Inferring the in vivo looping properties of DNA Journal Article
| Authors: | Saiz, L.; Rubi, J. M.; Vilar, J. M. G. |
| Article Title: | Inferring the in vivo looping properties of DNA |
| Abstract: | The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of the loop and found that, in addition to the intrinsic periodicity of the DNA double helix, the free energy has an oscillatory component of about half the helical period. Moreover, the oscillations have such an amplitude that the effects of regulatory molecules become strongly dependent on their precise DNA positioning and yet easily tunable by their cooperative interactions. These unexpected results can confer to the physical properties of DNA a more prominent role at shaping the properties of gene regulation than previously thought. © 2005 by The National Academy of Sciences of the USA. |
| Keywords: | complex formation; gene expression; in vivo study; gene expression regulation; dna; escherichia coli; binding site; thermodynamics; regulation; molecular interaction; nucleic acid conformation; dna helix; dna binding; mathematical computing; dna determination; protein dna interaction; lac operon; oscillation; dna looping; computational modeling; periodicity |
| Journal Title: | Proceedings of the National Academy of Sciences of the United States of America |
| Volume: | 102 |
| Issue: | 49 |
| ISSN: | 0027-8424 |
| Publisher: | National Academy of Sciences |
| Date Published: | 2005-01-01 |
| Start Page: | 17642 |
| End Page: | 17645 |
| Language: | English |
| DOI: | 10.1073/pnas.0505693102 |
| PUBMED: | 16303869 |
| PROVIDER: | scopus |
| PMCID: | PMC1287912 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 32" - "Export Date: 24 October 2012" - "CODEN: PNASA" - "Source: Scopus" |
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13Saiz-Ardanaz -
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Gomez Vilar
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