Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments
Tethered particle motion (TPM) has become an important tool for single‐molecule studies of biomolecules; however, concerns remain that the method may alter the dynamics of the biophysical process under study. We investigate the effect of the attached microsphere on an illustrative biological example...
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| Veröffentlicht in: | Biopolymers 2011-02, Vol.95 (2), p.144-150 |
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| creator | Milstein, J. N. Chen, Y. F. Meiners, J.-C. |
| description | Tethered particle motion (TPM) has become an important tool for single‐molecule studies of biomolecules; however, concerns remain that the method may alter the dynamics of the biophysical process under study. We investigate the effect of the attached microsphere on an illustrative biological example: the formation and breakdown of protein‐mediated DNA loops in the lac repressor system. By comparing data from a conventional TPM experiment with 800 nm polystyrene beads and dark‐field TPM using 50 nm Au nanoparticles, we found that the lifetimes of the looped and unlooped states are only weakly modified, less than two‐fold, by the presence of the large bead. This is consistent with our expectation of weak excluded‐volume effects and hydrodynamic surface interactions from the cover glass and microsphere. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 144–150, 2011. |
| doi_str_mv | 10.1002/bip.21547 |
| format | Article |
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N.</creatorcontrib><creatorcontrib>Chen, Y. F.</creatorcontrib><creatorcontrib>Meiners, J.-C.</creatorcontrib><title>Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments</title><title>Biopolymers</title><addtitle>Biopolymers</addtitle><description>Tethered particle motion (TPM) has become an important tool for single‐molecule studies of biomolecules; however, concerns remain that the method may alter the dynamics of the biophysical process under study. We investigate the effect of the attached microsphere on an illustrative biological example: the formation and breakdown of protein‐mediated DNA loops in the lac repressor system. By comparing data from a conventional TPM experiment with 800 nm polystyrene beads and dark‐field TPM using 50 nm Au nanoparticles, we found that the lifetimes of the looped and unlooped states are only weakly modified, less than two‐fold, by the presence of the large bead. This is consistent with our expectation of weak excluded‐volume effects and hydrodynamic surface interactions from the cover glass and microsphere. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 144–150, 2011.</description><subject>Beads</subject><subject>Biomolecules</subject><subject>Biophysical Phenomena</subject><subject>Biopolymers</subject><subject>Deoxyribonucleic acid</subject><subject>DNA - chemistry</subject><subject>DNA looping</subject><subject>Dynamical systems</subject><subject>Dynamics</subject><subject>Hydrodynamics</subject><subject>In Vitro Techniques</subject><subject>Kinetics</subject><subject>Lac Repressors - chemistry</subject><subject>Metal Nanoparticles</subject><subject>Microspheres</subject><subject>Models, Molecular</subject><subject>Motion</subject><subject>Nucleic Acid Conformation</subject><subject>Particle Size</subject><subject>Proteins - chemistry</subject><subject>Reproduction</subject><subject>single molecule techniques</subject><subject>TPM</subject><issn>0006-3525</issn><issn>1097-0282</issn><issn>1097-0282</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU1v1DAQhi0EokvhwB9AvgGHtDN2_LHHftBSaVUQAiG4WE48AUM2SWOv-vHrMWzbG4jDaC7P-2g0L2PPEfYQQOw3cdoTqGrzgC0QlqYCYcVDtgAAXUkl1A57ktIPgLqWCI_ZjgBrhZJqwb4ckg88xRvi1HXU5sTHgU_zmCkO1ZpC9JkCPz4_4P04TnH4xuPAM-XvNFOoJj_n2PbE12OOJUhXE81xTUNOT9mjzveJnt3uXfbp5M3Ho7fV6t3p2dHBqmprLUylbROUImF8AKmC9ctO49KT9tqitooQu1Z1vqXGhjLQgLEdQtBqqTUouctebr3l6IsNpezWMbXU936gcZOctRZB1vo_SBQoNBhZyFf_JFEblNpaowv6eou285jSTJ2bygP8fO0Q3O92XGnH_WmnsC9utZumvPaevKujAPtb4DL2dP13kzs8e3-nrLaJmDJd3Sf8_NNpI41yn89PnfqAUh2vTtxX-QseNadi</recordid><startdate>201102</startdate><enddate>201102</enddate><creator>Milstein, J. N.</creator><creator>Chen, Y. F.</creator><creator>Meiners, J.-C.</creator><general>Wiley Subscription Services, Inc., A Wiley Company</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7U5</scope><scope>8FD</scope><scope>L7M</scope><scope>7X8</scope><scope>7QO</scope><scope>7TM</scope><scope>FR3</scope><scope>P64</scope></search><sort><creationdate>201102</creationdate><title>Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments</title><author>Milstein, J. N. ; Chen, Y. F. ; Meiners, J.-C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4627-68bd55e27ad035d8a9f619ae6a681685e11fc5faceb8deb80b078f10d65966053</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Beads</topic><topic>Biomolecules</topic><topic>Biophysical Phenomena</topic><topic>Biopolymers</topic><topic>Deoxyribonucleic acid</topic><topic>DNA - chemistry</topic><topic>DNA looping</topic><topic>Dynamical systems</topic><topic>Dynamics</topic><topic>Hydrodynamics</topic><topic>In Vitro Techniques</topic><topic>Kinetics</topic><topic>Lac Repressors - chemistry</topic><topic>Metal Nanoparticles</topic><topic>Microspheres</topic><topic>Models, Molecular</topic><topic>Motion</topic><topic>Nucleic Acid Conformation</topic><topic>Particle Size</topic><topic>Proteins - chemistry</topic><topic>Reproduction</topic><topic>single molecule techniques</topic><topic>TPM</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Milstein, J. 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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Beads Biomolecules Biophysical Phenomena Biopolymers Deoxyribonucleic acid DNA - chemistry DNA looping Dynamical systems Dynamics Hydrodynamics In Vitro Techniques Kinetics Lac Repressors - chemistry Metal Nanoparticles Microspheres Models, Molecular Motion Nucleic Acid Conformation Particle Size Proteins - chemistry Reproduction single molecule techniques TPM |
| title | Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments |
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