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Tandem Affinity Purification of Protein Complexes in Mouse Embryonic Stem Cells Using In Vivo Biotinylation

Abstract Table of Contents Materials Figures Literature Cited Abstract Streptavidin affinity purification of protein complexes, in combination with in vivo biotinylation of critical transcription factors,

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Introduction to Atomic Force Microscopy (AFM) in Biology

Abstract Table of Contents Figures Literature Cited Abstract The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical ima

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TRAF‐Mediated TNFR‐Family Signaling

Abstract Table of Contents Figures Literature Cited Abstract The tumor necrosis factor (TNF) superfamily consists of a wide variety of cell?bound and secreted proteins that regulate numerous cellular processes. In particular, TNF?family pr

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Carbohydrate‐Oligonucleotide Conjugates

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes a strategy for attaching two mannose and two galactose residues to an oligonucleotide. This conjugation can be pe

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Fluorescence Spectroscopy

Abstract Table of Contents Materials Figures Literature Cited Abstract Fluorescence is an extremely powerful tool in modern biology, physics, and chemistry laboratories. This unit focuses on methods that

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Spatiotemporal Dynamics of Kinase Signaling Visualized by Targeted Reporters

Abstract Table of Contents Materials Figures Literature Cited Abstract The advent of genetically encoded FRET?based kinase activity reporters has ushered in a new era of signal transduction research. Such

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Generation of Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) Using Directed Molecular Evolution

Abstract Table of Contents Materials Figures Literature Cited Abstract G protein?coupled receptors (GPCRs) and their signal transductions are important for both physiological and pathological processes in

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Methylation‐Sensitive Single‐Molecule Analysis of Chromatin Structure

Abstract Table of Contents Materials Figures Literature Cited Abstract Methylation?sensitive single?molecule analysis of chromatin structure is a high?resolution method for studying nucleosome positioning

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Mapping Networks of Protein‐Mediated Physical Interactions Between Chromatin Elements

Abstract Table of Contents Materials Figures Literature Cited Abstract Understanding of transcriptional regulation has advanced in recent years in part due to development of technologies which allow deter

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Chromatin Interaction Analysis Using Paired‐End Tag Sequencing

Abstract Table of Contents Materials Figures Literature Cited Abstract Chromatin Interaction Analysis using Paired?End Tag sequencing (ChIA?PET) is a technique developed for large?scale, de novo analysis

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Use of Flow Cytometric Methods to Quantify Protein‐Protein Interactions

Abstract Table of Contents Materials Figures Literature Cited Abstract A method is described for the quantitative analysis of protein?protein interactions using the flow cytometry protein interaction assa

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Construction and Use of Glycan Microarrays

Abstract Table of Contents Materials Figures Literature Cited Abstract Glycosylation is an important post?translational modification that influences many biological processes critical for development, nor

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Biosensors for Characterizing the Dynamics of Rho Family GTPases in Living Cells

Abstract Table of Contents Materials Figures Literature Cited Abstract The biosensors developed in the authors' laboratory have been based on different designs, each imparting specific strengths and weakn

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Visualization of G Protein−Coupled Receptor (GPCR) Interactions in Living Cells Using Bimolecular Fluorescence Complementation (BiFC)

Abstract Table of Contents Materials Figures Literature Cited Abstract Members of the G protein?coupled receptor (GPCR) superfamily have been shown to homo? and hetero?oligomerize both in vitro and in viv

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Installation of Site‐Specific Methylation into Histones Using Methyl Lysine Analogs

Abstract Table of Contents Materials Figures Literature Cited Abstract Chromatin structure is influenced by post?translational modifications on histones, the principal basic protein component of chromatin

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Overview on the Rule of Five

Abstract Table of Contents Literature Cited Abstract In the mid? to late 1990s, because of the drug discovery paradigm shift from phenotypic screens to combinatorial chemistry and high?throughput screening, the physicochemical properties of exploratory drug molecules displa

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Nucleotide Analogues as Probes for DNA and RNA Polymerases

Abstract Table of Contents Figures Literature Cited Abstract Nucleotide analogues represent a major class of anti?cancer and anti?viral drugs, and provide an extremely powerful tool for dissecting the mechanisms of DNA and RNA polymerases.

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Analyzing Binding Data

Abstract Table of Contents Materials Figures Literature Cited Abstract Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and acce

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ChIP‐Seq: A Method for Global Identification of Regulatory Elements in the Genome

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes ChIP?Seq methodology, which involves chromatin immunoprecipitation (ChIP) followed by high?throughput sequencing

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Visualization of Kinase Activity with FRET‐Based Activity Biosensors

Abstract Table of Contents Materials Figures Literature Cited Abstract Genetically encodable FRET?based kinase activity reporters (KARs) enable real?time monitoring of kinase activity dynamics in living c

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