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Onoa B, Díaz-Celis C, Cañari-Chumpitaz C, Lee A, Bustamante C. Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy. ACS CENTRAL SCIENCE 2024; 10:122-137. [PMID: 38292612 PMCID: PMC10823521 DOI: 10.1021/acscentsci.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/30/2023] [Accepted: 11/30/2023] [Indexed: 02/01/2024]
Abstract
During replication, expression, and repair of the eukaryotic genome, cellular machinery must access the DNA wrapped around histone proteins forming nucleosomes. These octameric protein·DNA complexes are modular, dynamic, and flexible and unwrap or disassemble either spontaneously or by the action of molecular motors. Thus, the mechanism of formation and regulation of subnucleosomal intermediates has gained attention genome-wide because it controls DNA accessibility. Here, we imaged nucleosomes and their more compacted structure with the linker histone H1 (chromatosomes) using high-speed atomic force microscopy to visualize simultaneously the changes in the DNA and the histone core during their disassembly when deposited on mica. Furthermore, we trained a neural network and developed an automatic algorithm to track molecular structural changes in real time. Our results show that nucleosome disassembly is a sequential process involving asymmetrical stepwise dimer ejection events. The presence of H1 restricts DNA unwrapping, significantly increases the nucleosomal lifetime, and affects the pathway in which heterodimer asymmetrical dissociation occurs. We observe that tetrasomes are resilient to disassembly and that the tetramer core (H3·H4)2 can diffuse along the nucleosome positioning sequence. Tetrasome mobility might be critical to the proper assembly of nucleosomes and can be relevant during nucleosomal transcription, as tetrasomes survive RNA polymerase passage. These findings are relevant to understanding nucleosome intrinsic dynamics and their modification by DNA-processing enzymes.
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Affiliation(s)
- Bibiana Onoa
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
| | - César Díaz-Celis
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
| | - Cristhian Cañari-Chumpitaz
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
| | - Antony Lee
- Laboratoire
Photonique Numérique et Nanosciences, LP2N UMR 5298, Université de Bordeaux, Institut d’Optique,
CNRS, F-33400 Talence, France
| | - Carlos Bustamante
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Kavli
Energy Nanoscience Institute, University
of California, Berkeley, California 94720, United States
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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