Waves of DNA: Propagating excitations in extended nanoconfined polymers
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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American Physical Society
2016
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| Online Access: | http://hdl.handle.net/1721.1/105191 |
| _version_ | 1811081953903902720 |
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| author | de Haan, Hendrick W. Reisner, Walter W. Klotz, Alexander |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering de Haan, Hendrick W. Reisner, Walter W. Klotz, Alexander |
| author_sort | de Haan, Hendrick W. |
| collection | MIT |
| description | We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain occupies multiple cavities. Fluorescent video-microscopy data shows fluctuations in intensity between cavities, including waves of excess fluorescence that propagate across the cavity-straddling molecule, corresponding to propagating fluctuations of contour overdensity in the cavities. The transfer of DNA between neighboring pits is quantified by examining the correlation in intensity fluctuations between neighboring cavities. Correlations grow from an anticorrelated minimum to a correlated maximum before decaying, corresponding to a transfer of contour between neighboring cavities at a fixed transfer time scale. The observed dynamics can be modeled using Langevin dynamics simulations and a minimal lattice model of coupled diffusion. This study shows how confinement-based sculpting of the polymer equilibrium configuration, by renormalizing the physical system into a series of discrete cavity states, can lead to new types of dynamic collective phenomena. |
| first_indexed | 2024-09-23T11:55:03Z |
| format | Article |
| id | mit-1721.1/105191 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T11:55:03Z |
| publishDate | 2016 |
| publisher | American Physical Society |
| record_format | dspace |
| spelling | mit-1721.1/1051912022-10-01T06:57:43Z Waves of DNA: Propagating excitations in extended nanoconfined polymers de Haan, Hendrick W. Reisner, Walter W. Klotz, Alexander Massachusetts Institute of Technology. Department of Chemical Engineering Klotz, Alexander We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain occupies multiple cavities. Fluorescent video-microscopy data shows fluctuations in intensity between cavities, including waves of excess fluorescence that propagate across the cavity-straddling molecule, corresponding to propagating fluctuations of contour overdensity in the cavities. The transfer of DNA between neighboring pits is quantified by examining the correlation in intensity fluctuations between neighboring cavities. Correlations grow from an anticorrelated minimum to a correlated maximum before decaying, corresponding to a transfer of contour between neighboring cavities at a fixed transfer time scale. The observed dynamics can be modeled using Langevin dynamics simulations and a minimal lattice model of coupled diffusion. This study shows how confinement-based sculpting of the polymer equilibrium configuration, by renormalizing the physical system into a series of discrete cavity states, can lead to new types of dynamic collective phenomena. Natural Sciences and Engineering Research Council of Canada (Grant NSERC-DG, 386212-10) Canada Foundation for Innovation Natural Sciences and Engineering Research Council of Canada (Postdoctoral Fellowship) 2016-11-03T20:56:28Z 2016-11-03T20:56:28Z 2016-10 2016-06 2016-10-17T23:00:05Z Article http://purl.org/eprint/type/JournalArticle 2470-0045 2470-0053 http://hdl.handle.net/1721.1/105191 Klotz, Alexander R., Hendrick W. de Haan, and Walter W. Reisner. “Waves of DNA: Propagating Excitations in Extended Nanoconfined Polymers.” Physical Review E 94.4 (2016): n. pag. © 2016 American Physical Society en http://dx.doi.org/10.1103/PhysRevE.94.042603 Physical Review E Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. American Physical Society application/pdf American Physical Society American Physical Society |
| spellingShingle | de Haan, Hendrick W. Reisner, Walter W. Klotz, Alexander Waves of DNA: Propagating excitations in extended nanoconfined polymers |
| title | Waves of DNA: Propagating excitations in extended nanoconfined polymers |
| title_full | Waves of DNA: Propagating excitations in extended nanoconfined polymers |
| title_fullStr | Waves of DNA: Propagating excitations in extended nanoconfined polymers |
| title_full_unstemmed | Waves of DNA: Propagating excitations in extended nanoconfined polymers |
| title_short | Waves of DNA: Propagating excitations in extended nanoconfined polymers |
| title_sort | waves of dna propagating excitations in extended nanoconfined polymers |
| url | http://hdl.handle.net/1721.1/105191 |
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