Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning
Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation...
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| Format: | Article |
| Language: | en_US |
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American Institute of Physics
2011
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| Online Access: | http://hdl.handle.net/1721.1/60669 |
| _version_ | 1811082278154010624 |
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| author | Doyle, Patrick S. Trahan, Daniel Warner |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Doyle, Patrick S. Trahan, Daniel Warner |
| author_sort | Doyle, Patrick S. |
| collection | MIT |
| description | Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation model to study the deformation of DNA chains in a microcontraction preceded by an array of cylindrical obstacles. We compare our data to the experimental results and find good qualitative, and even quantitative, agreement concerning the behavior of the chains in the array; however, the simulations overpredict the mean stretch of the chains as they leave the contraction. We examine the amount of stretch gained between leaving the array and reaching the end of the contraction and speculate that the differences seen are caused by nonlinear electrokinetic effects that become important in the contraction due to a combination of field gradients and high field strengths. |
| first_indexed | 2024-09-23T12:00:34Z |
| format | Article |
| id | mit-1721.1/60669 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T12:00:34Z |
| publishDate | 2011 |
| publisher | American Institute of Physics |
| record_format | dspace |
| spelling | mit-1721.1/606692022-10-01T07:35:09Z Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning Doyle, Patrick S. Trahan, Daniel Warner Massachusetts Institute of Technology. Department of Chemical Engineering Doyle, Patrick S. Doyle, Patrick S. Trahan, Daniel Warner Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation model to study the deformation of DNA chains in a microcontraction preceded by an array of cylindrical obstacles. We compare our data to the experimental results and find good qualitative, and even quantitative, agreement concerning the behavior of the chains in the array; however, the simulations overpredict the mean stretch of the chains as they leave the contraction. We examine the amount of stretch gained between leaving the array and reaching the end of the contraction and speculate that the differences seen are caused by nonlinear electrokinetic effects that become important in the contraction due to a combination of field gradients and high field strengths. Singapore-MIT Alliance National Institute of Biomedical Imaging and Bioengineering (U.S.) (Award No. T32EB006348) 2011-01-19T19:40:50Z 2011-01-19T19:40:50Z 2009-01 2008-09 Article http://purl.org/eprint/type/JournalArticle 1932-1058 http://hdl.handle.net/1721.1/60669 Trahan, Daniel W., and Patrick S. Doyle. “Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning.” Biomicrofluidics 3.1 (2009): 012803-14. © 2009 American Institute of Physics. en_US http://dx.doi.org/10.1063/1.3055275 Biomicrofluidics 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 Institute of Physics MIT web domain |
| spellingShingle | Doyle, Patrick S. Trahan, Daniel Warner Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning |
| title | Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning |
| title_full | Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning |
| title_fullStr | Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning |
| title_full_unstemmed | Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning |
| title_short | Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning |
| title_sort | simulation of electrophoretic stretching of dna in a microcontraction using an obstacle array for conformational preconditioning |
| url | http://hdl.handle.net/1721.1/60669 |
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