Amplified stretch of bottlebrush-coated DNA in nanofluidic channels
The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA...
| Main Authors: | , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Oxford University Press
2013
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| Online Access: | http://hdl.handle.net/1721.1/81342 |
| _version_ | 1826212163997401088 |
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| author | Doyle, Patrick S. Zhang, Ce Hernandez-Garcia, Armando Jiang, Kai Gong, Zongying Guttula, Durgarao Ng, Siow Yee Malar, Piravi P. van Kan, Jeroen A. Dai, Liang de Vries, Renko van der Maarel, Johan R. C. |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Doyle, Patrick S. Zhang, Ce Hernandez-Garcia, Armando Jiang, Kai Gong, Zongying Guttula, Durgarao Ng, Siow Yee Malar, Piravi P. van Kan, Jeroen A. Dai, Liang de Vries, Renko van der Maarel, Johan R. C. |
| author_sort | Doyle, Patrick S. |
| collection | MIT |
| description | The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica. |
| first_indexed | 2024-09-23T15:17:22Z |
| format | Article |
| id | mit-1721.1/81342 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:17:22Z |
| publishDate | 2013 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/813422022-10-02T01:57:28Z Amplified stretch of bottlebrush-coated DNA in nanofluidic channels Doyle, Patrick S. Zhang, Ce Hernandez-Garcia, Armando Jiang, Kai Gong, Zongying Guttula, Durgarao Ng, Siow Yee Malar, Piravi P. van Kan, Jeroen A. Dai, Liang de Vries, Renko van der Maarel, Johan R. C. Massachusetts Institute of Technology. Department of Chemical Engineering Doyle, Patrick S. The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica. Singapore-MIT Alliance for Research and Technology National Science Foundation (U.S.) 2013-10-07T15:09:30Z 2013-10-07T15:09:30Z 2013-09 2013-08 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/81342 Zhang, C., A. Hernandez-Garcia, K. Jiang, Z. Gong, D. Guttula, S. Y. Ng, P. P. Malar, et al. “Amplified stretch of bottlebrush-coated DNA in nanofluidic channels.” Nucleic Acids Research (September 3, 2013). en_US http://dx.doi.org/10.1093/nar/gkt783 Nucleic Acids Research http://creativecommons.org/licenses/by-nc/3.0/ application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Doyle, Patrick S. Zhang, Ce Hernandez-Garcia, Armando Jiang, Kai Gong, Zongying Guttula, Durgarao Ng, Siow Yee Malar, Piravi P. van Kan, Jeroen A. Dai, Liang de Vries, Renko van der Maarel, Johan R. C. Amplified stretch of bottlebrush-coated DNA in nanofluidic channels |
| title | Amplified stretch of bottlebrush-coated DNA in nanofluidic channels |
| title_full | Amplified stretch of bottlebrush-coated DNA in nanofluidic channels |
| title_fullStr | Amplified stretch of bottlebrush-coated DNA in nanofluidic channels |
| title_full_unstemmed | Amplified stretch of bottlebrush-coated DNA in nanofluidic channels |
| title_short | Amplified stretch of bottlebrush-coated DNA in nanofluidic channels |
| title_sort | amplified stretch of bottlebrush coated dna in nanofluidic channels |
| url | http://hdl.handle.net/1721.1/81342 |
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