Book contents
- Single-Molecule Science
- Single-Molecule Science
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Super-Resolution Microscopy and Molecular Imaging Techniques to Probe Biology
- 1 Introduction on Single-Molecule Science
- 2 One Molecule, Two Molecules, Red Molecules, Blue Molecules
- 3 Multiscale Fluorescence Imaging
- 4 Long-Read Single-Molecule Optical Maps
- Part II Protein Folding, Structure, Confirmation, and Dynamics
- Part III Mapping DNA Molecules at the Single-Molecule Level
- Part IV Single-Molecule Biology to Study Gene Expression
- Index
- References
1 - Introduction on Single-Molecule Science
from Part I - Super-Resolution Microscopy and Molecular Imaging Techniques to Probe Biology
Published online by Cambridge University Press: 05 May 2022
Book contents
- Single-Molecule Science
- Single-Molecule Science
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Super-Resolution Microscopy and Molecular Imaging Techniques to Probe Biology
- 1 Introduction on Single-Molecule Science
- 2 One Molecule, Two Molecules, Red Molecules, Blue Molecules
- 3 Multiscale Fluorescence Imaging
- 4 Long-Read Single-Molecule Optical Maps
- Part II Protein Folding, Structure, Confirmation, and Dynamics
- Part III Mapping DNA Molecules at the Single-Molecule Level
- Part IV Single-Molecule Biology to Study Gene Expression
- Index
- References
Summary
Classical chemistry and biochemistry experiments in solution measure the properties of many molecules and/or interrogate them simultaneously – these are called ensemble measurements and tend to mask the underlying molecular dynamics. Studies at single-molecule level provide random, stochastic dynamics, and allow access to an incredible wealth of molecular information. Most importantly, previously “unanswerable” questions in the physical, chemical, and biological sciences can now be answered. The field of single-molecule science (SMS) can be roughly divided into two general areas: (1) improvements in single-molecule methodologies (technology development); and (2) use of these methodologies to address important scientific questions in fundamental biological research (applied research). Over the past decades, single-molecule research has fostered excellent collaboration and interdisciplinary research with input from biology, chemistry, and physics.
- Type
- Chapter
- Information
- Single-Molecule ScienceFrom Super-Resolution Microscopy to DNA Mapping and Diagnostics, pp. 3 - 19Publisher: Cambridge University PressPrint publication year: 2022
References
Aitken, C. E., Petrov, A., Puglisi, J. D., et al. (2010). Single Ribosome Dynamics and the Mechanism of Translation. Annual Reviews of Biophysics, 39 , 491–513.Google Scholar
Albrecht, T., Slabaugh, G., Alonso, E., et al. (2017). Deep Learning for Single-Molecule Science. Nanotechnology, 28, 42.Google Scholar
Ashkin, A. 1970. Acceleration and Trapping of Particles by Radiation Pressure. Physical Review Letters, 24 , 156–159.Google Scholar
Ashkin, A., Dziedzic, J. M., Bjorkholm, J. E., and Chu, S. (1986). Observation of a Single-Beam Gradient Force Optical Trap for Dielectric Particles. Optics Letters, 11 , 288–290.CrossRefGoogle ScholarPubMed
Benesch, R. E. and Benesch, R. (1953). Enzymatic Removal of Oxygen for Polarography and Related Methods. Science, 118 , 447–448.CrossRefGoogle ScholarPubMed
Betzig, E. and Chichester, R. J. (1993). Single Molecules Observed by Near-Field Scanning Optical Microscopy. Science, 262 , 1422–1425.Google Scholar
Betzig, E. and Trautman, J. K. (1992). Near-Field Optics: Microscopy, Spectroscopy, and Surface Modification beyond the Diffraction Limit. Science, 257, 189–195.Google Scholar
Binnig, G. and Rohrer, H. (1982). Scanning Tunnelling Microscopy. Helvetica Physics Acta, 55, 726–735.Google Scholar
Binnig, G., Quate, C. F., and Gerber, C. (1986). Atomic Force Microscope. Physical Reviews Letters, 56 , 930–933.CrossRefGoogle ScholarPubMed
Birk, U. J. (2019). Super-Resolution Microscopy of Chromatin. Genes (Basel), 10 , 493.Google Scholar
Block, S. M., Goldstein, L. S. B., Schnapp, B. J., et al. (1990). Bead Movement by Single Kinesin Molecules Studied with Optical Tweezers. Nature, 348 , 348–352. doi: 10.1038/348348a0Google Scholar
Bokinsky, G. and Zhuang, X. W. (2005). Single-Molecule RNA Folding. Accounts of Chemical Research, 38 , 566–573.Google Scholar
Brower-Toland, B. D., Smith, C. L., Yeh, R. C., et al. (2002). Mechanical Disruption of Individual Nucleosomes Reveals a Reversible Multistage Release of DNA. Proceedings of the National Academy of Sciences United States of America, 99 , 1960–1965.CrossRefGoogle ScholarPubMed
Bustamante, C., Chemla, Y. R, Forde, N. R., et al. (2004). Mechanical Processes in Biochemistry. Annual Reviews of Biochemistry, 73, 705–748.Google Scholar
Chemla, Y. R., Anderson, D. L., and Bustmante, C. (2005). Mechanism of Force Generation of a Viral DNA Packaging Motor. Cell, 122 , 683–692.CrossRefGoogle ScholarPubMed
Chen, J., Miller, J., Kirchmaier, A., et al. (2012). Single-Molecule Tools Elucidate H2A.Z Nucleosome Composition. Journal of Cell Science, 125, 2954–2964.Google Scholar
DeHaven, A. C., Norden, I. S., and Hoskins, A. A. (2016). Lights, Camera, Action! Capturing the Spliceosome and Pre-mRNA Splicing with Single-Molecule Fluorescence Microscopy. Wiley Interdisciplinary Reviews in RNA, 5, 683–701.Google Scholar
Dufrêne, Y. F., Ando, T., Garcia, R., et al. (2017). Imaging Modes of Atomic Force Microscopy for Application in Molecular and Cell Biology. Nature Nanotechnology, 12, 295–307.CrossRefGoogle ScholarPubMed
Engel, A. (1991). Biological applications of scanning probe microscopes. Annual Reviews Biophysics and Biophysical Chemistry, 20, 79–108.Google Scholar
Engel, A. and Muller, D. J. (2000). Observing Single Biomolecules at Work with the Atomic Force Microscope.Nature Structural Biology, 7 , 715–718.Google Scholar
Förster, T. (1948). Zwischenmolekulareenergiewanderung und fluoreszenz. Annalen Der Physik, 2 , 55–75.Google Scholar
Frank, J. and Agarwal, R. K. (2000). A Ratchet-Like Inter-Subunit Reorganization of the Ribosome during Translocation. Nature, 406, 318–322.Google Scholar
Frank, J. and Gonzalez, R. L. Jr. (2010). Structure and Dynamics of a Processive Brownian Motor: The Tyranslating Ribosome. Annual Reviews of Biochemistry, 79 , 381–412.Google Scholar
Fu, X., Moonschi, F. H., Fox-Loe, A. M., et al. (2019). Brain Region-Specific Single Molecule Fluorescence Imaging. Analytical Chemistry. doi: 10.1021/acs.analchem.9b02133.Google Scholar
Funatsu, T., Harada, Y., Higuchi, H., et al. (1997). Imaging and Nano-Manipulation of Single Biomolecules. Biophysical Chemistry, 68, 63–72.Google Scholar
Ha, T., Enderle, T., Weiss, S., et al. (1996). Probing the Interaction between Two Single Molecules: Fluorescence Resonance Energy Transfers between a Single Donor and a Single Acceptor. Proceedings of the National Academy of Sciences United States of America, 93 , 6264–6268.CrossRefGoogle Scholar
Ha, T., Zhuang, X. W., Kim, H. D., et al. (1999). Ligand-Induced Conformational Changes Observed in Single RNA Molecules. Proceedings of the National Academy of Sciences United States of America, 96, 9077–9082.Google Scholar
Hell, S. W., Byba, M., and Jakobs, S. (2004). Concepts for Nanoscale Resolution in Fluorescence Microscopy. Current Opinions in Neurobiology, 14 , 599–609.Google Scholar
Hirschfield, T. (1976). Optical Microscopic Observation of Single Small Molecules. Applied Optics, 15 , 2965–2966.Google Scholar
Howard, J., Hudspeth, A. J., Vale, R. D., et al. (1989). Movement of Microtubules by Single Kinesin Molecules.Nature, 342, 154–158.Google Scholar
Huang, B., Babcock, H., and Zhuang, X. (2010). Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells. Cell, 143, 1047–1058.Google Scholar
Hugel, T., Michaelis, J., Walter, J. M., et al. (2007). Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage Varphi29 Capsids. Public Library of Sciences Biology, 5 , e59. doi:10.1371/journal.pbio.0050059.Google Scholar
Kaledhonkar, S., Fu, Z., Caban, K., et. al. (2019). Late Steps in Bacterial Translation Initiation Visualized Using Time-Resolved Cryo-EM. Nature, 570, 400–404.Google Scholar
Kapanidis, A. N. and Weiss, S. (2004). Fluorescence-Aided Molecule Sorting: Analysis of Structure and Interactions by Alternating-Laser Excitation of Single Molecules. Proceedings of the National Academy of Sciences United States of America, 101 , 8936–8941.Google Scholar
Kapanidis, A. N., Laurence, T. A., Lee, N. K., et al. (2005). Alternating-Laser Excitation of Single Molecules. Accounts of Chemical Research, 38 , 523–533.Google Scholar
Kapanidis, A. N, Margeat, E., Weiss, S., et al. (2006). Initial Transcription by RNA Polymerase Proceeds through a DNA-Scrunching Mechanism. Science, 314 , 1144–1147.Google Scholar
Kim, P. S. and Baldwin, R. L. (1982). Specific Intermediates in the Folding Reactions of Small Proteins and the Mechanism of Protein Folding. Annual Reviews of Biochemistry, 51 , 459–489.Google Scholar
Kinosita, K., Itoh, H., Yoshida, M., et al. (2004). Mechanically Driven ATP Synthesis by F-1-ATPase. Nature, 427 , 465–468.Google Scholar
Ladoux, B., Quivy, J. P., Doyle, P., et al. (2000). Fast Kinetics of Chromatin Assemble Revealed by Single-Molecule Video-Microscopy and Scanning Force Microscopy. Proceedings of the National Academy of Sciences United States of America, 97 , 14251–14256.Google Scholar
Lindsay, S. M., Thundat, T., and Nagahara, L. (1988). Adsorbate Deformation as a Contrast Mechanism in STM Images of Bio-Polymers in an Aqueous Environment – Images of the Unstained. Hydrated DNA Double Helix. Journal of Microscopy, 152, 213–220.Google Scholar
Lindsay, S. M., Thundat, T., Nagahara, L., et al. (1989). Images of the DNA double helix in water. Science, 244, 1063–1064.Google Scholar
Lu, H. P., Xun, L. Y., and Xie, X. S. (1998). Single-Molecule Enzymatic Dynamics. Science, 282, 1877–1882.Google Scholar
Mallik, R., Gross, S. P., et al. (2004). Molecular Motors: Strategies to Get Along. Current Biology, 14 , R971–R982.Google Scholar
Mashanov, G. I., Tacon, D., Knight, A. E., et al. (2003). Visualizing Single Molecules inside Living Cells Using Total Internal Reflection Fluorescence Microscopy. Methods, 29 , 142–152.CrossRefGoogle ScholarPubMed
Mir, M., Reimer, A., Stadler, M., et al. (2018). Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Methods in Molecular Biology, 1814, 541–559.Google Scholar
Moerner, W. E. (1994). Examining Nano-Environments in Solids on the Scale of a Single, Isolated Impurity Molecule. Science, 265, 46–53.CrossRefGoogle Scholar
Moerner, W. E. and Kador, L. (1989). Finding a Single Molecule in a Haystack – Optical Detection and Spectroscopy of Single Absorbers in Solids. Analytical Chemistry, 61 , A1217-A1223.Google Scholar
Moerner, W. E. and Orrit, M. (1999). Illuminating Single Molecules in Condensed Matter. Science, 283, 1670–1676.Google Scholar
Morisaki, T., Lyon, K., Deluca, K. F., et al. (2016). Real-time Quantification of Single translation dynamics in living cells. Science, 352, 1425–1429.Google Scholar
Neher, E. and Sakmann, B. (1976). Single-Channel Currents Recorded from Membrane of Denervated Frog Muscle-Fibers. Nature, 260, 799–802.CrossRefGoogle Scholar
Orrit, M. and Bernard, J. (1990). Single Pentacene Molecules Detected by Fluorescence Excitation in a P-Terphenyl Crystal. Physical Review Letters, 65, 2716–2719.Google Scholar
Perkins, T. T., Smith, D. E., and Chu, S. (1994). Direct Observation of Tube-Like Motion of a Single Polymer-Chain. Science, 264, 819–822.Google Scholar
Psaltis, D., Quake, S. R., Yang, C. H., et al. (2006). Developing Optofluidic Technology through the Fusion of Microfluidics and Optics. Nature, 442, 381–386.Google Scholar
Revyakin, A., Liu, C. Y., Ebright, R. H., et al. (2006). Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching. Science, 314 , 1139–1143.Google Scholar
Rotman, B. (1961). Measurement of Activity of Single Molecules of ß-d-Galactosidase. Proceedings of the National Academy of Sciences United States of America, 47 , 1981-1991.Google Scholar
Rusimova, K. R., Purkiss, R. M., Howes, R., et al. (2018). Regulating the Femtosecond Excited-State Lifetime of a Single Molecule. Science, 361, 1012–1016.Google Scholar
Selvin, P. R. and Ha, T., eds. (2008). Single-Molecule Techniques, a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
Squires, T. M. and Quake, S. R. (2005). Microfluidics: Fluid Physics at the Nanoliter Scale. Reviews in Modern Physics, 77 , 977–1026.Google Scholar
Shashkova, S. and Leake, M. C. (2017). Single-Molecule Fluorescence Microscopy Review: Shedding New Light on Old Problems. Biosciences Reports, 37, pii: BSR20170031.Google Scholar
Sternberg, S. H., Redding, S., Jinek, M., et al. (2014). DNA Interrogation by the CRISPR RNA Guided Endonuclease Cas9. Nature, 507, 62–67.CrossRefGoogle ScholarPubMed
Vale, R. D., Funatsu, T., Pierce, D. W., et al. (1996). Direct Observation of Single Kinesin Molecules Moving along Microtubules. Nature, 380 , 451–453.CrossRefGoogle ScholarPubMed
Walter, N. G., Huang, C-Y., Manzo, A. J, and Sobhy, M. A. (2008). Do-It-Yourself Guide: How to Use Modern Single-Molecule Toolkit. Nature Methods, 5, 475–489.Google Scholar
Weiss, S. (2004). Photon Arrival-Time Interval Distribution (PAID): A Novel Tool for Analysing Interactions. Journal of Physical Chemistry B, 108 , 3051–3067.Google Scholar
Wollman, A. J. M., Hedlund, E. G., Shashkova, S., et al. (2019). Towards Mapping the 3D Genome through High Speed Single-Molecule Tracking of Functional Transcription Factors in Single Living Cells. Methods, pii, S1046–2023, 30473–30480.Google Scholar
Yanagida, T. (2000). Single-Molecule Imaging of EGFR Signalling on the Surface of Living Cells. Nature Cell Biology, 2 , 168–172.Google Scholar
Zhang, Y., Smith, C. L, Grill, S. W., et al. (2006). DNA Translocation and Loop Formation Mechanism of Chromatin Remodelling by SWI/SNF and RSC. Molecular Cell, 24 , 559–568.Google Scholar
Zhuang, X. B., Bartley, L. E., Babcock, H. P., et al. (2000). A Single-Molecule Study of RNA Catalysis and Folding. Science, 288 , 2048–2051.Google Scholar
Zhuang, X. W. (2003). Visualizing Infection of Individual Influenza Viruses. Proceedings of the National Academy of Sciences United States of America, 100 , 9280–9285.Google Scholar
Zlatanova, J. and Leuba, S. H. (2003). Chromatin Fibers, One-at-a-Time. Journal of Molecular Biology, 331, 1–19.Google Scholar
Zlatanova, J., Lindsay, S. M., and Leuba, S. H. (2000). Single Molecule Force Spectroscopy in Biology Using the Atomic Force Microscope. Progresses in Biophysics and Molecular Biology, 74 , 37–61.Google Scholar
Zlatanova, J., McAllister, W. T, Leuba, S. H., et al. 2006. Single-Molecule Approaches Reveal the Idiosyncrasies of RNA Polymerases. Structure, 14 , 953–966.Google Scholar