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Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers
We report that trivalent cobalt hexammine cations decrease the persistence length, stretching modulus, helical density, and size of plectonemes formed under torque of DNA but increase those of RNA. Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of p...
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| Published in: | Physical review letters 2020-02, Vol.124 (5), p.058101-058101, Article 058101 |
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| Main Authors: | , , , , , , |
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| cited_by | cdi_FETCH-LOGICAL-c339t-6f190e8b99632d1c352c3fdbfe76a922a6d2409fe20621eb97d4bddd41d167d43 |
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| cites | cdi_FETCH-LOGICAL-c339t-6f190e8b99632d1c352c3fdbfe76a922a6d2409fe20621eb97d4bddd41d167d43 |
| container_end_page | 058101 |
| container_issue | 5 |
| container_start_page | 058101 |
| container_title | Physical review letters |
| container_volume | 124 |
| creator | Fu, Hang Zhang, Chen Qiang, Xiao-Wei Yang, Ya-Jun Dai, Liang Tan, Zhi-Jie Zhang, Xing-Hua |
| description | We report that trivalent cobalt hexammine cations decrease the persistence length, stretching modulus, helical density, and size of plectonemes formed under torque of DNA but increase those of RNA. Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of plectonemes while increasing the helical densities of both DNA and RNA. The experimental results are explained by different binding modes of the cations on DNA and RNA in our all-atom molecular dynamics simulations. The significant variations of the helical densities and structures of DNA and RNA duplexes induced by high-valent cations may affect interactions of the duplexes with proteins. |
| doi_str_mv | 10.1103/PhysRevLett.124.058101 |
| format | article |
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Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of plectonemes while increasing the helical densities of both DNA and RNA. The experimental results are explained by different binding modes of the cations on DNA and RNA in our all-atom molecular dynamics simulations. The significant variations of the helical densities and structures of DNA and RNA duplexes induced by high-valent cations may affect interactions of the duplexes with proteins.</description><identifier>ISSN: 0031-9007</identifier><identifier>EISSN: 1079-7114</identifier><identifier>DOI: 10.1103/PhysRevLett.124.058101</identifier><identifier>PMID: 32083903</identifier><language>eng</language><publisher>United States: American Physical Society</publisher><subject>Cations ; Cations - chemistry ; Cobalt - chemistry ; Deoxyribonucleic acid ; DNA ; DNA - chemistry ; Elasticity ; Magnesium ; Magnesium - chemistry ; Magnetics - instrumentation ; Magnetics - methods ; Models, Chemical ; Models, Molecular ; Molecular dynamics ; Molecular Dynamics Simulation ; Optical Tweezers ; Ribonucleic acid ; RNA ; RNA - chemistry ; RNA, Double-Stranded - chemistry</subject><ispartof>Physical review letters, 2020-02, Vol.124 (5), p.058101-058101, Article 058101</ispartof><rights>Copyright American Physical Society Feb 7, 2020</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c339t-6f190e8b99632d1c352c3fdbfe76a922a6d2409fe20621eb97d4bddd41d167d43</citedby><cites>FETCH-LOGICAL-c339t-6f190e8b99632d1c352c3fdbfe76a922a6d2409fe20621eb97d4bddd41d167d43</cites><orcidid>0000-0002-9487-191X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,777,781,27905,27906</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32083903$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fu, Hang</creatorcontrib><creatorcontrib>Zhang, Chen</creatorcontrib><creatorcontrib>Qiang, Xiao-Wei</creatorcontrib><creatorcontrib>Yang, Ya-Jun</creatorcontrib><creatorcontrib>Dai, Liang</creatorcontrib><creatorcontrib>Tan, Zhi-Jie</creatorcontrib><creatorcontrib>Zhang, Xing-Hua</creatorcontrib><title>Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers</title><title>Physical review letters</title><addtitle>Phys Rev Lett</addtitle><description>We report that trivalent cobalt hexammine cations decrease the persistence length, stretching modulus, helical density, and size of plectonemes formed under torque of DNA but increase those of RNA. Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of plectonemes while increasing the helical densities of both DNA and RNA. The experimental results are explained by different binding modes of the cations on DNA and RNA in our all-atom molecular dynamics simulations. The significant variations of the helical densities and structures of DNA and RNA duplexes induced by high-valent cations may affect interactions of the duplexes with proteins.</description><subject>Cations</subject><subject>Cations - chemistry</subject><subject>Cobalt - chemistry</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - chemistry</subject><subject>Elasticity</subject><subject>Magnesium</subject><subject>Magnesium - chemistry</subject><subject>Magnetics - instrumentation</subject><subject>Magnetics - methods</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Optical Tweezers</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - chemistry</subject><subject>RNA, Double-Stranded - chemistry</subject><issn>0031-9007</issn><issn>1079-7114</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNpdkU1P3DAQhq2qqGyBv4As9dJLlhk7OPFxtdBSafkQWrhGTjxms8omIXZot7--bndBFacZjZ731UgPY6cIU0SQZ3errb-nlwWFMEWRTuE8R8APbIKQ6SRDTD-yCYDERANkh-yz92sAQKHyT-xQCsilBjlhz7d93_k6EL90jqrgeef4Vf20Sh5NQ23gcxPqro3nlodVpBrjQ13VoaZ_6MXNjJvW8vs4L8a-oV_xHh-jmLa83PJr89RSTPDlT6LfNPhjduBM4-lkP4_Yw7fL5fwqWdx-_zGfLZJKSh0S5VAD5aXWSgqLlTwXlXS2dJQpo4UwyooUtCMBSiCVOrNpaa1N0aKKuzxiX3e9_dA9j-RDsal9RU1jWupGXwipBMTyTEX0yzt03Y1DG7-LVJZihqnOI6V2VDV03g_kin6oN2bYFgjFXynFf1KKKKXYSYnB0339WG7IvsVeLcg__1OKQg</recordid><startdate>20200207</startdate><enddate>20200207</enddate><creator>Fu, Hang</creator><creator>Zhang, Chen</creator><creator>Qiang, Xiao-Wei</creator><creator>Yang, Ya-Jun</creator><creator>Dai, Liang</creator><creator>Tan, Zhi-Jie</creator><creator>Zhang, Xing-Hua</creator><general>American Physical 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>7U5</scope><scope>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-9487-191X</orcidid></search><sort><creationdate>20200207</creationdate><title>Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers</title><author>Fu, Hang ; Zhang, Chen ; Qiang, Xiao-Wei ; Yang, Ya-Jun ; Dai, Liang ; Tan, Zhi-Jie ; Zhang, Xing-Hua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c339t-6f190e8b99632d1c352c3fdbfe76a922a6d2409fe20621eb97d4bddd41d167d43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Cations</topic><topic>Cations - chemistry</topic><topic>Cobalt - chemistry</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - chemistry</topic><topic>Elasticity</topic><topic>Magnesium</topic><topic>Magnesium - chemistry</topic><topic>Magnetics - instrumentation</topic><topic>Magnetics - methods</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Optical Tweezers</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - chemistry</topic><topic>RNA, Double-Stranded - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fu, Hang</creatorcontrib><creatorcontrib>Zhang, Chen</creatorcontrib><creatorcontrib>Qiang, Xiao-Wei</creatorcontrib><creatorcontrib>Yang, Ya-Jun</creatorcontrib><creatorcontrib>Dai, Liang</creatorcontrib><creatorcontrib>Tan, Zhi-Jie</creatorcontrib><creatorcontrib>Zhang, Xing-Hua</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>Physical review letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fu, Hang</au><au>Zhang, Chen</au><au>Qiang, Xiao-Wei</au><au>Yang, Ya-Jun</au><au>Dai, Liang</au><au>Tan, Zhi-Jie</au><au>Zhang, Xing-Hua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers</atitle><jtitle>Physical review letters</jtitle><addtitle>Phys Rev Lett</addtitle><date>2020-02-07</date><risdate>2020</risdate><volume>124</volume><issue>5</issue><spage>058101</spage><epage>058101</epage><pages>058101-058101</pages><artnum>058101</artnum><issn>0031-9007</issn><eissn>1079-7114</eissn><abstract>We report that trivalent cobalt hexammine cations decrease the persistence length, stretching modulus, helical density, and size of plectonemes formed under torque of DNA but increase those of RNA. Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of plectonemes while increasing the helical densities of both DNA and RNA. The experimental results are explained by different binding modes of the cations on DNA and RNA in our all-atom molecular dynamics simulations. The significant variations of the helical densities and structures of DNA and RNA duplexes induced by high-valent cations may affect interactions of the duplexes with proteins.</abstract><cop>United States</cop><pub>American Physical Society</pub><pmid>32083903</pmid><doi>10.1103/PhysRevLett.124.058101</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-9487-191X</orcidid></addata></record> |
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| identifier | ISSN: 0031-9007 |
| ispartof | Physical review letters, 2020-02, Vol.124 (5), p.058101-058101, Article 058101 |
| issn | 0031-9007 1079-7114 |
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| source | American Physical Society:Jisc Collections:APS Read and Publish 2023-2025 (reading list) |
| subjects | Cations Cations - chemistry Cobalt - chemistry Deoxyribonucleic acid DNA DNA - chemistry Elasticity Magnesium Magnesium - chemistry Magnetics - instrumentation Magnetics - methods Models, Chemical Models, Molecular Molecular dynamics Molecular Dynamics Simulation Optical Tweezers Ribonucleic acid RNA RNA - chemistry RNA, Double-Stranded - chemistry |
| title | Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers |
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