein fusions within various subcellular locations. These tools open an avenue for precise localization of targets at high resolution by electron microscopy.

Recent Advances in Conventional Methods and Electrochemical Aptasensors for Mycotoxin Detection

The presence of mycotoxins in foodstuffs and feedstuffs is a serious concern for human health. The detection of mycotoxins is therefore necessary as a preventive action to avoid the harmful contamination of foodstuffs and animal feed. In comparison with the considerable expense of treating contaminated foodstuffs, early detection is a cost-effective way to ensure food safety. The high affinity of bio-recognition molecules to mycotoxins has led to the development of affinity columns for sample pre-treatment and the development of biosensors for the quantitative analysis of mycotoxins. Aptamers are a very attractive class of biological receptors that are currently in great demand for the development of new biosensors. In this review, the improvement in the materials and methodology, and the working principles and performance of both conventional and recently developed methods are discussed. The key features and applications of the fundamental recognition elements, such as antibodies and aptamers are addressed. Recent advances in aptasensors that are based on different electrochemical (EC) transducers are reviewed in detail, especially from the perspective of the diagnostic mechanism; in addition, a brief introduction of some commercially available mycotoxin detection kits is provided.

Unique Benefits of Tumor-Specific Nanobodies for Fluorescence Guided Surgery

Tumor-specific fluorescence labeling is promising for real-time visualization of solid malignancies during surgery. There are a number of technologies to confer tumor-specific fluorescence. Antibodies have traditionally been used due to their versatility in modifications; however, their large size hampers efficient fluorophore delivery. Nanobodies are a novel class of molecules, derived from camelid heavy-chain only antibodies, that have shown promise for tumor-specific fluorescence labeling. Nanobodies are ten times smaller than standard antibodies, while maintaining antigen-binding capacity and have advantageous features, including rapidity of tumor labeling, that are reviewed in the present report. The present report reviews special considerations needed in developing nanobody probes, the status of current literature on the use of nanobody probes in fluorescence guided surgery, and potential challenges to be addressed for clinical translation.

An Inside Job: Applications of Intracellular Single Domain Antibodies

Sera of camelid species contain a special kind of antibody that consists only of heavy chains. The variable antigen binding domain of these heavy chain antibodies can be expressed as a separate entity, called a single domain antibody that is characterized by its small size, high solubility and oftentimes exceptional stability. Because of this, most single domain antibodies fold correctly when expressed in the reducing environment of the cytoplasm, and thereby retain their antigen binding specificity. Single domain antibodies can thus be used to target a broad range of intracellular proteins. Such intracellular single domain antibodies are also known as intrabodies, and have proven to be highly useful tools for basic research by allowing visualization, disruption and even targeted degradation of intracellular proteins. Furthermore, intrabodies can be used to uncover prospective new therapeutic targets and have the potential to be applied in therapeutic settings in the future. In this review we provide a brief overview of recent advances in the field of intracellular single domain antibodies, focusing on their use as research tools and potential therapeutic applications. Special attention is given to the available methods that allow delivery of single domain antibodies into cells.

Nanobody-Based Probes for Subcellular Protein Identification and Visualization

Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.