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Single molecule tools. Part B, Super-resolution, particle tracking, multiparameter and force based methods /
Single molecule tools have begun to revolutionize the molecular sciences, from biophysics to chemistry to cell biology. They hold the promise to be able to directly observe previously unseen molecular heterogeneities, quantitatively dissect complex reaction kinetics, ultimately miniaturize enzyme as...
| Clasificación: | Libro Electrónico |
|---|---|
| Otros Autores: | |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
San Diego, CA :
Academic Press/Elsevier,
2010.
|
| Edición: | 1st ed. |
| Colección: | Methods in enzymology ;
v. 475. |
| Temas: | |
| Acceso en línea: | Texto completo Texto completo Texto completo Texto completo |
MARC
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| 245 | 0 | 0 | |a Single molecule tools. |n Part B, |p Super-resolution, particle tracking, multiparameter and force based methods / |c edited by Nils G. Walter. |
| 246 | 3 | 0 | |a Super-resolution, particle tracking, multiparameter and force based methods |
| 250 | |a 1st ed. | ||
| 260 | |a San Diego, CA : |b Academic Press/Elsevier, |c 2010. | ||
| 300 | |a 1 online resource (l, 663 pages) : |b illustrations (some color) | ||
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| 490 | 1 | |a Methods in enzymology, |x 0076-6879 ; |v v. 475 | |
| 504 | |a Includes bibliographical references and indexes. | ||
| 588 | 0 | |a Print version record. | |
| 520 | |a Single molecule tools have begun to revolutionize the molecular sciences, from biophysics to chemistry to cell biology. They hold the promise to be able to directly observe previously unseen molecular heterogeneities, quantitatively dissect complex reaction kinetics, ultimately miniaturize enzyme assays, image components of spatially distributed samples, probe the mechanical properties of single molecules in their native environment, and "just look at the thing" as anticipated by the visionary Richard Feynman already half a century ago. This volume captures a snapshot of this vibrant, rapidly expanding field, presenting articles from pioneers in the field intended to guide both the newcomer and the expert through the intricacies of getting single molecule tools. * Includes time-tested core methods and new innovations applicable to any researcher employing single molecule tools * Methods included are useful to both established researchers and newcomers to the field * Relevant background and reference information given for procedures can be used as a guide to developing protocols in a number of disciplines. | ||
| 505 | 0 | |a 1.Super-Accuracy and Super-Resolution: Getting Around the Diffraction Limit / Paul R. Selvin -- 1.Overview: Accuracy and Resolution -- 2.Getting Super-Accuracy -- 3.Calculating Super-Accuracy -- 4.Reaching Super-Resolution -- 5.Future Directions -- References -- 2.Molecules and Methods for Super-Resolution Imaging / W. E. Moerner -- 1.Introduction -- 2.Molecules for Super-Resolution Imaging -- 3.Selected Methods for Super-Resolution Imaging -- Acknowledgments -- References -- 3.Tracking Single Proteins in Live Cells Using Single-Chain Antibody Fragment-Fluorescent Quantum Dot Affinity Pair / Shimon Weiss -- 1.Introduction -- 2.The Method: Targeting QDs via a Single-Chain Variable Fragment-Hapten Pair -- 3.Functionalization of QDs -- 4.Quantification of the Number of FL Molecules per FL-pc-QD -- 5.Binding of FL-QDs to Anti-scFv Fusion Constructs -- 6.DNA Constructs for Single FL-QD Imaging in Live Cells -- 7.Single-Molecule Imaging of Live Mammalian Cells -- Acknowledgments -- References -- 4.Recording Single Motor Proteins in the Cytoplasm of Mammalian Cells / Edgar Meyhofer -- 1.Introduction -- 2.Basic Principles -- 3.Labeling Molecular Motors for in Vivo Observations -- 4.Instrumentation for Tracking Single Motors in Vivo -- 5.Detailed Experimental Procedures -- 6.Summary and Conclusions -- Acknowledgments -- References -- 5.Single-Particle Tracking Photoactivated Localization Microscopy for Mapping Single-Molecule Dynamics / Jennifer Lippincott-Schwartz -- 1.Introduction -- 2.Description of the sptPalm Method -- 3.Labeling with Photoactivatable Fluorescent Probes -- 4.Tracking Single Molecules -- 5.Experimental Example: sptPalm on a Membrane Protein -- 6.Conclusions -- References -- 6.A Bird's Eye View: Tracking Slow Nanometer-Scale Movements of Single Molecular Nano-Assemblies / Nils G. Walter -- 1.Introduction -- 2.DNA-Based Nanowalkers -- 3.Considerations for Fluorescence Imaging of Slowly Moving Particles -- 4.Single-Molecule Fluorescence Tracking of Nanowalkers -- 5.Extracting Super-Resolution Position Information -- 6.Concluding Remarks -- Acknowledgments -- References -- 7.Anti-Brownian Traps for Studies on Single Molecules / Adam E. Cohen -- 1.Theoretical Overview -- 2.Anti-Brownian Trapping Systems -- 3.The ABEL Trap -- 4.Applications -- 5.Future Work: En Route to Single Fluorophores -- Acknowledgments -- References -- 8.Plasmon Rulers as Dynamic Molecular Rulers in Enzymology / Jan Liphardt -- 1.Introduction -- 2.The Basic Idea: Distance Dependence of Plasmon Coupling -- 3.Hardware Needed for Single Particle Rayleigh Scattering Spectroscopy -- 4.Which Readout -- Intensity, Polarization, or Color? -- 5.Ruler Calibration? -- 6.Plasmon Ruler Assembly and Purification -- 7.Example 1: Dynamics of DNA Bending and Cleavage by Single EcoRV Restriction Enzymes -- 8.Example 2: Spermidine Modulated Ribonuclease Activity Probed by RNA Plasmon Rulers -- 9.Outlook -- References -- 9.Quantitative Analysis of DNA-Looping Kinetics from Tethered Particle Motion Experiments / Laura Finzi -- 1.Introduction -- 2.Change-Point Algorithm -- 3.Data Clustering and Expectation-Maximization Algorithm -- 4.Adaptation of the Method to the Case of TPM Data Analysis -- 5.Performance of the Method -- 6.Comparison with the Threshold Method -- 7.Application to TPM Experiments: Cl-Induced Looping in [MARC+6E]-DNA -- 8.Conclusions -- Acknowledgments -- References -- 10.Methods in Statistical Kinetics / Carlos Bustamante -- 1.Introduction -- 2.The Formalism of Statistical Kinetics -- 3.Characterizing Fluctuations -- 4.Extracting Mechanistic Constraints from Moments -- 5.Conclusions and Future Outlook -- References -- 11.Visualizing DNA Replication at the Single-Molecule Level / Antoine M. van Oijen -- 1.Introduction -- 2.Observing Replication Loops with Tethered Bead Motion -- 3.Fluorescence Visualization of DNA Replication -- Acknowledgments -- References -- 12.Measurement of the Conformational State of F1-ATPase by Single-Molecule Rotation / Hiroyuki Noji -- 1.Introduction -- 2.Sample Preparation -- 3.Single-Molecule Cross-Link Experiment -- 4.Pausing with AMP-PNP or/and N3- -- Acknowledgments -- References -- 13.Magnetic Tweezers for the Study of DNA Tracking Motors / Vincent Croquette -- 1.Introduction -- 2.Experimental Setup -- 3.Methods and Protocols -- 4.Application to the Study of FtsK -- 5.Application to the Study of the GP41 Helicase -- 6.Conclusions -- Acknowledgments -- References -- 14.Single-Molecule Dual-Beam Optical Trap Analysis of Protein Structure and Function / James A. Spudich -- 1.Introduction -- 2.Insights into Myosin Function Using a Dual-Beam Optical Trap -- 3.Optical Trap Instrumentation -- 4.Optical Trapping Experiment -- 5.Data Analysis -- 6.Conclusion -- Acknowledgments -- References -- 15.An Optical Apparatus for Rotation and Trapping / Steven M. Block -- 1.Introduction -- 2.Optical Trapping and Rotation of Microparticles -- 3.The Instrument -- 4.Fabrication of Anisotropic Particles -- 5.Instrument Calibration -- 6.Simultaneous Application of Force and Torque Using Optical Tweezers -- 7.Conclusions -- Acknowledgments -- References -- 16.Force-Fluorescence Spectroscopy at the Single-Molecule Level / Taekjip Ha -- 1.Introduction -- 2.Setup -- 3.Optical Trapping -- 4.Fluorescence Detection -- 5.Coalignment of Confocal and Optical Trapping -- 6.Sample Preparation Protocols -- 7.Applications to Biological Systems -- 8.Outlook -- Acknowledgments -- References -- 17.Combining Optical Tweezers, Single-Molecule Fluorescence Microscopy, and Microfluidics for Studies of DNA-Protein Interactions / Gijs J. L. Wuite -- 1.Introduction -- 2.Instrumentation -- 3.Preparation of Reagents -- 4.Combining Optical Trapping, Fluorescence Microscopy, and Microfluidics: Example Protocols -- 5.Conclusions -- Acknowledgments -- References -- 18.Accurate Single-Molecule FRET Studies Using Multiparameter Fluorescence Detection / Claus A. M. Seidel -- 1.Introduction -- 2.FRET Theory -- 3.Fluorescence Properties and Measurement Techniques -- 4.Qualitative Description of smFRET -- 5.Quantitative Description of smFRET -- 6.Discussion -- Acknowledgments -- References -- 19.Atomic Force Microscopy Studies of Human Rhinovirus: Topology and Molecular Forces / Peter Hinterdorfer -- 1.Introduction -- 2.Results and Discussion -- References -- 20.High-Speed Atomic Force Microscopy Techniques for Observing Dynamic Biomolecular Processes / Toshio Ando -- 1.Introduction -- 2.Survey of Requirements for High-Speed Bio-AFM Imaging -- 3.Substrate Surfaces -- 4.Control of Diffusional Mobility -- 5.Protein 2D Crystals as Targets to Study -- 6.Low-Invasive Imaging -- 7.UV Flash-Photolysis of Caged Compounds -- 8.Cantilever Tip -- References -- 21.Nanopore Force Spectroscopy Tools for Analyzing Single Biomolecular Complexes / Amit Meller -- 1.Introduction -- 2.The Nanopore Method -- 3.DNA Unzipping Kinetics Studied Using Nanopore Force Spectroscopy -- 4.Conclusions and Summary -- Acknowledgments -- References -- 22.Analysis of Single Nucleic Acid Molecules with Protein Nanopores / Hagan Bayley -- 1.Background: Analysis of Nucleic Acids with Nanopores -- 2.Electrical Recording with Planar Lipid Bilayers -- 3.Nanopores -- 4.Materials -- 5.Data Acquisition and Analysis -- References. | |
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| 830 | 0 | |a Methods in enzymology ; |v v. 475. | |
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