Contents

1. The New Era of Biology In Singulo

T. Ha and P.R. Selvin

IN VITRO FLUORESCENCE

2. Single-Molecule FRET with Total Internal Reflection Microscopy

C. Joo and T. Ha

3. In Vitro and In Vivo FIONA and Other Acronyms for Watching Molecular Motors Walk

P.R. Selvin, T. Lougheed, M.T. Hoffman, H. Park, H. Balci, B.H. Blehm, and E. Toprak

4. Colocalization of Fluorescent Probes: Accurate and Precise Registration with Nanometer Resolution

L.S. Churchman and J.A. Spudich

5. Alternating-Laser Excitation of Single Molecules

A.N. Kapanidis, M. Heilemann, E. Margeat, X. Kong, E. Nir, and S. Weiss

6. Orientation and Rotational Motions of Single Molecules by Polarized Total Internal Reflection Fluorescence Microscopy

J.F. Beausang, Y. Sun, M.E. Quinlan, J.N. Forkey, and Y.E. Goldman

FLUORESCENCE IN LIVING CELLS

7. Imaging Gene Expression in Living Cells at the Single-Molecule Level

J. Xiao, J. Elf, G.-W. Li, J. Yu, and X.S. Xie

8. Single-Virus Tracking in Live Cells

M.J. Rust, M. Lakadamyali, B. Brandenburg, and X. Zhuang

9. Ultrasensitive Imaging in Live Cells Using Fluorescent Quantum Dots

S. Courty and M. Dahan

10. Imaging Real-Time Gene Expression in Living Systems

A.L. Wells, J.S. Condeelis, R.H. Singer, and D. Zenklusen

11. Single-Molecule Imaging of Stochastic Signaling Events in Living Cells

S. Matsuoka, Y. Miyanaga, T. Yanagida, and M. Ueda

12. Fluorescence Correlation Spectroscopy In Vitro and In Vivo

E. Haustein and P. Schwille

OPTICAL TRAPS

13. Optical Traps to Study Properties of Molecular Motors

J.A. Spudich, S.E. Rice, R.S. Rock, T.J. Purcell, and H.M. Warrick

14. High-Resolution Dual-Trap Optical Tweezers with Differential Detection

C. Bustamante, Y.R. Chemla, and J.R. Moffitt

15. Imaging and Nanomanipulation of an Actomyosin Motor

S. Nishikawa, T. Komori, T. Ariga, T. Okada, M. Morimatsu, Y. Ishii, and T. Yanagida

MAGNETIC TRAPS

16. Single-Molecule Studies Using Magnetic Traps

T. Lionnet, J.-F. Allemand, A. Revyakin, T.R. Strick, O.A. Saleh, D. Bensimon, and V. Croquette

FORCE PROBES/ATOMIC FORCE MICROSCOPY

17. Probing Polysaccharide and Protein Mechanics by Atomic Force Microscopy

M. Rabbi and P.E. Marszalek

CHANNELS

18. Single-Molecule Analysis of Nucleic Acids and DNA–Protein Interactions Using Nanopores

M. Wanunu and A. Meller

OTHER TECHNIQUES

19. Single-Molecule Gold-Nanoparticle Tracking with High Temporal and Spatial Resolution and without an Applied Load

A.R. Dunn and J. A. Spudich

20. Advances in Surface-based Assays for Single Molecules

P.M. Fordyce, M.T. Valentine, and S.M. Block

21. Hydrodynamic Flow-stretching Assay for Single-Molecule Studies of Nucleic Acid–Protein Interactions

C.M. Schroeder, P.C. Blainey, S. Kim, and X.S. Xie

APPENDIX: Cautions

INDEX

  “I don't believe I have ever before read a microscopy textbook from cover to cover — but this one, reader, I did. Its two editors, Taekjip Ha and Paul Selvin, have set out to assemble a manual for cell biologists who want to extend their technical repertoires to include single-molecule techniques. They have succeeded admirably, and as a bonus the book provides a fascinating insight into where the technical limits lie, of how we stand — as the authors suggest in their introduction — at the beginning of a new era of single-molecule-based cell biology...This excellent book will be invaluable to anyone who is already competent at multimolecule data collection and interested in getting down to molecular mechanisms.”
      —Nature Cell Biology