Is DNA a Good Model Polymer?
The details surrounding the crossover from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy, and Kirkwood diffusivity fo...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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American Chemical Society (ACS)
2014
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| Online Access: | http://hdl.handle.net/1721.1/91257 |
| _version_ | 1826202022176620544 |
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| author | Tree, Douglas R. Muralidhar, Abhiram Doyle, Patrick S. Dorfman, Kevin D. |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Tree, Douglas R. Muralidhar, Abhiram Doyle, Patrick S. Dorfman, Kevin D. |
| author_sort | Tree, Douglas R. |
| collection | MIT |
| description | The details surrounding the crossover from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy, and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈1 000 000, base pairs depending on the choice of size metric) are required to reach flexible, swollen nondraining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48 500, base pairs) does not exhibit “ideal” scaling but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior. |
| first_indexed | 2024-09-23T12:00:39Z |
| format | Article |
| id | mit-1721.1/91257 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T12:00:39Z |
| publishDate | 2014 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/912572022-10-01T07:35:17Z Is DNA a Good Model Polymer? Tree, Douglas R. Muralidhar, Abhiram Doyle, Patrick S. Dorfman, Kevin D. Massachusetts Institute of Technology. Department of Chemical Engineering Doyle, Patrick S. The details surrounding the crossover from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy, and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈1 000 000, base pairs depending on the choice of size metric) are required to reach flexible, swollen nondraining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48 500, base pairs) does not exhibit “ideal” scaling but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior. National Science Foundation (U.S.) (Grant 0852235) National Institutes of Health (U.S.) (R01-HG005216) National Institutes of Health (U.S.) (R01-HG06851) 2014-11-03T14:08:51Z 2014-11-03T14:08:51Z 2013-10 2013-08 Article http://purl.org/eprint/type/JournalArticle 0024-9297 1520-5835 http://hdl.handle.net/1721.1/91257 Tree, Douglas R., Abhiram Muralidhar, Patrick S. Doyle, and Kevin D. Dorfman. “Is DNA a Good Model Polymer?” Macromolecules 46, no. 20 (October 22, 2013): 8369–8382. en_US http://dx.doi.org/10.1021/ma401507f Macromolecules 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. application/pdf American Chemical Society (ACS) MIT web domain |
| spellingShingle | Tree, Douglas R. Muralidhar, Abhiram Doyle, Patrick S. Dorfman, Kevin D. Is DNA a Good Model Polymer? |
| title | Is DNA a Good Model Polymer? |
| title_full | Is DNA a Good Model Polymer? |
| title_fullStr | Is DNA a Good Model Polymer? |
| title_full_unstemmed | Is DNA a Good Model Polymer? |
| title_short | Is DNA a Good Model Polymer? |
| title_sort | is dna a good model polymer |
| url | http://hdl.handle.net/1721.1/91257 |
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