I. Developing Single Molecule Technologies to Study Nanomachines
II. Combining FRET and Optical Trap to Study the Nucleosome
III. Investigating DNA Helicases Using Single Molecule Technologies
Part I: Developing Single Molecule Technologies to Study Nanomachines
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Recent improvements in single molecule technologies have enhanced our understanding of nanomachines; the cells’ tiny engines. Dr. Taekjip Ha explains how scientists have used fluorescence microscopy, in combination with other tools, to study nanomachines. For example, by tagging the protein myosin with a fluorescent dye, his laboratory was able to provide conclusive evidence that this protein does not “crawl”, but “walks” along actin. Ha explains the basis of Fluorescence Resonance Energy Transfer (FRET) and how it can be used to measure conformational changes within a protein (intramolecular) or movement between two molecules (intermolecular).
In his second lecture, Ha shows the value of combining FRET with optical trapping. An optical trap uses focused light to “grab” a particle and “pull” allowing scientists to measure the force required to move a molecule. Ha’s lab used this combination of technologies to study the dynamics of nucleosome binding to DNA. His lab was able to show that nucleosome “unwrapping” from the DNA is asymmetrical, unidirectional, and sequence dependent. Combining FRET and optical trapping technologies with other tools, like whole genome sequencing, scientists can predict novel areas of high transcriptional activity.
In Part 3, Ha explains how his laboratory used optical tweezers (a variation on an optical trap) to study helicases and their regulation. Their data confirmed that the closed conformation of the 3’-5’ DNA helicase is the active form of the enzyme. They combined optical tweezers with FRET to further understand the role of the open conformation of the helicase. Ha encourages scientists to continue combining these single molecule technologies to better understand nature’s complex nanomachines.
Dr. Taekjip Ha is the Bloomberg Distinguished Professor of Biophysics and Biophysical Chemistry, Biophysics, and Biomedical Engineering at Johns Hopkins University. Ha has been a Howard Hughes Medical Institute Investigator since 2005. Today his laboratory continues with his passion of developing novel single molecule technologies to investigate complex biological systems.
After completing his Bachelor’s degree from the Seoul National University in South Korea, Ha continued his graduate education in physics at the University of California, Berkeley where he started to develop new single molecule spectroscopy technologies. Ha was briefly a postdoctoral fellow at Lawrence Berkeley National Laboratory, after which he joined Steven Chu’s laboratory at Stanford University. Ha joined the Department of Physics at the University of Illinois in 2000 and moved to Johns Hopkins University in 2015.
Ha was a pioneer in the use of FRET to study conformational changes at the single molecule level in enzymes. In recognition of his scientific contributions, he was elected as a member of the National Academy of Sciences and the American Academy of arts and Sciences in 2015.
Learn more about Dr. Ha here.
- Nico Stuurman iBioSeminar: Fluorescence Microscopy
- Xiaowei Zhuang iBioSeminar: Fluorescence Imaging at Nanoscale
- Carlos Bustamante iBioSeminar: Single Molecule Manipulation in Biochemistry
- Nico Stuurman iBioEducation: Introduction to Fluorescence Microscopy
- Philippe Bastiaens iBioEducation: Förster Resonance Energy Transfer (FRET) Microscopy
- Roger Tsien iBioEducation: Fluorescent Protein Indicators
- Carlos Bustamante iBioEducation: Optical Traps
Ha, T. Enderle , D.F. Ogletree, D.S. Chemla, P.R. Selvin, S. Weiss. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proceedings of the National Academy of Sciences of the United States of America 93, 6264-6268 (1996).
Yildiz, J.N. Forkey, S.A. McKinney, T. Ha, Y.E. Goldman, P.R. Selvin. Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization. Science 300, 2061-2065 (2003).
Joo, H. Balci, Y. Ishitsuka, C. Buranachai, T. Ha. Advances in Single-Molecule Fluorescence Methods for Molecular Biology. Annual Review of Biochemistry 77, 51-76 (2008).
C. Neuman, S. M. Block. Optical trapping. Review of Scientific Instruments 75, 2787-2809 (2004).
T. M. Ngo, Q. Zhang, R. Zhou, J. G. Yodh, T. Ha. Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility. Cell 160, 1135-1144 (2015).
Vafabakhsh, T. Ha, Extreme bendability of sub-100 bp long DNA revealed by single molecule cyclization. Science 337, 1097-1101 (2012).
M.R. Singleton, M.S. Dillingham, D. B. Wigley. Structure and Mechanism of Helicases and Nucleic Acid Translocases. Annual Review of Biochemistry 76, 23-50 (2007).
S. Arslan, R. Khafizov, C. D. Thomas, Y. R. Chemla, T. Ha, Engineering of a superhelicase through conformational control. Science 348, 344-347 (2015).