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Conjugation of oligosaccharides to probes and surfaces is useful in the development of biochemical assays to assess carbohydrate–protein interactions. In this protocol, conjugation is enabled by using a bifunctional oligo(ethylene glycol) linker.
Many intra- and extracellular signals induce structural changes in proteins. Schopper et al., describe a limited proteolysis–based mass spectrometry (LiP-MS) approach to characterizing these changes at a proteome-wide scale.
Flow chemistry is an attractive alternative to batch chemistry in cases in which improved safety and reaction efficiency can be achieved. This protocol describes the assembly of a continuous flow apparatus from readily available and affordable parts.
The levels of monoamines and their cofactors in cerebrospinal fluid are strong indicators for dopamine and serotonin biosynthesis and turnover. This protocol describes a set of HPLC-based approaches for the quantitative detection of these molecules.
Recent studies have uncovered substantial cross talk between the ubiquitylation and SUMOylation pathways. Using sequential affinity purification and mass spectrometry, this protocol enables the identification of proteins that are modified by both pathways.
This protocol describes how to produce cell-derived matrices from fibroblasts. These matrices can be used to provide a 3D scaffold for cell culture and to investigate cell behavior in complex microenvironments.
This protocol describes the construction and use of the Activity Recording CAFE, an automated image-tracking-based system for the integrated measurement of sleep and feeding in individual Drosophila.
Crystal-phase-controlled synthesis of noble metal nanomaterials is a promising strategy to tune their physicochemical properties. Gold nanomaterials with unusual crystal structures (e.g., hcp, hcp/fcc and 4H) can be prepared under mild conditions.
DNase I hypersensitive sites (DHSs) are regions of accessible chromatin that are indicative of regions involved in the regulation of gene expression. scDNase-seq allows genome-wide detection of DHSs from a low number of cells, including single cells.
This protocol describes how to combine confocal and atomic force microscopy (AFM) to study the interactions between single viruses and their cell-surface receptors on live cells.
This massively parallel pipeline enables high-throughput generation and confirmation of variants by Gateway cloning, barcoding, and next-generation sequencing, and their stratification by multiplexed interaction profiling and experimental validation.
Chemical synthesis of proteins (e.g., histones) allows precise insertion of modified amino acids. This protocol uses palladium chemistry to remove protecting groups and a removable solubilizing tag for the synthesis of lipophilic peptide segments.
In this protocol, the skull overlying the cerebellum is removed and a window is applied, enabling intravital imaging to provide a detailed characterization of dynamic processes in this region of the mouse brain.
This protocol describes the synthesis and application of hydrogel matrices comprising a poly(ethylene glycol) backbone, functionalized with cell adhesion cues and laminin-111. Uses include expanding stem cells and differentiating them into organoids.
This protocol details the construction and use of the ichip, a platform developed to isolate previously uncultivable microorganisms from a range of environmental samples, by enabling exposure to natural growth factors through in situ culture.
This protocol describes a two-stage ‘post-translational mutagenesis’ approach for the site-specific installation of natural and unnatural amino acid side chains into recombinant proteins.
High-affinity magnetic immunocapture is used to rapidly purify HA-tagged mitochondria from cells for metabolite profiling. Matrix concentrations of mitochondrial metabolites are determined through LC/MS, immunoblotting, confocal microscopy, and volumetric analysis.
This protocol describes strategies for the characterization of transient protein–protein interactions and their interaction interfaces via genetically encoded releasable photo-cross-linkers.
Humanized bone-marrow-ossicle niches are formed in mice via in situ differentiation of bone-marrow-derived mesenchymal stromal cells and can be used for transplantation of normal and malignant human hematopoietic cells.
This protocol describes HyCoSuL, an approach that uses tetrapeptides containing natural and >100 unnatural amino acids to screen for protease substrate specificity and to engineer highly active and selective substrates and activity-based probes.