Compaction of Plasmid DNA by Macromolecular Crowding

Amar Nath Gupta; Johan R. C. van der Maarel

doi:10.1021/acs.macromol.6b02742

Compaction of Plasmid DNA by Macromolecular Crowding

Macromolecules ◽

10.1021/acs.macromol.6b02742 ◽

2017 ◽

Vol 50 (4) ◽

pp. 1666-1671 ◽

Cited By ~ 6

Author(s):

Amar Nath Gupta ◽

Johan R. C. van der Maarel

Keyword(s):

Plasmid Dna ◽

Macromolecular Crowding

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Plasmid DNA Undergoes Two Compaction Regimes under Macromolecular Crowding

ACS Macro Letters ◽

10.1021/acsmacrolett.1c00593 ◽

2022 ◽

pp. 186-192

Author(s):

Suparna Khatun ◽

Anurag Singh ◽

Kumari Shikha ◽

Agneyo Ganguly ◽

Amar Nath Gupta

Keyword(s):

Plasmid Dna ◽

Macromolecular Crowding

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Synergistic interactions between confinement and macromolecular crowding spatially order transcription and translation in cell-free expression

10.1101/445544 ◽

2018 ◽

Author(s):

S. Elizabeth Norred ◽

Rosemary M. Dabbs ◽

Gaurav Chauhan ◽

Patrick M. Caveney ◽

C. Patrick Collier ◽

...

Keyword(s):

Plasmid Dna ◽

Spatial Organization ◽

Macromolecular Crowding ◽

Self Organization ◽

Free Expression ◽

Control Of Gene Expression ◽

Free System ◽

Synergistic Interactions ◽

Transcriptional Dynamics ◽

In Cells

ABSTRACTSynergistic interactions between macromolecular crowding and confinement spatially organize transcription and translation in cells. Yet, reproducing such spatial ordering in cell-free expression platforms has proven to be elusive. Here we report crowding- and confinement-driven spatial self-organization of cell-free expression that mimics expression behavior within and around the nucleoid of prokaryotes. These experiments use Ficoll-70 to approximate cellular macromolecular crowding conditions within cell-size lipid vesicles. Intriguingly, there was an abrupt change in transcriptional dynamics when crowding reached physiologically relevant levels. Imaging experiments revealed that this change in transcriptional dynamics was coincident with localization of plasmid DNA and mRNA at the vesicle wall. Computer simulations demonstrated that crowding leads to an entropically induced attraction between plasmid DNA and the wall, causing localization of DNA near the wall at sufficiently high crowding levels. The experiments demonstrate cell-like spatial organization of translation, where translational activity is controlled by chromosomally-templated positioning of mRNA. This cell-free system provides a flexible experimental platform to probe the underlying mechanisms of self-organization of membrane-less structures in cells and the spatial control of gene expression.

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