ArticleProceedings of the National Academy of Sciences of the United States of America2010
Compartmentalization by directional gene expression.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Autonomous biogenesis of all thirty proteins of the Escherichia coli translation machinery.Nature communications · 2025Article
- Toward Memory in a DNA Brush: Site-Specific Recombination Responsive to Polymer Density, Orientation, and Conformation.Journal of the American Chemical Society · 2023Article
- Noncanonical DNA Cleavage by BamHI Endonuclease in Laterally Confined DNA Monolayers Is a Step Function of DNA Density and Sequence.Molecules (Basel, Switzerland) · 2022Article
- Cell-Free Gene Expression from DNA Brushes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface.ACS synthetic biology · 2021Article
- Spatiotemporally programmable cascade hybridization of hairpin DNA in polymeric nanoframework for precise siRNA delivery.Nature communications · 2021Article
- Programming multi-protein assembly by gene-brush patterns and two-dimensional compartment geometry.Nature nanotechnology · 2020Article
- Functional Surface-immobilization of Genes Using Multistep Strand Displacement Lithography.Journal of visualized experiments : JoVE · 2018Article
- Crowding-induced cooperativity in DNA surface hybridization.Scientific reports · 2015Article
- Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Entropy-driven collective interactions in DNA brushes on a biochip.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Development of an artificial cell, from self-organization to computation and self-reproduction.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The coalescence of basic biochemical reactions into compartments is a major hallmark of a living cell. Using surface-bound DNA and a transcription reaction, we investigate the conditions for boundary-free compartmentalization. The DNA self-organizes into a dense and ordered phase with coding sequences aligned at well-defined distances and orientation relative to the surface, imposing directionality on transcription. Unique to the surface in comparison to dilute homogeneous DNA solution, the reaction slows down early, is inhibited with increased DNA density, is favorable for surface-oriented promoters, and is robust against DNA condensation. We interpret these results to suggest that macromolecules (RNA polymerase and RNA), but not solutes (ions and nucleotides), are partitioned between immobilized DNA and the reservoir. Without any physical barrier, a nonequilibrium directional DNA transaction forms macromolecular gradients that define a compartment, thus offering a boundary-free approach to the assembly of a synthetic cell.
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