Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum...
Gespeichert in:
| Veröffentlicht in: | The journal of physical chemistry letters 2016-11, Vol.7 (21), p.4391-4397 |
|---|---|
| Hauptverfasser: | , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 4397 |
|---|---|
| container_issue | 21 |
| container_start_page | 4391 |
| container_title | The journal of physical chemistry letters |
| container_volume | 7 |
| creator | Mendieta-Moreno, Jesús I Trabada, Daniel G Mendieta, Jesús Lewis, James P Gómez-Puertas, Paulino Ortega, José |
| description | The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems. |
| doi_str_mv | 10.1021/acs.jpclett.6b02168 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_osti_</sourceid><recordid>TN_cdi_osti_scitechconnect_1534702</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1835519240</sourcerecordid><originalsourceid>FETCH-LOGICAL-a372t-78d626c5f2482fe502a4cd2d5908c5cbdd3c63cee45ff100231cd7e31ed4ed7b3</originalsourceid><addsrcrecordid>eNp9kU1vEzEQhi0EoiXwC5CQxYlLEn_srjfcqrSlSE35KmfLO54lrnbt1PYe8jf4xbhN-DhxmtH4fWY88xLymrMFZ4IvDaTF3Q4GzHnRdKXStE_IKV9V7Vzxtn76T35CXqR0x1izYq16Tk6EUk0rGTslP79MxudppBuErfEO0nITBoRpMPFvjV5GRHrhMf7Y043ZJWq8pTfBG-tMZ7ID-s2Nhcku-ET7EKmhn7chB9ji6MAM9CsaeHilztPzm7P3dL2HIXRTNh7p7XY_uhLP3YjxJXnWmyHhq2Ocke-XF7frq_n1pw8f12fXcyOVyHPV2kY0UPeiakWPNROmAitsXXaEGjprJTQSEKu67zljQnKwCiVHW6FVnZyRt4e-IWWnE7hc1oXgPULWvJaVKsyMvDuIdjHcT5iyHl0CHIby7TAlzVtZ13wlKlak8iCFGFKK2OtddKOJe82ZfnBMF8f00TF9dKxQb44Dpm5E-4f5bVERLA-CRzpM0Zej_LflL011puI</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1835519240</pqid></control><display><type>article</type><title>Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer</title><source>American Chemical Society (ACS) Journals</source><creator>Mendieta-Moreno, Jesús I ; Trabada, Daniel G ; Mendieta, Jesús ; Lewis, James P ; Gómez-Puertas, Paulino ; Ortega, José</creator><creatorcontrib>Mendieta-Moreno, Jesús I ; Trabada, Daniel G ; Mendieta, Jesús ; Lewis, James P ; Gómez-Puertas, Paulino ; Ortega, José ; West Virginia Univ., Morgantown, WV (United States)</creatorcontrib><description>The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.</description><identifier>ISSN: 1948-7185</identifier><identifier>EISSN: 1948-7185</identifier><identifier>DOI: 10.1021/acs.jpclett.6b02168</identifier><identifier>PMID: 27768300</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Chemistry ; Materials Science ; Physics ; Science & Technology - Other Topics</subject><ispartof>The journal of physical chemistry letters, 2016-11, Vol.7 (21), p.4391-4397</ispartof><rights>Copyright © 2016 American Chemical Society</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a372t-78d626c5f2482fe502a4cd2d5908c5cbdd3c63cee45ff100231cd7e31ed4ed7b3</citedby><cites>FETCH-LOGICAL-a372t-78d626c5f2482fe502a4cd2d5908c5cbdd3c63cee45ff100231cd7e31ed4ed7b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.6b02168$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.jpclett.6b02168$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>230,314,776,780,881,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27768300$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1534702$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Mendieta-Moreno, Jesús I</creatorcontrib><creatorcontrib>Trabada, Daniel G</creatorcontrib><creatorcontrib>Mendieta, Jesús</creatorcontrib><creatorcontrib>Lewis, James P</creatorcontrib><creatorcontrib>Gómez-Puertas, Paulino</creatorcontrib><creatorcontrib>Ortega, José</creatorcontrib><creatorcontrib>West Virginia Univ., Morgantown, WV (United States)</creatorcontrib><title>Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer</title><title>The journal of physical chemistry letters</title><addtitle>J. Phys. Chem. Lett</addtitle><description>The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.</description><subject>Chemistry</subject><subject>Materials Science</subject><subject>Physics</subject><subject>Science & Technology - Other Topics</subject><issn>1948-7185</issn><issn>1948-7185</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><recordid>eNp9kU1vEzEQhi0EoiXwC5CQxYlLEn_srjfcqrSlSE35KmfLO54lrnbt1PYe8jf4xbhN-DhxmtH4fWY88xLymrMFZ4IvDaTF3Q4GzHnRdKXStE_IKV9V7Vzxtn76T35CXqR0x1izYq16Tk6EUk0rGTslP79MxudppBuErfEO0nITBoRpMPFvjV5GRHrhMf7Y043ZJWq8pTfBG-tMZ7ID-s2Nhcku-ET7EKmhn7chB9ji6MAM9CsaeHilztPzm7P3dL2HIXRTNh7p7XY_uhLP3YjxJXnWmyHhq2Ocke-XF7frq_n1pw8f12fXcyOVyHPV2kY0UPeiakWPNROmAitsXXaEGjprJTQSEKu67zljQnKwCiVHW6FVnZyRt4e-IWWnE7hc1oXgPULWvJaVKsyMvDuIdjHcT5iyHl0CHIby7TAlzVtZ13wlKlak8iCFGFKK2OtddKOJe82ZfnBMF8f00TF9dKxQb44Dpm5E-4f5bVERLA-CRzpM0Zej_LflL011puI</recordid><startdate>20161103</startdate><enddate>20161103</enddate><creator>Mendieta-Moreno, Jesús I</creator><creator>Trabada, Daniel G</creator><creator>Mendieta, Jesús</creator><creator>Lewis, James P</creator><creator>Gómez-Puertas, Paulino</creator><creator>Ortega, José</creator><general>American Chemical Society</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>OTOTI</scope></search><sort><creationdate>20161103</creationdate><title>Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer</title><author>Mendieta-Moreno, Jesús I ; Trabada, Daniel G ; Mendieta, Jesús ; Lewis, James P ; Gómez-Puertas, Paulino ; Ortega, José</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a372t-78d626c5f2482fe502a4cd2d5908c5cbdd3c63cee45ff100231cd7e31ed4ed7b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Chemistry</topic><topic>Materials Science</topic><topic>Physics</topic><topic>Science & Technology - Other Topics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mendieta-Moreno, Jesús I</creatorcontrib><creatorcontrib>Trabada, Daniel G</creatorcontrib><creatorcontrib>Mendieta, Jesús</creatorcontrib><creatorcontrib>Lewis, James P</creatorcontrib><creatorcontrib>Gómez-Puertas, Paulino</creatorcontrib><creatorcontrib>Ortega, José</creatorcontrib><creatorcontrib>West Virginia Univ., Morgantown, WV (United States)</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><jtitle>The journal of physical chemistry letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mendieta-Moreno, Jesús I</au><au>Trabada, Daniel G</au><au>Mendieta, Jesús</au><au>Lewis, James P</au><au>Gómez-Puertas, Paulino</au><au>Ortega, José</au><aucorp>West Virginia Univ., Morgantown, WV (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer</atitle><jtitle>The journal of physical chemistry letters</jtitle><addtitle>J. Phys. Chem. Lett</addtitle><date>2016-11-03</date><risdate>2016</risdate><volume>7</volume><issue>21</issue><spage>4391</spage><epage>4397</epage><pages>4391-4397</pages><issn>1948-7185</issn><eissn>1948-7185</eissn><abstract>The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>27768300</pmid><doi>10.1021/acs.jpclett.6b02168</doi><tpages>7</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1948-7185 |
| ispartof | The journal of physical chemistry letters, 2016-11, Vol.7 (21), p.4391-4397 |
| issn | 1948-7185 1948-7185 |
| language | eng |
| recordid | cdi_osti_scitechconnect_1534702 |
| source | American Chemical Society (ACS) Journals |
| subjects | Chemistry Materials Science Physics Science & Technology - Other Topics |
| title | Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-01T04%3A46%3A00IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_osti_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Quantum%20Mechanics/Molecular%20Mechanics%20Free%20Energy%20Maps%20and%20Nonadiabatic%20Simulations%20for%20a%20Photochemical%20Reaction%20in%20DNA:%20Cyclobutane%20Thymine%20Dimer&rft.jtitle=The%20journal%20of%20physical%20chemistry%20letters&rft.au=Mendieta-Moreno,%20Jesu%CC%81s%20I&rft.aucorp=West%20Virginia%20Univ.,%20Morgantown,%20WV%20(United%20States)&rft.date=2016-11-03&rft.volume=7&rft.issue=21&rft.spage=4391&rft.epage=4397&rft.pages=4391-4397&rft.issn=1948-7185&rft.eissn=1948-7185&rft_id=info:doi/10.1021/acs.jpclett.6b02168&rft_dat=%3Cproquest_osti_%3E1835519240%3C/proquest_osti_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1835519240&rft_id=info:pmid/27768300&rfr_iscdi=true |