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Li JY, Liu F, Xu J, Kim YJ, Kwon OH, Xia B, Wang H, Granick S. The ergodicity question when imaging DNA conformation using liquid cell electron microscopy. Proc Natl Acad Sci U S A 2024; 121:e2314797121. [PMID: 38194452 PMCID: PMC10801859 DOI: 10.1073/pnas.2314797121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
Assessing the ergodicity of graphene liquid cell electron microscope measurements, we report that loop states of circular DNA interconvert reversibly and that loop numbers follow the Boltzmann distribution expected for this molecule in bulk solution, provided that the electron dose is low (80-keV electron energy and electron dose rate 1-20 e- Å-2 s-1). This imaging technique appears to act as a "slow motion" camera that reveals equilibrated distributions by imaging the time average of a few molecules without the need to image a spatial ensemble.
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Affiliation(s)
- Jia-Ye Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, National Biomedical Imaging Center, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing100871, China
| | - Fan Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, National Biomedical Imaging Center, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing100871, China
- Beijing NMR Center, School of Life Science, Peking University, Beijing100871, China
| | - Jing Xu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, National Biomedical Imaging Center, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing100871, China
- Beijing NMR Center, School of Life Science, Peking University, Beijing100871, China
| | - Ye-Jin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan44919, South Korea
| | - Oh-Hoon Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan44919, South Korea
| | - Bin Xia
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, National Biomedical Imaging Center, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing100871, China
- Beijing NMR Center, School of Life Science, Peking University, Beijing100871, China
| | - Huan Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, National Biomedical Imaging Center, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing100871, China
| | - Steve Granick
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan44919, South Korea
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan44919, South Korea
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
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