Synthetic gene brushes: a structure–function relationship
Abstract We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end‐immobilized linear double‐stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relax...
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| Format: | Article |
| Language: | English |
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Springer Nature
2008-04-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2008.20 |
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| author | Amnon Buxboim Shirley S Daube Roy Bar‐Ziv |
| author_facet | Amnon Buxboim Shirley S Daube Roy Bar‐Ziv |
| author_sort | Amnon Buxboim |
| collection | DOAJ |
| description | Abstract We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end‐immobilized linear double‐stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relaxed conformations, down to 30 nm, where steric repulsion at dense packing forces stretching out. We investigated the gene‐to‐protein relationship of firefly luciferase under the T7/E.Coli‐extract expression system, as well as transcription‐only reactions with T7 RNA polymerase, and found both systems to be highly sensitive to brush density, conformation, and orientation. A ‘structure–function’ picture emerges in which extension of genes induced by moderate packing exposes coding sequences and improves their interaction with the transcription/translation machinery. However, tighter packing impairs the penetration of the machinery into the brush. The response of expression to two‐dimensional gene crowding at the nanoscale identifies gene brushes as basic controllable units en route to multicomponent synthetic systems. In turn, these brushes could deepen our understanding of biochemical reactions taking place under confinement and molecular crowding in living cells. |
| format | Article |
| id | doaj-art-9a1d233f3a2145c4935bba0730d57fb2 |
| institution | OA Journals |
| issn | 1744-4292 |
| language | English |
| publishDate | 2008-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-9a1d233f3a2145c4935bba0730d57fb22025-08-20T02:18:27ZengSpringer NatureMolecular Systems Biology1744-42922008-04-01411810.1038/msb.2008.20Synthetic gene brushes: a structure–function relationshipAmnon Buxboim0Shirley S Daube1Roy Bar‐Ziv2Department of Materials and Interfaces, The Weizmann Institute of ScienceChemical Research Support Unit, The Weizmann Institute of ScienceDepartment of Materials and Interfaces, The Weizmann Institute of ScienceAbstract We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end‐immobilized linear double‐stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relaxed conformations, down to 30 nm, where steric repulsion at dense packing forces stretching out. We investigated the gene‐to‐protein relationship of firefly luciferase under the T7/E.Coli‐extract expression system, as well as transcription‐only reactions with T7 RNA polymerase, and found both systems to be highly sensitive to brush density, conformation, and orientation. A ‘structure–function’ picture emerges in which extension of genes induced by moderate packing exposes coding sequences and improves their interaction with the transcription/translation machinery. However, tighter packing impairs the penetration of the machinery into the brush. The response of expression to two‐dimensional gene crowding at the nanoscale identifies gene brushes as basic controllable units en route to multicomponent synthetic systems. In turn, these brushes could deepen our understanding of biochemical reactions taking place under confinement and molecular crowding in living cells.https://doi.org/10.1038/msb.2008.20in vitro synthetic biologynano‐biotechnologycell‐free gene expressionmolecular crowdingbiochip |
| spellingShingle | Amnon Buxboim Shirley S Daube Roy Bar‐Ziv Synthetic gene brushes: a structure–function relationship Molecular Systems Biology in vitro synthetic biology nano‐biotechnology cell‐free gene expression molecular crowding biochip |
| title | Synthetic gene brushes: a structure–function relationship |
| title_full | Synthetic gene brushes: a structure–function relationship |
| title_fullStr | Synthetic gene brushes: a structure–function relationship |
| title_full_unstemmed | Synthetic gene brushes: a structure–function relationship |
| title_short | Synthetic gene brushes: a structure–function relationship |
| title_sort | synthetic gene brushes a structure function relationship |
| topic | in vitro synthetic biology nano‐biotechnology cell‐free gene expression molecular crowding biochip |
| url | https://doi.org/10.1038/msb.2008.20 |
| work_keys_str_mv | AT amnonbuxboim syntheticgenebrushesastructurefunctionrelationship AT shirleysdaube syntheticgenebrushesastructurefunctionrelationship AT roybarziv syntheticgenebrushesastructurefunctionrelationship |