Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics
Ultraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new a...
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| creator | Goto, Noriko Bazar, Gyorgy Kovacs, Zoltan Kunisada, Makoto Morita, Hiroyuki Kizaki, Seiichiro Sugiyama, Hiroshi Tsenkova, Roumiana Nishigori, Chikako |
| description | Ultraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn TTs; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400–1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn TTs increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn TTs in isolated DNA aqueous solutions upon UVC exposure. |
| doi_str_mv | 10.1038/srep11808 |
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Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn TTs; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400–1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn TTs increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn TTs in isolated DNA aqueous solutions upon UVC exposure.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep11808</identifier><identifier>PMID: 26133899</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/1647/527/1989 ; 631/67/1813 ; Cyclobutane pyrimidine dimers ; Cyclobutane thymine dimers ; Deoxyribonucleic acid ; DNA ; DNA - radiation effects ; DNA damage ; DNA Damage - radiation effects ; Genetic testing ; Humanities and Social Sciences ; I.R. radiation ; Infrared spectroscopy ; multidisciplinary ; Multivariate analysis ; Mutagenesis - radiation effects ; Mutation - radiation effects ; Pyrimidine Dimers - isolation & purification ; Pyrimidine Dimers - radiation effects ; Science ; Spectroscopy, Near-Infrared ; Spectrum analysis ; Thymine ; Ultraviolet radiation ; Ultraviolet Rays</subject><ispartof>Scientific reports, 2015-07, Vol.5 (1), p.11808-11808, Article 11808</ispartof><rights>The Author(s) 2015</rights><rights>Copyright Nature Publishing Group Jul 2015</rights><rights>Copyright © 2015, Macmillan Publishers Limited 2015 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c632t-98a181b861b4f2133bf3d91cddf59181e4cc0828d61fcac4116a17a235af3ab03</citedby><cites>FETCH-LOGICAL-c632t-98a181b861b4f2133bf3d91cddf59181e4cc0828d61fcac4116a17a235af3ab03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488872/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488872/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26133899$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Goto, Noriko</creatorcontrib><creatorcontrib>Bazar, Gyorgy</creatorcontrib><creatorcontrib>Kovacs, Zoltan</creatorcontrib><creatorcontrib>Kunisada, Makoto</creatorcontrib><creatorcontrib>Morita, Hiroyuki</creatorcontrib><creatorcontrib>Kizaki, Seiichiro</creatorcontrib><creatorcontrib>Sugiyama, Hiroshi</creatorcontrib><creatorcontrib>Tsenkova, Roumiana</creatorcontrib><creatorcontrib>Nishigori, Chikako</creatorcontrib><title>Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Ultraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn TTs; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400–1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn TTs increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn TTs in isolated DNA aqueous solutions upon UVC exposure.</description><subject>631/1647/527/1989</subject><subject>631/67/1813</subject><subject>Cyclobutane pyrimidine dimers</subject><subject>Cyclobutane thymine dimers</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - radiation effects</subject><subject>DNA damage</subject><subject>DNA Damage - radiation effects</subject><subject>Genetic testing</subject><subject>Humanities and Social Sciences</subject><subject>I.R. radiation</subject><subject>Infrared spectroscopy</subject><subject>multidisciplinary</subject><subject>Multivariate analysis</subject><subject>Mutagenesis - radiation effects</subject><subject>Mutation - radiation effects</subject><subject>Pyrimidine Dimers - isolation & purification</subject><subject>Pyrimidine Dimers - radiation effects</subject><subject>Science</subject><subject>Spectroscopy, Near-Infrared</subject><subject>Spectrum analysis</subject><subject>Thymine</subject><subject>Ultraviolet radiation</subject><subject>Ultraviolet Rays</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNplkUtr3TAQhUVoSUKaRf5AMXTTFNx6JNlX2hRK0hcEukmyFbIeiYItOZJd8L_vhJtcblttZmA-js7MIeQMmo_QMPGpZDcBiEYckGPa8LamjNJXe_0ROS3locHXUslBHpIj2gFjQspj4i7d7MwcUqySr25u6xDtYpytzGqG1C-zjq6a1hzGYAO2Nowul6pfq-h0RtpnnREvE6rkVEya1kpHW-nHRU_3aU5jMOUNee31UNzpcz0hN9--Xl_8qK9-ff958eWqNh2jcy2FBgG96KDnnqLF3jMrwVjrW4kTx41pBBW2A2-04QCdho2mrNWe6b5hJ-TzVnda-tFZ4-Kc9aAmtK_zqpIO6u9JDPfqLv1WnAshNhQF3j8L5PS4uDKrMRTjhgHPkJaioJNcdu1Gtoi--wd9SEuOuJ4CPC3HLcSTo_MtZfA4GJXfmYFGPeWndvkh-3bf_Y58SQuBD1ug4Cjeubz35X9qfwAX_qah</recordid><startdate>20150702</startdate><enddate>20150702</enddate><creator>Goto, Noriko</creator><creator>Bazar, Gyorgy</creator><creator>Kovacs, Zoltan</creator><creator>Kunisada, Makoto</creator><creator>Morita, Hiroyuki</creator><creator>Kizaki, Seiichiro</creator><creator>Sugiyama, Hiroshi</creator><creator>Tsenkova, Roumiana</creator><creator>Nishigori, Chikako</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150702</creationdate><title>Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics</title><author>Goto, Noriko ; Bazar, Gyorgy ; Kovacs, Zoltan ; Kunisada, Makoto ; Morita, Hiroyuki ; Kizaki, Seiichiro ; Sugiyama, Hiroshi ; Tsenkova, Roumiana ; Nishigori, Chikako</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c632t-98a181b861b4f2133bf3d91cddf59181e4cc0828d61fcac4116a17a235af3ab03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>631/1647/527/1989</topic><topic>631/67/1813</topic><topic>Cyclobutane pyrimidine dimers</topic><topic>Cyclobutane thymine dimers</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - radiation effects</topic><topic>DNA damage</topic><topic>DNA Damage - radiation effects</topic><topic>Genetic testing</topic><topic>Humanities and Social Sciences</topic><topic>I.R. radiation</topic><topic>Infrared spectroscopy</topic><topic>multidisciplinary</topic><topic>Multivariate analysis</topic><topic>Mutagenesis - radiation effects</topic><topic>Mutation - radiation effects</topic><topic>Pyrimidine Dimers - isolation & purification</topic><topic>Pyrimidine Dimers - radiation effects</topic><topic>Science</topic><topic>Spectroscopy, Near-Infrared</topic><topic>Spectrum analysis</topic><topic>Thymine</topic><topic>Ultraviolet radiation</topic><topic>Ultraviolet Rays</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Goto, Noriko</creatorcontrib><creatorcontrib>Bazar, Gyorgy</creatorcontrib><creatorcontrib>Kovacs, Zoltan</creatorcontrib><creatorcontrib>Kunisada, Makoto</creatorcontrib><creatorcontrib>Morita, Hiroyuki</creatorcontrib><creatorcontrib>Kizaki, Seiichiro</creatorcontrib><creatorcontrib>Sugiyama, Hiroshi</creatorcontrib><creatorcontrib>Tsenkova, Roumiana</creatorcontrib><creatorcontrib>Nishigori, Chikako</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection (ProQuest)</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Goto, Noriko</au><au>Bazar, Gyorgy</au><au>Kovacs, Zoltan</au><au>Kunisada, Makoto</au><au>Morita, Hiroyuki</au><au>Kizaki, Seiichiro</au><au>Sugiyama, Hiroshi</au><au>Tsenkova, Roumiana</au><au>Nishigori, Chikako</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-07-02</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>11808</spage><epage>11808</epage><pages>11808-11808</pages><artnum>11808</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Ultraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn TTs; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400–1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn TTs increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn TTs in isolated DNA aqueous solutions upon UVC exposure.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26133899</pmid><doi>10.1038/srep11808</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 631/1647/527/1989 631/67/1813 Cyclobutane pyrimidine dimers Cyclobutane thymine dimers Deoxyribonucleic acid DNA DNA - radiation effects DNA damage DNA Damage - radiation effects Genetic testing Humanities and Social Sciences I.R. radiation Infrared spectroscopy multidisciplinary Multivariate analysis Mutagenesis - radiation effects Mutation - radiation effects Pyrimidine Dimers - isolation & purification Pyrimidine Dimers - radiation effects Science Spectroscopy, Near-Infrared Spectrum analysis Thymine Ultraviolet radiation Ultraviolet Rays |
| title | Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics |
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