Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays
Identifieur interne : 002434 ( Main/Exploration ); précédent : 002433; suivant : 002435Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays
Auteurs : Christy Agbavwe ; Mark M. SomozaSource :
- PLoS ONE [ 1932-6203 ] ; 2011.
Descripteurs français
- KwdFr :
- ADN (génétique), ADN (métabolisme), Biotine (analogues et dérivés), Biotine (métabolisme), Carbocyanines (), Carbocyanines (métabolisme), Composés organiques du phosphore (métabolisme), Génomique, Oligodésoxyribonucléotides (génétique), Oligodésoxyribonucléotides (métabolisme), Spectrométrie de fluorescence, Séquence nucléotidique, Séquençage par oligonucléotides en batterie ().
- MESH :
- analogues et dérivés : Biotine.
- génétique : ADN, Oligodésoxyribonucléotides.
- métabolisme : ADN, Biotine, Carbocyanines, Composés organiques du phosphore, Oligodésoxyribonucléotides.
- Carbocyanines, Génomique, Spectrométrie de fluorescence, Séquence nucléotidique, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Base Sequence, Biotin (analogs & derivatives), Biotin (metabolism), Carbocyanines (chemistry), Carbocyanines (metabolism), DNA (genetics), DNA (metabolism), Genomics, Oligodeoxyribonucleotides (genetics), Oligodeoxyribonucleotides (metabolism), Oligonucleotide Array Sequence Analysis (methods), Organophosphorus Compounds (metabolism), Spectrometry, Fluorescence.
- MESH :
- chemical , analogs & derivatives : Biotin.
- chemical , chemistry : Carbocyanines.
- chemical , genetics : DNA, Oligodeoxyribonucleotides.
- chemical , metabolism : Biotin, Carbocyanines, DNA, Oligodeoxyribonucleotides, Organophosphorus Compounds.
- methods : Oligonucleotide Array Sequence Analysis.
- Base Sequence, Genomics, Spectrometry, Fluorescence.
Abstract
Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed
Url:
DOI: 10.1371/journal.pone.0022177
PubMed: 21799789
PubMed Central: 3143128
Affiliations:
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Le document en format XML
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Somoza</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21799789</idno><idno type="pmc">3143128</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143128</idno><idno type="RBID">PMC:3143128</idno><idno type="doi">10.1371/journal.pone.0022177</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">001063</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001063</idno><idno type="wicri:Area/Pmc/Curation">001063</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001063</idno><idno type="wicri:Area/Pmc/Checkpoint">001323</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001323</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:21799789</idno><idno type="wicri:Area/PubMed/Corpus">001E55</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001E55</idno><idno type="wicri:Area/PubMed/Curation">001E55</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001E55</idno><idno type="wicri:Area/PubMed/Checkpoint">001D46</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001D46</idno><idno type="wicri:Area/Ncbi/Merge">000878</idno><idno type="wicri:Area/Ncbi/Curation">000878</idno><idno type="wicri:Area/Ncbi/Checkpoint">000878</idno><idno type="wicri:Area/Main/Merge">002459</idno><idno type="wicri:Area/Main/Curation">002434</idno><idno type="wicri:Area/Main/Exploration">002434</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays</title><author><name sortKey="Agbavwe, Christy" sort="Agbavwe, Christy" uniqKey="Agbavwe C" first="Christy" last="Agbavwe">Christy Agbavwe</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Somoza, Mark M" sort="Somoza, Mark M" uniqKey="Somoza M" first="Mark M." last="Somoza">Mark M. Somoza</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Biotin (analogs & derivatives)</term><term>Biotin (metabolism)</term><term>Carbocyanines (chemistry)</term><term>Carbocyanines (metabolism)</term><term>DNA (genetics)</term><term>DNA (metabolism)</term><term>Genomics</term><term>Oligodeoxyribonucleotides (genetics)</term><term>Oligodeoxyribonucleotides (metabolism)</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Organophosphorus Compounds (metabolism)</term><term>Spectrometry, Fluorescence</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term><term>ADN (métabolisme)</term><term>Biotine (analogues et dérivés)</term><term>Biotine (métabolisme)</term><term>Carbocyanines ()</term><term>Carbocyanines (métabolisme)</term><term>Composés organiques du phosphore (métabolisme)</term><term>Génomique</term><term>Oligodésoxyribonucléotides (génétique)</term><term>Oligodésoxyribonucléotides (métabolisme)</term><term>Spectrométrie de fluorescence</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analogs & derivatives" xml:lang="en"><term>Biotin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Carbocyanines</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Biotin</term><term>Carbocyanines</term><term>DNA</term><term>Oligodeoxyribonucleotides</term><term>Organophosphorus Compounds</term></keywords><keywords scheme="MESH" qualifier="analogues et dérivés" xml:lang="fr"><term>Biotine</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Oligodésoxyribonucléotides</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Biotine</term><term>Carbocyanines</term><term>Composés organiques du phosphore</term><term>Oligodésoxyribonucléotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Genomics</term><term>Spectrometry, Fluorescence</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Carbocyanines</term><term>Génomique</term><term>Spectrométrie de fluorescence</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed <italic>in-situ</italic> synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5′-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5′ guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5′-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Canales, Rd" uniqKey="Canales R">RD Canales</name></author><author><name sortKey="Luo, Y" uniqKey="Luo Y">Y Luo</name></author><author><name sortKey="Willey, Jc" uniqKey="Willey J">JC Willey</name></author><author><name sortKey="Austermiller, B" uniqKey="Austermiller B">B Austermiller</name></author><author><name sortKey="Barbacioru, Cc" uniqKey="Barbacioru C">CC Barbacioru</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Churchill, Ga" uniqKey="Churchill G">GA Churchill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shi, Lm" uniqKey="Shi L">LM Shi</name></author><author><name sortKey="Reid, Lh" uniqKey="Reid L">LH Reid</name></author><author><name 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Waggoner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mujumdar, Sr" uniqKey="Mujumdar S">SR Mujumdar</name></author><author><name sortKey="Mujumdar, Rb" uniqKey="Mujumdar R">RB Mujumdar</name></author><author><name sortKey="Grant, Cm" uniqKey="Grant C">CM Grant</name></author><author><name sortKey="Waggoner, As" uniqKey="Waggoner A">AS Waggoner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gruber, Hj" uniqKey="Gruber H">HJ Gruber</name></author><author><name sortKey="Hahn, Cd" uniqKey="Hahn C">CD Hahn</name></author><author><name sortKey="Kada, G" uniqKey="Kada G">G Kada</name></author><author><name sortKey="Riener, Ck" uniqKey="Riener C">CK Riener</name></author><author><name sortKey="Harms, Gs" uniqKey="Harms G">GS Harms</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, S" uniqKey="Chen S">S Chen</name></author><author><name sortKey="Phillips, Mf" uniqKey="Phillips M">MF Phillips</name></author><author><name sortKey="Cerrina, F" uniqKey="Cerrina F">F Cerrina</name></author><author><name sortKey="Smith, Lm" uniqKey="Smith L">LM Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fuller, Cw" uniqKey="Fuller C">CW Fuller</name></author><author><name sortKey="Middendorf, Lr" uniqKey="Middendorf L">LR Middendorf</name></author><author><name sortKey="Benner, Sa" uniqKey="Benner S">SA Benner</name></author><author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name></author><author><name sortKey="Harris, T" uniqKey="Harris T">T Harris</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Agbavwe, Christy" sort="Agbavwe, Christy" uniqKey="Agbavwe C" first="Christy" last="Agbavwe">Christy Agbavwe</name><name sortKey="Somoza, Mark M" sort="Somoza, Mark M" uniqKey="Somoza M" first="Mark M." last="Somoza">Mark M. 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