The thermodynamics and kinetics of a nucleotide base pair
The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The o...
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| Veröffentlicht in: | The Journal of chemical physics 2016-03, Vol.144 (11), p.115101-115101 |
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| container_title | The Journal of chemical physics |
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| creator | Wang, Yujie Gong, Sha Wang, Zhen Zhang, Wenbing |
| description | The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian. |
| doi_str_mv | 10.1063/1.4944067 |
| format | Article |
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The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.</description><identifier>ISSN: 0021-9606</identifier><identifier>EISSN: 1089-7690</identifier><identifier>DOI: 10.1063/1.4944067</identifier><identifier>PMID: 27004898</identifier><identifier>CODEN: JCPSA6</identifier><language>eng</language><publisher>United States: American Institute of Physics</publisher><subject>Base Pairing ; Computer simulation ; Diffusion barriers ; Disruption ; Enthalpy ; EXPERIMENTAL DATA ; FREE ENERGY ; Hydrogen bonding ; INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY ; KINETICS ; Melt temperature ; MELTING POINTS ; Molecular dynamics ; MOLECULAR DYNAMICS METHOD ; Molecular Dynamics Simulation ; Parameters ; Physics ; Ribonucleic acid ; RNA ; RNA - chemistry ; RNA Folding ; Temperature ; TEMPERATURE DEPENDENCE ; THERMODYNAMICS ; Time dependence ; Transition Temperature</subject><ispartof>The Journal of chemical physics, 2016-03, Vol.144 (11), p.115101-115101</ispartof><rights>AIP Publishing LLC</rights><rights>2016 AIP Publishing LLC.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c411t-47be4e7e2bb235302e78da286bdfd70a996cf580d2b54606a6144c6843bacf783</citedby><cites>FETCH-LOGICAL-c411t-47be4e7e2bb235302e78da286bdfd70a996cf580d2b54606a6144c6843bacf783</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://pubs.aip.org/jcp/article-lookup/doi/10.1063/1.4944067$$EHTML$$P50$$Gscitation$$H</linktohtml><link.rule.ids>230,314,780,784,794,885,4512,27924,27925,76384</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27004898$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/22660827$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Yujie</creatorcontrib><creatorcontrib>Gong, Sha</creatorcontrib><creatorcontrib>Wang, Zhen</creatorcontrib><creatorcontrib>Zhang, Wenbing</creatorcontrib><title>The thermodynamics and kinetics of a nucleotide base pair</title><title>The Journal of chemical physics</title><addtitle>J Chem Phys</addtitle><description>The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.</description><subject>Base Pairing</subject><subject>Computer simulation</subject><subject>Diffusion barriers</subject><subject>Disruption</subject><subject>Enthalpy</subject><subject>EXPERIMENTAL DATA</subject><subject>FREE ENERGY</subject><subject>Hydrogen bonding</subject><subject>INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY</subject><subject>KINETICS</subject><subject>Melt temperature</subject><subject>MELTING POINTS</subject><subject>Molecular dynamics</subject><subject>MOLECULAR DYNAMICS METHOD</subject><subject>Molecular Dynamics Simulation</subject><subject>Parameters</subject><subject>Physics</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - chemistry</subject><subject>RNA Folding</subject><subject>Temperature</subject><subject>TEMPERATURE DEPENDENCE</subject><subject>THERMODYNAMICS</subject><subject>Time dependence</subject><subject>Transition Temperature</subject><issn>0021-9606</issn><issn>1089-7690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp90F1LHDEUBuAglbq1vfAPlAFvbGHsSSabj0uRfgiCN3odMskZNrqTbJNMwX_vLLuuF0KvDoGHN-e8hJxRuKQguh_0kmvOQcgjsqCgdCuFhg9kAcBoqwWIE_KplEcAoJLxj-SESQCutFoQfb_Cpq4wj8k_RzsGVxobffMUItbtIw2NbeLk1phq8Nj0tmCzsSF_JseDXRf8sp-n5OHXz_vrP-3t3e-b66vb1nFKa8tljxwlsr5n3bIDhlJ5y5To_eAlWK2FG5YKPOuXfF7VCsq5E4p3vXWDVN0pOd_lplKDKS5UdCuXYkRXDWNCgGJyVhc7tcnp74SlmjEUh-u1jZimYqiUS8E0o_AWeKCPacpxvsEwyqjq5Bw5q2875XIqJeNgNjmMNj8bCmbbuqFm3_psv-4Tp35Ef5CvNc_g-w5s17c1pHgw_1J-SzIbP_wPv__6BXtXlVA</recordid><startdate>20160321</startdate><enddate>20160321</enddate><creator>Wang, Yujie</creator><creator>Gong, Sha</creator><creator>Wang, Zhen</creator><creator>Zhang, Wenbing</creator><general>American Institute of Physics</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>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><scope>OTOTI</scope></search><sort><creationdate>20160321</creationdate><title>The thermodynamics and kinetics of a nucleotide base pair</title><author>Wang, Yujie ; Gong, Sha ; Wang, Zhen ; Zhang, Wenbing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c411t-47be4e7e2bb235302e78da286bdfd70a996cf580d2b54606a6144c6843bacf783</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Base Pairing</topic><topic>Computer simulation</topic><topic>Diffusion barriers</topic><topic>Disruption</topic><topic>Enthalpy</topic><topic>EXPERIMENTAL DATA</topic><topic>FREE ENERGY</topic><topic>Hydrogen bonding</topic><topic>INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY</topic><topic>KINETICS</topic><topic>Melt temperature</topic><topic>MELTING POINTS</topic><topic>Molecular dynamics</topic><topic>MOLECULAR DYNAMICS METHOD</topic><topic>Molecular Dynamics Simulation</topic><topic>Parameters</topic><topic>Physics</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - chemistry</topic><topic>RNA Folding</topic><topic>Temperature</topic><topic>TEMPERATURE DEPENDENCE</topic><topic>THERMODYNAMICS</topic><topic>Time dependence</topic><topic>Transition Temperature</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Yujie</creatorcontrib><creatorcontrib>Gong, Sha</creatorcontrib><creatorcontrib>Wang, Zhen</creatorcontrib><creatorcontrib>Zhang, Wenbing</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><jtitle>The Journal of chemical physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Yujie</au><au>Gong, Sha</au><au>Wang, Zhen</au><au>Zhang, Wenbing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The thermodynamics and kinetics of a nucleotide base pair</atitle><jtitle>The Journal of chemical physics</jtitle><addtitle>J Chem Phys</addtitle><date>2016-03-21</date><risdate>2016</risdate><volume>144</volume><issue>11</issue><spage>115101</spage><epage>115101</epage><pages>115101-115101</pages><issn>0021-9606</issn><eissn>1089-7690</eissn><coden>JCPSA6</coden><abstract>The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.</abstract><cop>United States</cop><pub>American Institute of Physics</pub><pmid>27004898</pmid><doi>10.1063/1.4944067</doi><tpages>7</tpages></addata></record> |
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| ispartof | The Journal of chemical physics, 2016-03, Vol.144 (11), p.115101-115101 |
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| source | MEDLINE; AIP Journals Complete; Alma/SFX Local Collection |
| subjects | Base Pairing Computer simulation Diffusion barriers Disruption Enthalpy EXPERIMENTAL DATA FREE ENERGY Hydrogen bonding INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY KINETICS Melt temperature MELTING POINTS Molecular dynamics MOLECULAR DYNAMICS METHOD Molecular Dynamics Simulation Parameters Physics Ribonucleic acid RNA RNA - chemistry RNA Folding Temperature TEMPERATURE DEPENDENCE THERMODYNAMICS Time dependence Transition Temperature |
| title | The thermodynamics and kinetics of a nucleotide base pair |
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