Oligonucleotide chip assay for quantification of gamma ray-induced single strand breaks.
Identifieur interne : 002040 ( PubMed/Corpus ); précédent : 002039; suivant : 002041Oligonucleotide chip assay for quantification of gamma ray-induced single strand breaks.
Auteurs : Hyeon A. Ki ; Min Jung Kim ; Sukdeb Pal ; Joon Myong SongSource :
- Journal of pharmaceutical and biomedical analysis [ 0731-7085 ] ; 2009.
English descriptors
- KwdEn :
- Biotin (metabolism), Biotinylation, Calibration, DNA Damage (radiation effects), DNA, Single-Stranded (analysis), DNA, Single-Stranded (genetics), DNA, Single-Stranded (radiation effects), Dose-Response Relationship, Radiation, Fluorescein (metabolism), Fluorescent Dyes (metabolism), Gamma Rays, Oligonucleotide Array Sequence Analysis (methods), Oligonucleotides (genetics), Silicon (chemistry), Surface Properties, Time Factors.
- MESH :
- chemical , analysis : DNA, Single-Stranded.
- chemical , chemistry : Silicon.
- chemical , genetics : DNA, Single-Stranded, Oligonucleotides.
- chemical , metabolism : Biotin, Fluorescein, Fluorescent Dyes.
- methods : Oligonucleotide Array Sequence Analysis.
- radiation effects : DNA Damage, DNA, Single-Stranded.
- Biotinylation, Calibration, Dose-Response Relationship, Radiation, Gamma Rays, Surface Properties, Time Factors.
Abstract
An oligonucleotide chip assay was designed for direct quantification of single strand breaks (SSBs) induced by gamma-ray irradiation. The oligonucleotides used were 20-mers, which were short enough to produce only a single strand break within a single oligonucleotide. The two ends of the oligonucleotides were labeled with fluorescein and biotin, respectively. The biotinylated ends of the oligonucleotides were immobilized on a silicon wafer chip treated with (3-aminopropyl)triethoxysilane (APTES), glutaraldehyde, and avidin. The DNA fragments cleaved by gamma-ray irradiation were detected by a laser-induced fluorescence (LIF) detection system. The gamma-ray-induced SSBs were quantified using a calibration curve (fluorescence intensity versus gamma-ray dose) without the need for complicated mathematical calculation based on gel-based separation. The experimentally determined gamma-ray-induced SSBs yield was almost equal to the theoretical value derived from gel electrophoresis of plasmid DNAs and DNA surface coverage.
DOI: 10.1016/j.jpba.2008.11.031
PubMed: 19128912
Links to Exploration step
pubmed:19128912Le document en format XML
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Ki</name><affiliation><nlm:affiliation>Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, Seoul, South Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Min Jung" sort="Kim, Min Jung" uniqKey="Kim M" first="Min Jung" last="Kim">Min Jung Kim</name></author><author><name sortKey="Pal, Sukdeb" sort="Pal, Sukdeb" uniqKey="Pal S" first="Sukdeb" last="Pal">Sukdeb Pal</name></author><author><name sortKey="Song, Joon Myong" sort="Song, Joon Myong" uniqKey="Song J" first="Joon Myong" last="Song">Joon Myong Song</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19128912</idno><idno type="pmid">19128912</idno><idno type="doi">10.1016/j.jpba.2008.11.031</idno><idno type="wicri:Area/PubMed/Corpus">002040</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002040</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Oligonucleotide chip assay for quantification of gamma ray-induced single strand breaks.</title><author><name sortKey="Ki, Hyeon A" sort="Ki, Hyeon A" uniqKey="Ki H" first="Hyeon A" last="Ki">Hyeon A. Ki</name><affiliation><nlm:affiliation>Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, Seoul, South Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Min Jung" sort="Kim, Min Jung" uniqKey="Kim M" first="Min Jung" last="Kim">Min Jung Kim</name></author><author><name sortKey="Pal, Sukdeb" sort="Pal, Sukdeb" uniqKey="Pal S" first="Sukdeb" last="Pal">Sukdeb Pal</name></author><author><name sortKey="Song, Joon Myong" sort="Song, Joon Myong" uniqKey="Song J" first="Joon Myong" last="Song">Joon Myong Song</name></author></analytic><series><title level="j">Journal of pharmaceutical and biomedical analysis</title><idno type="ISSN">0731-7085</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biotin (metabolism)</term><term>Biotinylation</term><term>Calibration</term><term>DNA Damage (radiation effects)</term><term>DNA, Single-Stranded (analysis)</term><term>DNA, Single-Stranded (genetics)</term><term>DNA, Single-Stranded (radiation effects)</term><term>Dose-Response Relationship, Radiation</term><term>Fluorescein (metabolism)</term><term>Fluorescent Dyes (metabolism)</term><term>Gamma Rays</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotides (genetics)</term><term>Silicon (chemistry)</term><term>Surface Properties</term><term>Time Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Single-Stranded</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Silicon</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Single-Stranded</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Biotin</term><term>Fluorescein</term><term>Fluorescent Dyes</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="radiation effects" xml:lang="en"><term>DNA Damage</term><term>DNA, Single-Stranded</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biotinylation</term><term>Calibration</term><term>Dose-Response Relationship, Radiation</term><term>Gamma Rays</term><term>Surface Properties</term><term>Time Factors</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">An oligonucleotide chip assay was designed for direct quantification of single strand breaks (SSBs) induced by gamma-ray irradiation. The oligonucleotides used were 20-mers, which were short enough to produce only a single strand break within a single oligonucleotide. The two ends of the oligonucleotides were labeled with fluorescein and biotin, respectively. The biotinylated ends of the oligonucleotides were immobilized on a silicon wafer chip treated with (3-aminopropyl)triethoxysilane (APTES), glutaraldehyde, and avidin. The DNA fragments cleaved by gamma-ray irradiation were detected by a laser-induced fluorescence (LIF) detection system. The gamma-ray-induced SSBs were quantified using a calibration curve (fluorescence intensity versus gamma-ray dose) without the need for complicated mathematical calculation based on gel-based separation. The experimentally determined gamma-ray-induced SSBs yield was almost equal to the theoretical value derived from gel electrophoresis of plasmid DNAs and DNA surface coverage.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19128912</PMID><DateCompleted><Year>2009</Year><Month>04</Month><Day>30</Day></DateCompleted><DateRevised><Year>2015</Year><Month>11</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0731-7085</ISSN><JournalIssue CitedMedium="Print"><Volume>49</Volume><Issue>2</Issue><PubDate><Year>2009</Year><Month>Feb</Month><Day>20</Day></PubDate></JournalIssue><Title>Journal of pharmaceutical and biomedical analysis</Title><ISOAbbreviation>J Pharm Biomed Anal</ISOAbbreviation></Journal><ArticleTitle>Oligonucleotide chip assay for quantification of gamma ray-induced single strand breaks.</ArticleTitle><Pagination><MedlinePgn>562-6</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jpba.2008.11.031</ELocationID><Abstract><AbstractText>An oligonucleotide chip assay was designed for direct quantification of single strand breaks (SSBs) induced by gamma-ray irradiation. The oligonucleotides used were 20-mers, which were short enough to produce only a single strand break within a single oligonucleotide. The two ends of the oligonucleotides were labeled with fluorescein and biotin, respectively. The biotinylated ends of the oligonucleotides were immobilized on a silicon wafer chip treated with (3-aminopropyl)triethoxysilane (APTES), glutaraldehyde, and avidin. The DNA fragments cleaved by gamma-ray irradiation were detected by a laser-induced fluorescence (LIF) detection system. The gamma-ray-induced SSBs were quantified using a calibration curve (fluorescence intensity versus gamma-ray dose) without the need for complicated mathematical calculation based on gel-based separation. The experimentally determined gamma-ray-induced SSBs yield was almost equal to the theoretical value derived from gel electrophoresis of plasmid DNAs and DNA surface coverage.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ki</LastName><ForeName>Hyeon A</ForeName><Initials>HA</Initials><AffiliationInfo><Affiliation>Research Institute of Pharmaceutical Sciences and College of Pharmacy, Seoul National University, Seoul, South Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Min Jung</ForeName><Initials>MJ</Initials></Author><Author ValidYN="Y"><LastName>Pal</LastName><ForeName>Sukdeb</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Joon Myong</ForeName><Initials>JM</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>11</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Pharm Biomed Anal</MedlineTA><NlmUniqueID>8309336</NlmUniqueID><ISSNLinking>0731-7085</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004277">DNA, Single-Stranded</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005456">Fluorescent Dyes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>6SO6U10H04</RegistryNumber><NameOfSubstance UI="D001710">Biotin</NameOfSubstance></Chemical><Chemical><RegistryNumber>TPY09G7XIR</RegistryNumber><NameOfSubstance UI="D019793">Fluorescein</NameOfSubstance></Chemical><Chemical><RegistryNumber>Z4152N8IUI</RegistryNumber><NameOfSubstance UI="D012825">Silicon</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001710" MajorTopicYN="N">Biotin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019921" MajorTopicYN="N">Biotinylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002138" MajorTopicYN="N">Calibration</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004249" MajorTopicYN="N">DNA Damage</DescriptorName><QualifierName UI="Q000528" MajorTopicYN="Y">radiation effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004277" MajorTopicYN="N">DNA, Single-Stranded</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000528" MajorTopicYN="Y">radiation effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004307" MajorTopicYN="N">Dose-Response Relationship, Radiation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019793" MajorTopicYN="N">Fluorescein</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005456" MajorTopicYN="N">Fluorescent Dyes</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005720" MajorTopicYN="Y">Gamma Rays</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009841" 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