Current Protocols in Chemical Biology

Current Protocols in Chemical Biology

Online ISBN: 9780470559277

DOI: 10.1002/9780470559277

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  1. Volume 8
    1. Issue 1
      1. RNA Imaging with Dimeric Broccoli in Live Bacterial and Mammalian Cells
      2. Hollow-Fiber Methodology for Pharmacokinetic/Pharmacodynamic Studies of Antimalarial Compounds
      3. Isotope Targeted Glycoproteomics (IsoTaG) to Characterize Intact, Metabolically Labeled Glycopeptides from Complex Proteomes
    2. Issue 2
      1. Pseudo-Ligandless Click Chemistry for Oligonucleotide Conjugation
      2. Liquid Exfoliation of Layered Transition Metal Dichalcogenides for Biological Applications
      3. Combinatorial Library Screening Coupled to Mass Spectrometry to Identify Valuable Cyclic Peptides
      4. Optogenetic Control of Nuclear Protein Import in Living Cells Using Light-Inducible Nuclear Localization Signals (LINuS)
    3. Issue 3
      1. Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC)
      2. Reverse Phase Protein Arrays for Compound Profiling
      3. Nanoparticle-Templated Molecular Recognition Platforms for Detection of Biological Analytes
    4. Issue 4
      1. Tracking the Activity of mTORC1 in Living Cells Using Genetically Encoded FRET-based Biosensor TORCAR
      2. Enriching s4U-RNA Using Methane Thiosulfonate (MTS) Chemistry
      3. Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging
      4. Biochemical, Biophysical and Cellular Techniques to Study the Guanine Nucleotide Exchange Factor, GIV/Girdin
  2. Volume 7
    1. Issue 1
      1. SNIPER Peptide-Mediated Degradation of Endogenous Proteins
      2. Universal Non-Antibody Detection of Protein Phosphorylation Using pIMAGO
      3. Diffraction-Unlimited Fluorescence Microscopy of Living Biological Samples Using pcSOFI
      4. Preparation and Separation of DNA-Wrapped Carbon Nanotubes
    2. Issue 2
      1. Biosensing with Virus Electrode Hybrids
      2. SELMA: Selection with Modified Aptamers
      3. In Vivo Delivery of Nitric Oxide-Sensing, Single-Walled Carbon Nanotubes
      4. Point by Point: An Introductory Guide to Sample Preparation for Single-Molecule, Super-Resolution Fluorescence Microscopy
      5. Identifying Direct Protein Targets of Poly-ADP-Ribose Polymerases (PARPs) Using Engineered PARP Variants—Orthogonal Nicotinamide Adenine Dinucleotide (NAD+) Analog Pairs
    3. Issue 3
      1. Use of Human Induced Pluripotent Stem Cell–Derived Cardiomyocytes (hiPSC-CMs) to Monitor Compound Effects on Cardiac Myocyte Signaling Pathways
      2. Genetic Code Expansion of Mammalian Cells with Unnatural Amino Acids
      3. Digestion, Purification, and Enrichment of Protein Samples for Mass Spectrometry
    4. Issue 4
      1. Molecular Evolution Directs Protein Translation Using Unnatural Amino Acids
      2. Chemical Synthesis of Ubiquitin Chains
      3. Corking Nitrogen-Doped Carbon Nanotube Cups with Gold Nanoparticles for Biodegradable Drug Delivery Applications
      4. A Bead-Based Proximity Assay for BRD4 Ligand Discovery
  3. Volume 6
    1. Issue 1
      1. A One-Step Imaging Assay to Monitor Cell Cycle State and Apoptosis in Mammalian Cells
      2. Luciferase Reporter Assay in Drosophila and Mammalian Tissue Culture Cells
      3. High-Throughput Screening for Novel Anti-Infectives Using a C. elegans Pathogenesis Model
      4. Label-Free Cell-Based Dynamic Mass Redistribution Assays
    2. Issue 2
      1. Nanolithography Based on Metalized DNA Templates for Graphene Patterning
      2. Manipulating Natural Product Biosynthetic Pathways via DNA Assembler
      3. Synthesis of Hydrogen-Bond Surrogate α-Helices as Inhibitors of Protein-Protein Interactions
      4. Rapid Assays for Lectin Toxicity and Binding Changes that Reflect Altered Glycosylation in Mammalian Cells
    3. Issue 3
      1. Quantification of Protein Kinase Enzymatic Activity in Unfractionated Cell Lysates Using CSox-Based Sensors
      2. Evaluation of Compounds in Primary Human Islet Cell Culture
      3. A Biocompatible “Split Luciferin” Reaction and Its Application for Non-Invasive Bioluminescent Imaging of Protease Activity in Living Animals
      4. Glycomic Analysis of Glycans Released from Glycoproteins Using Chemical Immobilization and Mass Spectrometry
    4. Issue 4
      1. Probing Small-Molecule Microarrays with Tagged Proteins in Cell Lysates
      2. Real-Time Chemiluminescence Imaging Using Nano-Lantern Probes
      3. Determination of the Cytostatic and Cytocidal Activities of Antimalarial Compounds and Their Combination Interactions
  4. Volume 5
    1. Issue 1
      1. Advances in Lectin Microarray Technology: Optimized Protocols for Piezoelectric Print Conditions
      2. In Vivo Imaging and Biochemical Characterization of Protease Function Using Fluorescent Activity-Based Probes
      3. Bioorthogonal Profiling of Protein Methylation (BPPM) Using an Azido Analog of S-Adenosyl-L-Methionine
      4. Profiling Protein Methylation with Cofactor Analog Containing Terminal Alkyne Functionality
    2. Issue 2
      1. Chemoenzymatic Site-Specific Reversible Immobilization and Labeling of Proteins from Crude Cellular Extract Without Prior Purification Using Oxime and Hydrazine Ligation
      2. Spatiotemporal Control of Gene Expression in Mammalian Cells and in Mice Using the LightOn System
      3. Design, Synthesis, and Application of the Trimethoprim-Based Chemical Tag for Live-Cell Imaging
      4. Determining Lectin Specificity from Glycan Array Data Using Motif Segregation and GlycoSearch Software
    3. Issue 3
      1. Phage Selection of Peptide “Microantibodies”
      2. Multiplexing High-Content Flow (HCF) and Quantitative High-Throughput Screening (qHTS) to Identify Compounds Capable of Decreasing Cell Viability, Activating Caspase 3/7, Expressing Annexin V, and Changing Mitochondrial Membrane Integrity
      3. Profiling Native Kinases by Immuno-Assisted Activity-Based Profiling
      4. Using a Kinase-Inducible Bimolecular Switch to Control Enzyme Activity in Living Cells
    4. Issue 4
      1. Penicillin-Binding Protein Imaging Probes
      2. Saturation Transfer Difference NMR for Fragment Screening
      3. Chemiluminescent Nitrogen Detection (CLND) to Measure Kinetic Aqueous Solubility
      4. Visualization of O-GlcNAc Glycosylation Stoichiometry and Dynamics Using Resolvable Poly(ethylene glycol) Mass Tags
  5. Volume 4
    1. Issue 1
      1. Gene Assembly from Chip-Synthesized Oligonucleotides
      2. Labeling Substrate Proteins of Poly(ADP-ribose) Polymerases with Clickable NAD Analog
      3. On-Bead Two-Color (OBTC) Cell Screen for Direct Identification of Highly Selective Cell Surface Receptor Ligands
      4. High-Throughput RT-PCR for Small-Molecule Screening Assays
      5. Measurement of Protein Phosphorylation Stoichiometry by SRM-MS
      6. Kinase-Catalyzed Biotinylation of Peptides, Proteins, and Lysates
    2. Issue 2
      1. Bioorthogonal Chemical Reporters for Analyzing Protein Sulfenylation in Cells
      2. Nanostructure-Initiator Mass Spectrometry (NIMS) for the Analysis of Enzyme Activities
      3. In Situ Hybridization Assay-Based Small-Molecule Screening in Zebrafish
      4. High-Throughput Phosphoproteomics from Formalin-Fixed, Paraffin-Embedded Tissues
    3. Issue 3
      1. Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening
      2. Dealing with the Data Deluge: Handling the Multitude of Chemical Biology Data Sources
      3. Functional Assays on High-Content Protein Microarrays
      4. One-Pot Multienzyme Synthesis of Lewis x and Sialyl Lewis x Antigens
      5. Metallomics Using Inductively Coupled Plasma Mass Spectrometry
    4. Issue 4
      1. SHAPE–Seq: High-Throughput RNA Structure Analysis
      2. In Vivo Rapid Assessment of Compound Exposure (RACE) for Profiling the Pharmacokinetics of Novel Chemical Probes
      3. A High-Throughput Screening Method for Identification of Inhibitors of the Deubiquitinating Enzyme USP14
      4. Specificity Profiling of Protein-Binding Domains Using One-Bead-One-Compound Peptide Libraries
      5. A Screening Protocol for Identification of Functional Mutants of RNA Editing Adenosine Deaminases
  6. Volume 3
    1. Issue 1
      1. Parallel High-Throughput Automated Assays to Measure Cell Growth and Beta-Galactosidase Reporter Gene Expression in the Yeast Saccharomyces cerevisiae
      2. Development of Chemical Probes for Biochemical Detection and Cellular Imaging of Myristoylated and Palmitoylated Proteins
      3. Imaging of Endogenous RNA Using Genetically Encoded Probes
      4. Development of In-Cell Western Assays Using Far-Red Fluorophores
    2. Issue 2
      1. Derivatization of Free Natural Glycans for Incorporation onto Glycan Arrays: Derivatizing Glycans on the Microscale for Microarray and Other Applications
      2. Visualization and Identification of Fatty Acylated Proteins Using Chemical Reporters
      3. Miniaturized High-Throughput Fluorescent Assay for Conversion of NAD(P)H to NAD(P)
    3. Issue 3
      1. Chemical Synthesis of Hydrocarbon-Stapled Peptides for Protein Interaction Research and Therapeutic Targeting
      2. Triple-Addition Assay Protocols for Detecting and Characterizing Modulators of Seven-Transmembrane Receptors
      3. Compound Management: Guidelines for Compound Storage, Provision, and Quality Control
    4. Issue 4
      1. Copper-Catalyzed Azide–Alkyne Click Chemistry for Bioconjugation
      2. Target Identification Using Drug Affinity Responsive Target Stability (DARTS)
      3. Analyzing In Vivo Metabolite-Protein Interactions by Large-Scale Systematic Analyses
  7. Volume 2
    1. Issue 1
      1. Cross-Coupling Modification of Nucleoside Triphosphates, PEX, and PCR Construction of Base-Modified DNA
      2. Chemical Genetic Approach for Kinase-Substrate Mapping by Covalent Capture of Thiophosphopeptides and Analysis by Mass Spectrometry
      3. Construction and Use of Glycan Microarrays
    2. Issue 2
      1. Quantitative Glycomics of Cultured Cells Using Isotopic Detection of Aminosugars with Glutamine (IDAWG)
      2. Targeted Degradation of Proteins by PROTACs
      3. Directed Evolution of DNA Polymerases: Construction and Screening of DNA Polymerase Mutant Libraries
      4. Nucleotide Analogues as Probes for DNA and RNA Polymerases
      5. Site-Specific Protein Bioconjugation via a Pyridoxal 5′-Phosphate-Mediated N-Terminal Transamination Reaction
    3. Issue 3
      1. Small-Molecule Library Synthesis on Silicon-Functionalized SynPhase Lanterns
      2. High-Throughput Assessment of Mammalian Cell Viability by Determination of Adenosine Triphosphate Levels
      3. Preparation, Characterization, and Application of Optical Switch Probes
      4. Experimental Design Considerations for In Vitro Non-Natural Glycan Display via Metabolic Oligosaccharide Engineering
    4. Issue 4
      1. High-Throughput Assessment of Bacterial Growth Inhibition by Optical Density Measurements
      2. Mass Spectrometry-Based Identification of Protein Kinase Substrates Utilizing Engineered Kinases and Thiophosphate Labeling
      3. Supported Membrane Formation, Characterization, Functionalization, and Patterning for Application in Biological Science and Technology
  8. Volume 1
    1. Issue 1
      1. Fluorescence Polarization (FP) Assays for Monitoring Peptide-Protein or Nucleic Acid-Protein Binding
      2. Spatiotemporal Dynamics of Kinase Signaling Visualized by Targeted Reporters
      3. Activity-Based Protein Profiling (ABPP) and Click Chemistry (CC)–ABPP by MudPIT Mass Spectrometry
      4. Overview of Liquid Handling Instrumentation for High-Throughput Screening Applications
      5. Target Identification by Diazirine Photo-Cross-Linking and Click Chemistry