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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<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>
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<author><name sortKey="Kim, Min Jung" sort="Kim, Min Jung" uniqKey="Kim M" first="Min Jung" last="Kim">Min Jung Kim</name>
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<author><name sortKey="Pal, Sukdeb" sort="Pal, Sukdeb" uniqKey="Pal S" first="Sukdeb" last="Pal">Sukdeb Pal</name>
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<author><name sortKey="Song, Joon Myong" sort="Song, Joon Myong" uniqKey="Song J" first="Joon Myong" last="Song">Joon Myong Song</name>
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<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>
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<author><name sortKey="Kim, Min Jung" sort="Kim, Min Jung" uniqKey="Kim M" first="Min Jung" last="Kim">Min Jung Kim</name>
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<author><name sortKey="Pal, Sukdeb" sort="Pal, Sukdeb" uniqKey="Pal S" first="Sukdeb" last="Pal">Sukdeb Pal</name>
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<author><name sortKey="Song, Joon Myong" sort="Song, Joon Myong" uniqKey="Song J" first="Joon Myong" last="Song">Joon Myong Song</name>
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<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>
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<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>
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<term>Fluorescent Dyes</term>
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<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>
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<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>
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<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>
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