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DNA Scissors Device Used to Measure MutS Binding to DNA Mis-pairs
MutS is a DNA repair protein that recognizes unpaired and bulged bases. When it binds to DNA, it bends the double helix. We have developed a novel DNA-based nanomechanical device that measures the amount of work that a DNA-bending protein can do when it binds to the double helix. The device we repor...
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Published in: | Journal of the American Chemical Society 2010-03, Vol.132 (12), p.4352-4357 |
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container_title | Journal of the American Chemical Society |
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creator | Gu, Hongzhou Yang, Wei Seeman, Nadrian C |
description | MutS is a DNA repair protein that recognizes unpaired and bulged bases. When it binds to DNA, it bends the double helix. We have developed a novel DNA-based nanomechanical device that measures the amount of work that a DNA-bending protein can do when it binds to the double helix. The device we report here is a scissors-like device consisting of two double-crossover (DX) molecules connected to each other by a flexible Holliday junction. The two DX components are connected by a double helix that contains the binding site for MutS; when the binding site duplex is bent, the scissors contracts. The two DX molecules are also joined by sticky ends on an edge adjacent to the binding site; the sticky ends can be disrupted if the protein binds with sufficient free energy. Those sticky ends are flanked by a pair of dyes; when the sticky ends are disrupted, the dyes separate, and the fluorescence resonance energy transfer signal can monitor the disruption. The strength of the sticky ends is readily varied, so that the ability of the protein to disrupt them can be quantitated. We use this device to measure work in conjunction with a second device that measures the bending angle resulting from protein binding, so as to calibrate the system. Our data are in good agreement with previous measurements of MutS binding, indicating that this device is able to measure the strength of binding correctly. |
doi_str_mv | 10.1021/ja910188p |
format | article |
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When it binds to DNA, it bends the double helix. We have developed a novel DNA-based nanomechanical device that measures the amount of work that a DNA-bending protein can do when it binds to the double helix. The device we report here is a scissors-like device consisting of two double-crossover (DX) molecules connected to each other by a flexible Holliday junction. The two DX components are connected by a double helix that contains the binding site for MutS; when the binding site duplex is bent, the scissors contracts. The two DX molecules are also joined by sticky ends on an edge adjacent to the binding site; the sticky ends can be disrupted if the protein binds with sufficient free energy. Those sticky ends are flanked by a pair of dyes; when the sticky ends are disrupted, the dyes separate, and the fluorescence resonance energy transfer signal can monitor the disruption. The strength of the sticky ends is readily varied, so that the ability of the protein to disrupt them can be quantitated. We use this device to measure work in conjunction with a second device that measures the bending angle resulting from protein binding, so as to calibrate the system. Our data are in good agreement with previous measurements of MutS binding, indicating that this device is able to measure the strength of binding correctly.</description><identifier>ISSN: 0002-7863</identifier><identifier>EISSN: 1520-5126</identifier><identifier>DOI: 10.1021/ja910188p</identifier><identifier>PMID: 20205420</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Base Pair Mismatch ; Base Sequence ; DNA - chemistry ; Electrophoresis, Polyacrylamide Gel ; Hydrogen Bonding ; Intercalating Agents - chemistry ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein - chemistry ; Nanotechnology - instrumentation ; Protein Binding ; Thermodynamics</subject><ispartof>Journal of the American Chemical Society, 2010-03, Vol.132 (12), p.4352-4357</ispartof><rights>Copyright © 2010 American Chemical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a470t-7afab5a4d4d418dee49141564cea7d5fb5cf699d6f50e27f1476b3c903e2fa093</citedby><cites>FETCH-LOGICAL-a470t-7afab5a4d4d418dee49141564cea7d5fb5cf699d6f50e27f1476b3c903e2fa093</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20205420$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gu, Hongzhou</creatorcontrib><creatorcontrib>Yang, Wei</creatorcontrib><creatorcontrib>Seeman, Nadrian C</creatorcontrib><title>DNA Scissors Device Used to Measure MutS Binding to DNA Mis-pairs</title><title>Journal of the American Chemical Society</title><addtitle>J. Am. Chem. Soc</addtitle><description>MutS is a DNA repair protein that recognizes unpaired and bulged bases. When it binds to DNA, it bends the double helix. We have developed a novel DNA-based nanomechanical device that measures the amount of work that a DNA-bending protein can do when it binds to the double helix. The device we report here is a scissors-like device consisting of two double-crossover (DX) molecules connected to each other by a flexible Holliday junction. The two DX components are connected by a double helix that contains the binding site for MutS; when the binding site duplex is bent, the scissors contracts. The two DX molecules are also joined by sticky ends on an edge adjacent to the binding site; the sticky ends can be disrupted if the protein binds with sufficient free energy. Those sticky ends are flanked by a pair of dyes; when the sticky ends are disrupted, the dyes separate, and the fluorescence resonance energy transfer signal can monitor the disruption. The strength of the sticky ends is readily varied, so that the ability of the protein to disrupt them can be quantitated. We use this device to measure work in conjunction with a second device that measures the bending angle resulting from protein binding, so as to calibrate the system. Our data are in good agreement with previous measurements of MutS binding, indicating that this device is able to measure the strength of binding correctly.</description><subject>Base Pair Mismatch</subject><subject>Base Sequence</subject><subject>DNA - chemistry</subject><subject>Electrophoresis, Polyacrylamide Gel</subject><subject>Hydrogen Bonding</subject><subject>Intercalating Agents - chemistry</subject><subject>Molecular Sequence Data</subject><subject>MutS DNA Mismatch-Binding Protein - chemistry</subject><subject>Nanotechnology - instrumentation</subject><subject>Protein Binding</subject><subject>Thermodynamics</subject><issn>0002-7863</issn><issn>1520-5126</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><recordid>eNptkE1PwzAMhiMEYmNw4A-gXhDiUHDStGkvSGPjS9rgMHaO0tQdmbq2JO0k_j2dNiaQkA-W7cevrZeQcwo3FBi9XaqEAo3j-oD0acjADymLDkkfAJgv4ijokRPnll3JWUyPSY8Bg5Az6JPh-HXozbRxrrLOG-PaaPTmDjOvqbwpKtda9KZtM_PuTZmZcrHpb3amxvm1MtadkqNcFQ7PdnlA5o8P76Nnf_L29DIaTnzFBTS-ULlKQ8WzLmicIfKEchpGXKMSWZinoc6jJMmiPARkIqdcRGmgEwiQ5QqSYEDutrp1m64w01g2VhWytmal7JeslJF_J6X5kItqLVnMYwHQCVztBGz12aJr5Mo4jUWhSqxaJ0UQRAETCe3I6y2pbeWcxXx_hYLcOC73jnfsxe-39uSPxR1wuQWUdnJZtbbsXPpH6Bu9TIbe</recordid><startdate>20100331</startdate><enddate>20100331</enddate><creator>Gu, Hongzhou</creator><creator>Yang, Wei</creator><creator>Seeman, Nadrian C</creator><general>American Chemical Society</general><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>7X8</scope><scope>5PM</scope></search><sort><creationdate>20100331</creationdate><title>DNA Scissors Device Used to Measure MutS Binding to DNA Mis-pairs</title><author>Gu, Hongzhou ; Yang, Wei ; Seeman, Nadrian C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a470t-7afab5a4d4d418dee49141564cea7d5fb5cf699d6f50e27f1476b3c903e2fa093</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Base Pair Mismatch</topic><topic>Base Sequence</topic><topic>DNA - chemistry</topic><topic>Electrophoresis, Polyacrylamide Gel</topic><topic>Hydrogen Bonding</topic><topic>Intercalating Agents - chemistry</topic><topic>Molecular Sequence Data</topic><topic>MutS DNA Mismatch-Binding Protein - chemistry</topic><topic>Nanotechnology - instrumentation</topic><topic>Protein Binding</topic><topic>Thermodynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gu, Hongzhou</creatorcontrib><creatorcontrib>Yang, Wei</creatorcontrib><creatorcontrib>Seeman, Nadrian C</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of the American Chemical Society</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gu, Hongzhou</au><au>Yang, Wei</au><au>Seeman, Nadrian C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA Scissors Device Used to Measure MutS Binding to DNA Mis-pairs</atitle><jtitle>Journal of the American Chemical Society</jtitle><addtitle>J. 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Those sticky ends are flanked by a pair of dyes; when the sticky ends are disrupted, the dyes separate, and the fluorescence resonance energy transfer signal can monitor the disruption. The strength of the sticky ends is readily varied, so that the ability of the protein to disrupt them can be quantitated. We use this device to measure work in conjunction with a second device that measures the bending angle resulting from protein binding, so as to calibrate the system. Our data are in good agreement with previous measurements of MutS binding, indicating that this device is able to measure the strength of binding correctly.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>20205420</pmid><doi>10.1021/ja910188p</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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source | American Chemical Society:Jisc Collections:American Chemical Society Read & Publish Agreement 2022-2024 (Reading list) |
subjects | Base Pair Mismatch Base Sequence DNA - chemistry Electrophoresis, Polyacrylamide Gel Hydrogen Bonding Intercalating Agents - chemistry Molecular Sequence Data MutS DNA Mismatch-Binding Protein - chemistry Nanotechnology - instrumentation Protein Binding Thermodynamics |
title | DNA Scissors Device Used to Measure MutS Binding to DNA Mis-pairs |
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