Effect of Nanochannel Geometry on DNA Structure in the Presence of Macromolecular Crowding Agent
We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics s...
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| Veröffentlicht in: | Nano letters 2011-11, Vol.11 (11), p.5047-5053 |
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| container_title | Nano letters |
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| creator | Jones, Jeremy J van der Maarel, Johan R. C Doyle, Patrick S |
| description | We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and allow us to develop a deeper understanding of the key physics at play in these systems. It is proposed that the occupancy of free volume next to the channel wall by crowders causes an effective reduction in confining dimensions of the channel that initially swells DNA in nanoconfinement. |
| doi_str_mv | 10.1021/nl203114f |
| format | Article |
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It is proposed that the occupancy of free volume next to the channel wall by crowders causes an effective reduction in confining dimensions of the channel that initially swells DNA in nanoconfinement.</description><identifier>ISSN: 1530-6984</identifier><identifier>EISSN: 1530-6992</identifier><identifier>DOI: 10.1021/nl203114f</identifier><identifier>PMID: 21988280</identifier><language>eng</language><publisher>Washington, DC: American Chemical Society</publisher><subject>Biological and medical sciences ; Biotechnology ; Channels ; Computer Simulation ; Condensed matter: structure, mechanical and thermal properties ; Confinement ; Confining ; Cross-disciplinary physics: materials science; rheology ; Crowding ; Deoxyribonucleic acid ; DNA - chemistry ; DNA - ultrastructure ; Dynamical systems ; Dynamics ; Exact sciences and technology ; Fundamental and applied biological sciences. Psychology ; Macromolecular Substances - chemistry ; Materials science ; Materials Testing ; Methods. 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C</creatorcontrib><creatorcontrib>Doyle, Patrick S</creatorcontrib><title>Effect of Nanochannel Geometry on DNA Structure in the Presence of Macromolecular Crowding Agent</title><title>Nano letters</title><addtitle>Nano Lett</addtitle><description>We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and allow us to develop a deeper understanding of the key physics at play in these systems. It is proposed that the occupancy of free volume next to the channel wall by crowders causes an effective reduction in confining dimensions of the channel that initially swells DNA in nanoconfinement.</description><subject>Biological and medical sciences</subject><subject>Biotechnology</subject><subject>Channels</subject><subject>Computer Simulation</subject><subject>Condensed matter: structure, mechanical and thermal properties</subject><subject>Confinement</subject><subject>Confining</subject><subject>Cross-disciplinary physics: materials science; rheology</subject><subject>Crowding</subject><subject>Deoxyribonucleic acid</subject><subject>DNA - chemistry</subject><subject>DNA - ultrastructure</subject><subject>Dynamical systems</subject><subject>Dynamics</subject><subject>Exact sciences and technology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Macromolecular Substances - chemistry</subject><subject>Materials science</subject><subject>Materials Testing</subject><subject>Methods. Procedures. Technologies</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Molecular Conformation</subject><subject>Nanoscale materials and structures: fabrication and characterization</subject><subject>Nanostructure</subject><subject>Nanostructures - chemistry</subject><subject>Nanostructures - ultrastructure</subject><subject>Nanotubes</subject><subject>Others</subject><subject>Particle Size</subject><subject>Physics</subject><subject>Solid surfaces and solid-solid interfaces</subject><subject>Surfaces and interfaces; thin films and whiskers (structure and nonelectronic properties)</subject><subject>Various methods and equipments</subject><subject>Walls</subject><issn>1530-6984</issn><issn>1530-6992</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0clKBDEQBuAgivvBF5BcRD2MVpZechzGFdxAPbeZpKIt3Ykm3Yhvb4vjeBE9VQ5fquD_CdlicMCAs0PfcBCMSbdAVlkmYJQrxRfn71KukLWUngFAiQyWyQpnqix5Cavk4dg5NB0Njl5pH8yT9h4beoqhxS6-0-Dp0dWY3naxN10fkdaedk9IbyIm9AY_P15qE0MbGjR9oyOdxPBma_9Ix4_ouw2y5HSTcHM218n9yfHd5Gx0cX16PhlfjLQs8m7kMuOkcYCWm6nILWeAzuopl9ygLlQmIddOGQkKpxkqbXjOrJDC2qywZSHWye7X3pcYXntMXdXWyWDTaI-hT5UaEpKSlXyQe39KVuQchuRk9j_NhCxFzgsY6P4XHbJIKaKrXmLd6vheMag-W6rmLQ12e7a2n7Zo5_K7lgHszIBORjcuam_q9ONkIRkU6sdpk6rn0Ec_RPzLwQ93faT7</recordid><startdate>20111109</startdate><enddate>20111109</enddate><creator>Jones, Jeremy J</creator><creator>van der Maarel, Johan R. 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C ; Doyle, Patrick S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a476t-f5cf4cf0ed2cb36d210efdab242cea795406af9c409eb5e9ac261d343dd57d873</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Biological and medical sciences</topic><topic>Biotechnology</topic><topic>Channels</topic><topic>Computer Simulation</topic><topic>Condensed matter: structure, mechanical and thermal properties</topic><topic>Confinement</topic><topic>Confining</topic><topic>Cross-disciplinary physics: materials science; rheology</topic><topic>Crowding</topic><topic>Deoxyribonucleic acid</topic><topic>DNA - chemistry</topic><topic>DNA - ultrastructure</topic><topic>Dynamical systems</topic><topic>Dynamics</topic><topic>Exact sciences and technology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Macromolecular Substances - chemistry</topic><topic>Materials science</topic><topic>Materials Testing</topic><topic>Methods. Procedures. Technologies</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Molecular Conformation</topic><topic>Nanoscale materials and structures: fabrication and characterization</topic><topic>Nanostructure</topic><topic>Nanostructures - chemistry</topic><topic>Nanostructures - ultrastructure</topic><topic>Nanotubes</topic><topic>Others</topic><topic>Particle Size</topic><topic>Physics</topic><topic>Solid surfaces and solid-solid interfaces</topic><topic>Surfaces and interfaces; thin films and whiskers (structure and nonelectronic properties)</topic><topic>Various methods and equipments</topic><topic>Walls</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jones, Jeremy J</creatorcontrib><creatorcontrib>van der Maarel, Johan R. 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C</au><au>Doyle, Patrick S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Effect of Nanochannel Geometry on DNA Structure in the Presence of Macromolecular Crowding Agent</atitle><jtitle>Nano letters</jtitle><addtitle>Nano Lett</addtitle><date>2011-11-09</date><risdate>2011</risdate><volume>11</volume><issue>11</issue><spage>5047</spage><epage>5053</epage><pages>5047-5053</pages><issn>1530-6984</issn><eissn>1530-6992</eissn><abstract>We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and allow us to develop a deeper understanding of the key physics at play in these systems. 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| subjects | Biological and medical sciences Biotechnology Channels Computer Simulation Condensed matter: structure, mechanical and thermal properties Confinement Confining Cross-disciplinary physics: materials science rheology Crowding Deoxyribonucleic acid DNA - chemistry DNA - ultrastructure Dynamical systems Dynamics Exact sciences and technology Fundamental and applied biological sciences. Psychology Macromolecular Substances - chemistry Materials science Materials Testing Methods. Procedures. Technologies Models, Chemical Models, Molecular Molecular Conformation Nanoscale materials and structures: fabrication and characterization Nanostructure Nanostructures - chemistry Nanostructures - ultrastructure Nanotubes Others Particle Size Physics Solid surfaces and solid-solid interfaces Surfaces and interfaces thin films and whiskers (structure and nonelectronic properties) Various methods and equipments Walls |
| title | Effect of Nanochannel Geometry on DNA Structure in the Presence of Macromolecular Crowding Agent |
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