Single Molecule Tools, Part B: Super-Resolution, Particle Tracking, Multiparameter, and Force Based Methods Methods in Enzymology Series

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. Single Molecule Tools, Part B: Super-Resolution, Particle Tracking, Multiparameter, and Force Based Methods 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.

1. Watching single DNA replication loops under flow extension

Antoine Van Oijen

2. Star polymer surface passivation for single molecule detection

Jürgen Groll , Martin Möller

3. Ultrahigh resolution detection of single active motor proteins in live cells

Paul Selvin, Erdal Toprak & Comert Kural

4. Molecules and Methods for Superresolution Imaging

W.E. Moerner, Michael Thompson, Sam Lord, Julie Biteen, and Nick Conley +…

5. Aqueous nanodroplets for studying single molecules

Lori Goldner

6. High-speed atomic force microscopy techniques for visualizing dynamic behavior of biological macromolecules

Toshio Ando

7. Single-Biomolecule Spectroscopy Using Microfluidic Platforms

Richard Zare, Dr. Olga Dudko, Dr. Jérôme Mathé

8. DNA Looping Kinetics Analyzed by Tethered Particle Microscopy

Laura Finzi

9. Single molecule observation of proteins in vivo

Shimon Weiss, Gopal Iyer

10. DNA curtains as a high-throughput approach to single molecule imaging

Eric Greene

11. Single-molecule enzymology of protein synthesis

Ruben Gonzalez

12. Single molecule fluorescence studies of intrinsically disordered proteins

Ashok Deniz

13. Nanovesicle trapping for studying transient protein-protein interactions by single molecule FRET

Peng Chen

14. Tracking single motor proteins in the cytoplasm of mammalian cells

Edgar Meyhöfer

15. Conformational States of F1-ATPase by Single-Molecule Rotation

Hiroyuki Noji

16. Single Molecule Sequencing by Fluorescence Imaging

Patrice Milos

17. Real-Time DNA Sequencing from Single Polymerase Molecules

Jonas Korlach

18. Micropatterning and single molecule imaging for quantitative analysis of protein-protein interactions in living cells

Gerhard Schütz

19. Probing virus-receptor interactions by atomic force spectroscopy

Peter Hinterdorfer

20. Single-Molecule Fluorescence Spectroscopy of Cytochrome P450 in Nanodiscs

Elizabeth Rhoades, William M. Atkins

21. Analysis of complex single molecule FRET time traces

Nils Walter, Mario Blanco

22. Application of super-resolution imaging to single particle tracking in nanotechnology

Nils Walter, Chamaree de Silva & Anthony Manzo

23. Scanning FCS for the characterization of protein dynamics in live cells

Petra Schwille

24. Single mRNA molecule tracking in live cells

Rob Singer

25. Single-molecule high-resolution colocalization (SHREC) or Single-molecule optical-trap analyses of protein structure

James Spudich

26. Nanopore force Spectroscopy tools for analyzing single bio-complexes

Amit Meller

27. Use of plasmon coupling to reveal DNA dynamics at the single molecule level

Jan Liphardt

28. "Fluorescence-force spectroscopy" or "Suppression of fluorophore blinking and bleaching" or "Spontaneous intersubunit rotation of the ribosome"

Taekjip Ha

29. Multiplexed single mRNA imaging in fixed cells

Sanjay Tyagi, Arjun Raj

30. Size-Minimized Quantum Dots for Single-Molecule and Intracellular Imaging

Shuming Nie

31. The ABEL trap

Adam Cohen, Alex Fields

32. An optical torque wrench

Steve Block, Arthur La Porta

33. Determining the Stoichiometry of Protein Hetero-complexes in Living Cells with Fluorescence Fluctuation Spectroscopy

Joachim Mueller

34. Fluorescent Visualization of Single Protein-DNA Complexes

Steve Kowalzcykowski

35. Direct Measurement of Tertiary Contact Cooperativity in RNA Folding by single molecule FRET

Daniel Herschlag

36. Nanometer-localized multiple single-molecule (NALMS) or Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments

Norbert Scherer

37. Multiparameter single molecule fluorescence detection with applications to FRET

Claus Seidel

38. single-particle tracking-photoactivated localization microscopy (sptPALM) within live cells

Jennifer Lippincott-Schwartz, Suliana Manley

39. Site-specific incoporation of fluorescent probes into RNA polymerase

Richard Ebright

40. Quantitative single-molecule imaging by confocal laser scanning microscopy

Rudolph Rigler

41. Studies of DNA-replication at the single molecule level using magnetic tweezers

David Bensimon, Vincent Croquette

42. RNA labeled for single molecule FRET analysis from ligation with T4 RNA ligases

John Abelson

43. Combining optical tweezers, single-molecule fluorescence microscopy and microfluidics for studying reversible protein-DNA interactions

Gijs Wuite, G. Farge, P. Gross & E.J.G. Peterman

44. How dwell time distributions and other such observables in single molecule analysis can be used to extract information from molecular systems

Carlos Bustamante, Jeff Moffitt & Yann Robert Chemla

45. Atomic force microscopy studies of human rhinovirus: topology and molecular forces

Peter Hinterdorfer

Biochemists, geneticists, molecular biologists, cell biologists, and biophysicists.

• 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