2018Lei DNABennet: Difference between revisions

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(Created page with "== Citation == Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032 == Abstract == It has been proposed that the intrinsic property of nucleosom...")
 
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== Citation ==
== Citation ==
Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032
3D Structural Dynamics of DNA Origami Mechanisms and Machines Using Individual-Particle Electron Tomography, Dongsheng Lei, Alex Marras, Jianfang Liu, Chaomin Huang, Lifeng Zhou, Carlos Castro, Hai-Jun Su, Gang Ren, Nature Communications, (2018), 9:592, DOI: 10.1038/s41467-018-03018-0


== Abstract ==
== Abstract ==
It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.
Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. Here we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~ 6–14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.


== Keywords ==
== Keywords ==
Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, nucleosome array, phase transition, aggregation
Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, DNA origami Bennett linkages, structural flexibility


== Paper links ==
== Paper links ==
https://pubmed.ncbi.nlm.nih.gov/35907400/
https://www.nature.com/articles/s41467-018-03018-0


== Related video ==
== Related video ==
https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/530f75ed-d615-46af-bdf6-255b34acf813/mmc2.mp4
https://www.youtube.com/watch?v=2Cjaxv9-btU
https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/d2ae50b4-cafd-40f1-95c6-355322774031/mmc3.mp4
https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/bc9def6c-803f-4938-83d7-c4fd72610fc8/mmc4.mp4


== Comments ==
== Comments ==

Latest revision as of 09:31, 12 November 2024

Citation

3D Structural Dynamics of DNA Origami Mechanisms and Machines Using Individual-Particle Electron Tomography, Dongsheng Lei, Alex Marras, Jianfang Liu, Chaomin Huang, Lifeng Zhou, Carlos Castro, Hai-Jun Su, Gang Ren, Nature Communications, (2018), 9:592, DOI: 10.1038/s41467-018-03018-0

Abstract

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. Here we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~ 6–14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.

Keywords

Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, DNA origami Bennett linkages, structural flexibility

Paper links

https://www.nature.com/articles/s41467-018-03018-0

Related video

https://www.youtube.com/watch?v=2Cjaxv9-btU

Comments

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