Advanced Fluorescent Polymer Probes for the Site-Specific Labeling of Proteins in Live Cells Using the HaloTag Technology

Design Parameters for a Mass Cytometry Detectable HaloTag Ligand

Mass cytometry permits the high dimensional analysis of complex biological samples; however, some techniques are not yet integrated into the mass cytometry workflow due to reagent availability. The use of self-labeling protein systems, such as HaloTag, are one such application. Here, we describe the design and implementation of the first mass cytometry ligands for use with HaloTag. "Click"-amenable HaloTag warheads were first conjugated onto poly(l-lysine) or poly(acrylic acid) polymers that were then functionalized with diethylenetriaminepentaacetic acid (DTPA) lutetium metal chelates. Kinetic analysis of the HaloTag labeling rates demonstrated that the structure appended to the 1-chlorohexyl warhead was key to success. A construct with a diethylene glycol spacer appended to a benzamide gave similar rates (kobs ∼ 102 M-1 s-1), regardless of the nature of the polymer. Comparison of the polymer with a small molecule chelate having rapid HaloTag labeling kinetics (kobs ∼ 104 M-1 s-1) suggests the polymers significantly reduced the HaloTag labeling rate. HEK293T cells expressing surface-exposed GFP-HaloTag fusions were labeled with the polymeric constructs and 175Lu content measured by cytometry by time-of-flight (CyTOF). Robust labeling was observed; however, significant nonspecific binding of the constructs to cells was also present. Heavily pegylated polymers demonstrated that nonspecific binding could be reduced to allow cells bearing the HaloTag protein to be distinguished from nonexpressing cells.

Bright and Stable Nanomaterials for Imaging and Sensing

This review covers strategies to prepare high-performance emissive polymer nanomaterials, combining very high brightness and photostability, to respond to the drive for better imaging quality and lower detection limits in fluorescence imaging and sensing applications. The more common approaches to obtaining high-brightness nanomaterials consist of designing polymer nanomaterials carrying a large number of fluorescent dyes, either by attaching the dyes to individual polymer chains or by encapsulating the dyes in nanoparticles. In both cases, the dyes can be covalently linked to the polymer during polymerization (by using monomers functionalized with fluorescent groups), or they can be incorporated post-synthesis, using polymers with reactive groups, or encapsulating the unmodified dyes. Silica nanoparticles in particular, obtained by the condensation polymerization of silicon alcoxides, provide highly crosslinked environments that protect the dyes from photodegradation and offer excellent chemical modification flexibility. An alternative and less explored strategy is to increase the brightness of each individual dye. This can be achieved by using nanostructures that couple dyes to plasmonic nanoparticles so that the plasmon resonance can act as an electromagnetic field concentrator to increase the dye excitation efficiency and/or interact with the dye to increase its emission quantum yield.

Lipophilic Anchors that Embed Bioconjugates in Bilayer Membranes: A Review

A wide range of biomaterials and engineered cell surfaces are composed of bioconjugates embedded in liposome membranes, surface-immobilized bilayers, or the plasma membranes of living cells. This review article summarizes the various ways that Nature anchors integral and peripheral proteins in a cell membrane and describes the strategies devised by chemical biologists to label a membrane protein in living cells. Also discussed are modern synthetic and semisynthetic methods to produce lipidated proteins. Subsequent sections describe methods to anchor a three-component synthetic construct that is composed of a lipophilic membrane anchor, hydrophilic linker, and exposed functional component. The surface exposed payload can be a fluorophore, aptamer, oligonucleotide, polypeptide, peptide nucleic acid, polysaccharide, branched dendrimer, or linear polymer. Hydrocarbon chains are commonly used as the membrane anchor, and a general experimental trend is that a two chain lipid anchor has higher membrane affinity than a cholesteryl or single chain lipid anchor. Amphiphilic fluorescent dyes are effective molecular probes for cell membrane imaging and a zwitterionic linker between the fluorophore and the lipid anchor promotes high persistence in the plasma membrane of living cells. A relatively new advance is the development of switchable membrane anchors as molecular tools for fundamental studies or as technology platforms for applied biomaterials.

Fluorescent Polymer-AS1411-Aptamer Probe for dSTORM Super-Resolution Imaging of Endogenous Nucleolin

Nucleolin is a multifunctional protein involved in essential biological processes. To precisely localize it and unravel its different roles in cells, fluorescence imaging is a powerful tool, especially super-resolution techniques. Here, we developed polymer-aptamer probes, both small and bright, adapted to direct stochastic optical reconstruction microscopy (dSTORM). Well-defined fluorescent polymer chains bearing fluorophores (AlexaFluor647) and a reactive end group were prepared via RAFT polymerization. The reactive end-group was then used for the oriented conjugation with AS1411, a DNA aptamer that recognizes nucleolin with high affinity. Conjugation via strain-promoted alkyne/azide click chemistry (SPAAC) between dibenzylcyclooctyne-ended fluorescent polymer chains and 3'-azido-functionalized nucleic acids proved to be the most efficient approach. In vitro and in cellulo evaluations demonstrated that selective recognition for nucleolin was retained. Their brightness and small size make these polymer-aptamer probes an appealing alternative to immunofluorescence, especially for super-resolution (10-20 nm) nanoscopy. dSTORM imaging demonstrated the ability of our fluorescent polymer-aptamer probe to provide selective and super-resolved detection of cell surface nucleolin.

Generation of Peptides for Highly Efficient Proximity Utilizing Site-Specific Biotinylation in Cells

Protein tags are peptide sequences genetically embedded into a recombinant protein for various purposes, such as affinity purification, Western blotting, and immunofluorescence. Another recent application of peptide tags is in vivo labeling and analysis of protein–protein interactions (PPI) by proteomics methods. One of the common workflows involves site-specific in vivo biotinylation of an AviTag-fused protein in the presence of the biotin ligase BirA. However, due to the rapid kinetics of labeling, this tag is not ideal for analysis of PPI. Here we describe the rationale, design, and protocol for the new biotin acceptor peptides BAP1070 and BAP1108 using modular assembling of biotin acceptor fragments, DNA sequencing, transient expression of proteins in cells, and Western blotting methods. These tags were used in the Proximity Utilizing Biotinylation (PUB) method, which is based on coexpression of BAP-X and BirA-Y in mammalian cells, where X or Y are candidate interacting proteins of interest. By changing the sequence of these peptides, a low level of background biotinylation is achieved, which occurs due to random collisions of proteins in cells. Over 100 plasmid constructs, containing genes of transcription factors, histones, gene repressors, and other nuclear proteins were obtained during implementation of projects related to this method.

End-functionalized polymers by controlled/living radical polymerizations: synthesis and applications

This review focuses on end-functionalized polymers synthesized by controlled/living radical polymerizations and the applications in fields including bioconjugate formation, surface modification, topology construction, and self-assembly.

Recent biomedical advances enabled by HaloTag technology

The knowledge of interactions among functional proteins helps researchers understand disease mechanisms and design potential strategies for treatment. As a general approach, the fluorescent and affinity tags were employed for exploring this field by labeling the Protein of Interest (POI). However, the autofluorescence and weak binding strength significantly reduce the accuracy and specificity of these tags. Conversely, HaloTag, a novel self-labeling enzyme (SLE) tag, could quickly form a covalent bond with its ligand, enabling fast and specific labeling of POI. These desirable features greatly increase the accuracy and specificity, making the HaloTag a valuable system for various applications ranging from imaging to immobilization of POI. Notably, the HaloTag technique has already been successfully employed in a series of studies with excellent efficiency. In this review, we summarize the development of HaloTag and recent advanced investigations associated with HaloTag, including in vitro imaging (e.g., POI imaging, cellular condition monitoring, microorganism imaging, system development), in vivo imaging, biomolecule immobilization (e.g., POI collection, protein/nuclear acid interaction and protein structure analysis), targeted degradation (e.g., L-AdPROM), and more. We also present a systematic discussion regarding the future direction and challenges of the HaloTag technique.

Fluorescent labeling of biocompatible block copolymers: synthetic strategies and applications in bioimaging

Among biocompatible materials, block copolymers (BCPs) possess several advantages due to the control of their chemistry and the possibility of combining various blocks with defined properties. Consequently, BCPs drew considerable attention as biocompatible materials in the fields of drug delivery, medicine and bioimaging. Fluorescent labeling of BCPs quickly appeared to be a method of choice to image and track these materials in order to better understand the nature of their interactions with biological media. However, incorporating fluorescent markers (FM) into BCPs can appear tricky; we thus intend to help chemists in this endeavor by reviewing recent advances made in the last 10 years. With the choice of the FM being of prior importance, we first reviewed their photophysical properties and functionalities for optimal labeling and imaging. In the second part the different chemical approaches that have been used in the literature to fluorescently label BCPs have been reviewed. We also report and discuss relevant applications of fluorescent BCPs in bioimaging.

Multifunctional, histidine-tagged polymers: antibody conjugation and signal amplification

A polymer scaffold, with multiple reactive centres, was synthesised by RAFT polymerisation and conjugated to the antibody herceptin. A hexahistidine RAFT agent enabled simple purification of polymer–protein conjugates.