| Contributors |
| Preface |
| Volume in Series |
| Star Polymer Surface Passivation for Single-Molecule Detection / Jürgen Groll ; Martin Moeller1： |
| Introduction |
| Surface Grafting of PEO and Protein Repellence / 2： |
| The NCO-sP(EO-stat-PO) System / 3： |
| Preparation of sP(EO-stat-PO)-Coated Substrates for Single-Molecule Experiments / 4： |
| Analysis of Protein Structure and Function on NCO-sP(EO-stat-PO) Surfaces / 5： |
| Acknowledgments |
| References |
| Azide-Specific Labeling of Biomolecules by Staudinger-Bertozzi Ligation: Phosphine Derivatives of Fluorescent Probes Suitable for Single-Molecule Fluorescence Spectroscopy / Anirban Chakraborty ; Dongye Wang ; Yon W. Ebright ; Richard H. Ebright |
| Materials and Methods |
| Preparation of Fluorescent Pre-mRNA Substrates for an smFRET Study of Pre-mRNA Splicing in Yeast / John Abelson ; Haralambos Hadjivassiliou ; Christine Guthrie |
| Identification of a Yeast Pre-mRNA with a Small Intron that is Spliced Efficiently In Vitro |
| Synthetic Fluorescent Ubc4 Pre-mRNA |
| Do the Dyes Affect the Efficiency of Splicing? |
| Mutant Pre-mRNAs |
| Tethering the Pre-mRNA to the Microscope Slide / 6： |
| Summary and Conclusion / 7： |
| Nanovesicle Trapping for Studying Weak Protein Interactions by Single-Molecule FRET / Jaime J. BenÃtez ; Aaron M. Keller ; Peng Chen |
| Nanovesicle Trapping Approach |
| smFRET Measurements of Weak Protein-Protein Interactions |
| Single-Molecule Kinetic Analysis of Three-State Protein-Protein Interactions |
| Further Developments |
| Concluding Remarks |
| Droplet Confinement and Fluorescence Measurement of Single Molecules / Lori S. Goldner ; Ana M. Jofre ; Jianyong Tang |
| Methods for Droplet Generation |
| Methods for Droplet Manipulation |
| Droplet Coalescence and Mixing |
| Experimental Considerations for Single Fluorophore Detection |
| Single-Molecule Measurements in Droplets |
| Future Prospects |
| Single-Molecule Fluorescence Spectroscopy Using Phospholipid Bilayer Nanodiscs / Abhinav Nath ; Adam J. Trexler ; Peter Koo ; Andrew D. Miranker ; William M. Atkins ; Elizabeth Rhoades |
| Nanodiscs and HDL Particles |
| Single-Molecule Techniques and Applications to Membrane Proteins |
| Cytochrome P450 3A4 and Its Allosteric Behavior |
| Image Filtering by Singular-Value Decomposition |
| Islet Amyloid Polypeptide Binding to Nanodiscs |
| ?-Synuclein Conformations on Nanodiscs |
| Summary / 8： |
| Single-Molecule Spectroscopy Using Microfluidic Platforms / Samuel Kim ; Richard N. Zare |
| Microchip Fabrication |
| Instrumentation for Fluorescence Detection |
| Detergent-Assisted Microchannel Electrophoresis |
| Fluorescence Correlation Spectroscopy |
| Detection of Protein-Protein Interactions in the Live Cell Plasma Membrane by Quantifying Prey Redistribution upon Bait Micropatterning / Julian Weghuber ; Mario Brameshuber ; Stefan Sunzenauer ; Manuela Lehner ; Christian Paar ; Thomas Haselgrübler ; Michaela Schwarzenbacher ; Martin Kaltenbrunner ; Clemens Hesch ; Wolfgang Paster ; Bettina Heise ; Alois Sonnleitner ; Hannes Stockinger ; Gerhard J. Schütz |
| Methodological Requirements |
| The Micropatterning Technique |
| Experimental Design |
| Procedure |
| Interpretation of Results |
| Figures of Merit |
| Conclusions |
| Analysis of Complex Single-Molecule FRET Time Trajectories / Mario Blanco ; Nils G. Walter9： |
| Analysis of Simple Trajectories |
| Analysis of Complex Trajectories |
| Post-HMM Processing and Data Visualization |
| Acknowledgment |
| Single-Molecule Fluorescence Studies of Intrinsically Disordered Proteins / Allan Chris M. Ferreon ; Crystal R. Moran ; Yann Gambin ; Ashok A. Deniz10： |
| Single-Molecule Fluorescence Methods |
| Site-Specific Labeling of Intrinsically Disordered Proteins |
| Examples of SMF Characterization of IDP Structure and Dynamics |
| Measuring the Energetic Coupling of Tertiary Contacts in RNA Folding using Single Molecule Fluorescence Resonance Energy Transfer / Max Greenfeld ; Daniel Herschlag11： |
| Thermodynamic Cooperativity Overview |
| Measuring Folding Equilibrium in RNA |
| Designing an smFRET Experiment to Measure Cooperativity |
| Additional Comments |
| A Highly Purified, Fluorescently Labeled In Vitro Translation System for Single-Molecule Studies of Protein Synthesis / Jingyi Fei ; Jiangning Wang ; Samuel H. Sternberg ; Daniel D. MacDougall ; Margaret M. Elvekrog ; Dileep K. Pulukkunat ; Michael T. Englander ; Ruben L. Gonzalez Jr12： |
| A Highly Purified, Escherichia coli-Based In Vitro Translation System |
| Biochemical Assays |
| Preparation of Fluorescently Labeled Translation Components |
| Conclusions and Future Perspectives |
| Watching Individual Proteins Acting on Single Molecules of DNA / Ichiro Amitani ; Bian Liu ; Christopher C. Dombrowski ; Ronald J. Baskin ; Stephen C. Kowalczykowski13： |
| Preparation of DNA Substrates |
| Preparation of Fluorescent Proteins |
| Instrument |
| Single-Molecule Imaging of Proteins on DNA |
| Data Analysis Methods |
| DNA Curtains for High-Throughput Single-Molecule Optical Imaging / Eric C. Greene ; Shalom Wind ; Teresa Fazio ; Jason Gorman ; Mari-Liis Visnapuu14： |
| Total Internal Reflection Fluorescence Microscopy |
| DNA Curtains |
| Visualizing Protein-DNA Interactions |
| Conclusions and Future Directions |
| Scanning FCS for the Characterization of Protein Dynamics in Live Cells / Zdenek Petrásek ; Jonas Ries ; Petra Schwille15： |
| Implementation |
| Data Analysis |
| Applications |
| Conclusion |
| Observing Protein Interactions and Their Stoichiometry in Living Cells by Brightness Analysis of Fluorescence Fluctuation Experiments / Yan Chen ; Jolene Johnson ; Patrick Macdonald ; Bin Wu ; Joachim D. Mueller16： |
| Brightness Classification of Fluorescent Molecules |
| Brightness Measurements in Cells |
| Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes / Arjun Raj ; Sanjay Tyagi17： |
| Design and Synthesis of Fluorescent Oligonucleotide Probe Sets |
| Preparation of Samples for In Situ Hybridization |
| Hybridization |
| Imaging |
| Image Analysis |
| Single mRNA Tracking in Live Cells / Hye Yoon Park ; Adina R. Buxbaum ; Robert H. Singer18： |
| Significance of Tracking mRNA |
| Labeling mRNA in Living Cells |
| Imaging mRNA Movements |
| Analyzing mRNA Motions |
| Single-Molecule Sequencing: Sequence Methods to Enable Accurate Quantitation / Christopher Hart ; Doron Lipson ; Fatih Ozsolak ; Tal Raz ; Kathleen Steinmann ; John Thompson ; Patrice M. Milos19： |
| Basic Principles of Single-Molecule Sequencing |
| Preparation of Genomic DNA for Single-Molecule Sequencing |
| Bacterial Genome Sequencing |
| Human Genome Sequencing and Quantitation |
| Chromatin Immunoprecipitation Studies |
| Digital Gene Expression for Transcriptome Quantitation |
| Real-Time DNA Sequencing from Single Polymerase Molecules / Jonas Korlach ; Keith P. Bjornson ; Bidhan P. Chaudhuri ; Ronald L. Cicero ; Benjamin A. Flusberg ; Jeremy J. Gray ; David Holden ; Ravi Saxena ; Jeffrey Wegener ; Stephen W. Turner20： |
| Principle of Single-Molecule, Real-Time DNA Sequencing |
| Components of SMRT Sequencing |
| Single-Molecule DNA Polymerase Dynamics |
| Author index |
| Subject Index |
| Contributors |
| Preface |
| Volume in Series |
| Star Polymer Surface Passivation for Single-Molecule Detection / Jürgen Groll ; Martin Moeller1： |
| Introduction |
| Surface Grafting of PEO and Protein Repellence / 2： |
