Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays
Identifieur interne : 001323 ( Pmc/Checkpoint ); précédent : 001322; suivant : 001324Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays
Auteurs : Christy Agbavwe ; Mark M. SomozaSource :
- PLoS ONE [ 1932-6203 ] ; 2011.
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
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DOI: 10.1371/journal.pone.0022177
PubMed: 21799789
PubMed Central: 3143128
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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></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></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></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 sortKey="Jones, Wd" uniqKey="Jones W">WD Jones</name></author><author><name sortKey="Shippy, R" uniqKey="Shippy R">R Shippy</name></author><author><name sortKey="Warrington, Ja" uniqKey="Warrington J">JA Warrington</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chain, B" uniqKey="Chain B">B Chain</name></author><author><name sortKey="Bowen, H" uniqKey="Bowen H">H Bowen</name></author><author><name sortKey="Hammond, J" uniqKey="Hammond J">J Hammond</name></author><author><name sortKey="Posch, W" uniqKey="Posch W">W Posch</name></author><author><name sortKey="Rasaiyaah, J" uniqKey="Rasaiyaah J">J Rasaiyaah</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dobbin, Kk" uniqKey="Dobbin K">KK Dobbin</name></author><author><name sortKey="Kawasaki, Es" uniqKey="Kawasaki E">ES Kawasaki</name></author><author><name sortKey="Petersen, Dw" uniqKey="Petersen D">DW Petersen</name></author><author><name sortKey="Simon, Rm" uniqKey="Simon R">RM Simon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dombkowski, Aa" uniqKey="Dombkowski A">AA Dombkowski</name></author><author><name sortKey="Thibodeau, Bj" uniqKey="Thibodeau B">BJ Thibodeau</name></author><author><name sortKey="Starcevic, Sl" uniqKey="Starcevic S">SL Starcevic</name></author><author><name sortKey="Novak, Rf" uniqKey="Novak R">RF Novak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gregory Cox, W" uniqKey="Gregory Cox W">W Gregory Cox</name></author><author><name sortKey="Beaudet, Mp" uniqKey="Beaudet M">MP Beaudet</name></author><author><name sortKey="Agnew, Jy" uniqKey="Agnew J">JY Agnew</name></author><author><name sortKey="Ruth, Jl" uniqKey="Ruth J">JL Ruth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin Magniette, Ml" uniqKey="Martin Magniette M">ML Martin-Magniette</name></author><author><name sortKey="Aubert, J" uniqKey="Aubert J">J Aubert</name></author><author><name sortKey="Cabannes, E" uniqKey="Cabannes E">E Cabannes</name></author><author><name sortKey="Daudin, Jj" uniqKey="Daudin J">JJ Daudin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Patterson, Ta" uniqKey="Patterson T">TA Patterson</name></author><author><name sortKey="Lobenhofer, Ek" uniqKey="Lobenhofer E">EK Lobenhofer</name></author><author><name sortKey="Fulmer Smentek, Sb" uniqKey="Fulmer Smentek S">SB Fulmer-Smentek</name></author><author><name sortKey="Collins, Pj" uniqKey="Collins P">PJ Collins</name></author><author><name sortKey="Chu, Tm" uniqKey="Chu T">TM Chu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jeon, H" uniqKey="Jeon H">H Jeon</name></author><author><name sortKey="Choi, S" uniqKey="Choi S">S Choi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luby Phelps, K" uniqKey="Luby Phelps K">K Luby-Phelps</name></author><author><name sortKey="Mujumdar, S" uniqKey="Mujumdar S">S Mujumdar</name></author><author><name sortKey="Mujumdar, Rb" uniqKey="Mujumdar R">RB Mujumdar</name></author><author><name sortKey="Ernst, La" uniqKey="Ernst L">LA Ernst</name></author><author><name sortKey="Galbraith, W" uniqKey="Galbraith W">W Galbraith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brauns, Eb" uniqKey="Brauns E">EB Brauns</name></author><author><name sortKey="Murphy, Cj" uniqKey="Murphy C">CJ Murphy</name></author><author><name sortKey="Berg, Ma" uniqKey="Berg M">MA Berg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Han, Jy" uniqKey="Han J">JY Han</name></author><author><name sortKey="Burgess, K" uniqKey="Burgess K">K Burgess</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Somoza, Mm" uniqKey="Somoza M">MM Somoza</name></author><author><name sortKey="Wiedersich, J" uniqKey="Wiedersich J">J Wiedersich</name></author><author><name sortKey="Friedrich, J" uniqKey="Friedrich J">J Friedrich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Somoza, Mm" uniqKey="Somoza M">MM Somoza</name></author><author><name sortKey="Andreatta, D" uniqKey="Andreatta D">D Andreatta</name></author><author><name sortKey="Murphy, Cj" uniqKey="Murphy C">CJ Murphy</name></author><author><name sortKey="Coleman, Rs" uniqKey="Coleman R">RS Coleman</name></author><author><name sortKey="Berg, Ma" uniqKey="Berg M">MA Berg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pawley, Jb" uniqKey="Pawley J">JB Pawley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, Zx" uniqKey="Huang Z">ZX Huang</name></author><author><name sortKey="Ji, Dm" uniqKey="Ji D">DM Ji</name></author><author><name sortKey="Wang, Sf" uniqKey="Wang S">SF Wang</name></author><author><name sortKey="Xia, Ad" uniqKey="Xia A">AD Xia</name></author><author><name sortKey="Koberling, F" uniqKey="Koberling F">F Koberling</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Widengren, J" uniqKey="Widengren J">J Widengren</name></author><author><name sortKey="Schwille, P" uniqKey="Schwille P">P Schwille</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dempster, Dn" uniqKey="Dempster D">DN Dempster</name></author><author><name sortKey="Thompson, Gf" uniqKey="Thompson G">GF Thompson</name></author><author><name sortKey="Morrow, T" uniqKey="Morrow T">T Morrow</name></author><author><name sortKey="Rankin, R" uniqKey="Rankin R">R Rankin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanborn, Me" uniqKey="Sanborn M">ME Sanborn</name></author><author><name sortKey="Connolly, Bk" uniqKey="Connolly B">BK Connolly</name></author><author><name sortKey="Gurunathan, K" uniqKey="Gurunathan K">K Gurunathan</name></author><author><name sortKey="Levitus, M" uniqKey="Levitus M">M Levitus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Iqbal, A" uniqKey="Iqbal A">A Iqbal</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author><author><name sortKey="Thompson, Kc" uniqKey="Thompson K">KC Thompson</name></author><author><name sortKey="Lilley, Dmj" uniqKey="Lilley D">DMJ Lilley</name></author><author><name sortKey="Norman, Dg" uniqKey="Norman D">DG Norman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Norman, Dg" uniqKey="Norman D">DG Norman</name></author><author><name sortKey="Grainger, Rj" uniqKey="Grainger R">RJ Grainger</name></author><author><name sortKey="Uhrin, D" uniqKey="Uhrin D">D Uhrin</name></author><author><name sortKey="Lilley, Dmj" uniqKey="Lilley D">DMJ Lilley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Harvey, Bj" uniqKey="Harvey B">BJ Harvey</name></author><author><name sortKey="Levitus, M" uniqKey="Levitus M">M Levitus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Harvey, Bj" uniqKey="Harvey B">BJ Harvey</name></author><author><name sortKey="Perez, C" uniqKey="Perez C">C Perez</name></author><author><name sortKey="Levitus, M" uniqKey="Levitus M">M Levitus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Singh Gasson, S" uniqKey="Singh Gasson S">S Singh-Gasson</name></author><author><name sortKey="Green, Rd" uniqKey="Green R">RD Green</name></author><author><name sortKey="Yue, Yj" uniqKey="Yue Y">YJ Yue</name></author><author><name sortKey="Nelson, C" uniqKey="Nelson C">C Nelson</name></author><author><name sortKey="Blattner, F" uniqKey="Blattner F">F Blattner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lackey, Jg" uniqKey="Lackey J">JG Lackey</name></author><author><name sortKey="Mitra, D" uniqKey="Mitra D">D Mitra</name></author><author><name sortKey="Somoza, Mm" uniqKey="Somoza M">MM Somoza</name></author><author><name sortKey="Cerrina, F" uniqKey="Cerrina F">F Cerrina</name></author><author><name sortKey="Damha, Mj" uniqKey="Damha M">MJ Damha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lackey, Jg" uniqKey="Lackey J">JG Lackey</name></author><author><name sortKey="Somoza, Mm" uniqKey="Somoza M">MM Somoza</name></author><author><name sortKey="Mitra, D" uniqKey="Mitra D">D Mitra</name></author><author><name sortKey="Cerrina, F" uniqKey="Cerrina F">F Cerrina</name></author><author><name sortKey="Damha, Mj" uniqKey="Damha M">MJ Damha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcgall, Gh" uniqKey="Mcgall G">GH McGall</name></author><author><name sortKey="Barone, Ad" uniqKey="Barone A">AD Barone</name></author><author><name sortKey="Diggelmann, M" uniqKey="Diggelmann M">M Diggelmann</name></author><author><name sortKey="Fodor, Spa" uniqKey="Fodor S">SPA Fodor</name></author><author><name sortKey="Gentalen, E" uniqKey="Gentalen E">E Gentalen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nuwaysir, Ef" uniqKey="Nuwaysir E">EF Nuwaysir</name></author><author><name sortKey="Huang, W" uniqKey="Huang W">W Huang</name></author><author><name sortKey="Albert, Tj" uniqKey="Albert T">TJ Albert</name></author><author><name sortKey="Singh, J" uniqKey="Singh J">J Singh</name></author><author><name sortKey="Nuwaysir, K" uniqKey="Nuwaysir K">K Nuwaysir</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Murphy, Mc" uniqKey="Murphy M">MC Murphy</name></author><author><name sortKey="Rasnik, I" uniqKey="Rasnik I">I Rasnik</name></author><author><name sortKey="Cheng, W" uniqKey="Cheng W">W Cheng</name></author><author><name sortKey="Lohman, Tm" uniqKey="Lohman T">TM Lohman</name></author><author><name sortKey="Ha, T" uniqKey="Ha T">T Ha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schneider, Td" uniqKey="Schneider T">TD Schneider</name></author><author><name sortKey="Stephens, Rm" uniqKey="Stephens R">RM Stephens</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mikelsons, L" uniqKey="Mikelsons L">L Mikelsons</name></author><author><name sortKey="Carra, C" uniqKey="Carra C">C Carra</name></author><author><name sortKey="Shaw, M" uniqKey="Shaw M">M Shaw</name></author><author><name sortKey="Schweitzer, C" uniqKey="Schweitzer C">C Schweitzer</name></author><author><name sortKey="Scaiano, Jc" uniqKey="Scaiano J">JC Scaiano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Crockett, Ao" uniqKey="Crockett A">AO Crockett</name></author><author><name sortKey="Wittwer, Ct" uniqKey="Wittwer C">CT Wittwer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shafirovich, Vy" uniqKey="Shafirovich V">VY Shafirovich</name></author><author><name sortKey="Courtney, Sh" uniqKey="Courtney S">SH Courtney</name></author><author><name sortKey="Ya, N" uniqKey="Ya N">N Ya</name></author><author><name sortKey="Geacintov, Ne" uniqKey="Geacintov N">NE Geacintov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seidel, Cam" uniqKey="Seidel C">CAM Seidel</name></author><author><name sortKey="Schulz, A" uniqKey="Schulz A">A Schulz</name></author><author><name sortKey="Sauer, Mhm" uniqKey="Sauer M">MHM Sauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Widengren, J" uniqKey="Widengren J">J Widengren</name></author><author><name sortKey="Dapprich, J" uniqKey="Dapprich J">J Dapprich</name></author><author><name sortKey="Rigler, R" uniqKey="Rigler R">R Rigler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Torimura, M" uniqKey="Torimura M">M Torimura</name></author><author><name sortKey="Kurata, S" uniqKey="Kurata S">S Kurata</name></author><author><name sortKey="Yamada, K" uniqKey="Yamada K">K Yamada</name></author><author><name sortKey="Yokomaku, T" uniqKey="Yokomaku T">T Yokomaku</name></author><author><name sortKey="Kamagata, Y" uniqKey="Kamagata Y">Y Kamagata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heinlein, T" uniqKey="Heinlein T">T Heinlein</name></author><author><name sortKey="Knemeyer, J P" uniqKey="Knemeyer J">J-P Knemeyer</name></author><author><name sortKey="Piestert, O" uniqKey="Piestert O">O Piestert</name></author><author><name sortKey="Sauer, M" uniqKey="Sauer M">M Sauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Turner, Dh" uniqKey="Turner D">DH Turner</name></author><author><name sortKey="Sugimoto, N" uniqKey="Sugimoto N">N Sugimoto</name></author><author><name sortKey="Freier, Sm" uniqKey="Freier S">SM Freier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Petersheim, M" uniqKey="Petersheim M">M Petersheim</name></author><author><name sortKey="Turner, Dh" uniqKey="Turner D">DH Turner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Solie, Tn" uniqKey="Solie T">TN Solie</name></author><author><name sortKey="Schellman, Ja" uniqKey="Schellman J">JA Schellman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sain, A" uniqKey="Sain A">A Sain</name></author><author><name sortKey="Chen, Jzy" uniqKey="Chen J">JZY Chen</name></author><author><name sortKey="Ha, B Y" uniqKey="Ha B">B-Y Ha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guckian, Km" uniqKey="Guckian K">KM Guckian</name></author><author><name sortKey="Schweitzer, Ba" uniqKey="Schweitzer B">BA Schweitzer</name></author><author><name sortKey="Ren, Rx F" uniqKey="Ren R">RX-F Ren</name></author><author><name sortKey="Sheils, Cj" uniqKey="Sheils C">CJ Sheils</name></author><author><name sortKey="Tahmassebi, Dc" uniqKey="Tahmassebi D">DC Tahmassebi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Doktycz, Mj" uniqKey="Doktycz M">MJ Doktycz</name></author><author><name sortKey="Paner, Tm" uniqKey="Paner T">TM Paner</name></author><author><name sortKey="Amaratunga, M" uniqKey="Amaratunga M">M Amaratunga</name></author><author><name sortKey="Benight, As" uniqKey="Benight A">AS Benight</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mujumdar, Rb" uniqKey="Mujumdar R">RB Mujumdar</name></author><author><name sortKey="Ernst, La" uniqKey="Ernst L">LA Ernst</name></author><author><name sortKey="Mujumdar, Sr" uniqKey="Mujumdar S">SR Mujumdar</name></author><author><name sortKey="Lewis, Cj" uniqKey="Lewis C">CJ Lewis</name></author><author><name sortKey="Waggoner, As" uniqKey="Waggoner A">AS 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><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21799789</article-id><article-id pub-id-type="pmc">3143128</article-id><article-id pub-id-type="publisher-id">PONE-D-11-00277</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0022177</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Biophysics</subject><subj-group><subject>Nucleic Acids</subject><subj-group><subject>DNA</subject><subject>Nucleic Acid Components</subject><subject>Nucleotides</subject><subject>Synthetic Nucleic Acids</subject></subj-group></subj-group></subj-group><subj-group><subject>Biotechnology</subject></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Chemistry</subject><subj-group><subject>Physical Chemistry</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Physics</subject><subj-group><subject>Biophysics</subject><subj-group><subject>Nucleic Acids</subject><subj-group><subject>DNA</subject><subject>Nucleic Acid Components</subject><subject>Nucleotides</subject><subject>Synthetic Nucleic Acids</subject></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays</article-title><alt-title alt-title-type="running-head">Sequence-Dependent Fluorescence of Cyanine Dyes</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Agbavwe</surname><given-names>Christy</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Somoza</surname><given-names>Mark M.</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><addr-line>Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Gibas</surname><given-names>Cynthia</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">University of North Carolina at Charlotte, United States of America</aff><author-notes><corresp id="cor1">* E-mail: <email>mark.somoza@univie.ac.at</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: MMS. Performed the experiments: CA MMS. Analyzed the data: MMS. Wrote the paper: MMS.</p></fn></author-notes><pub-date pub-type="collection"><year>2011</year></pub-date><pub-date pub-type="epub"><day>25</day><month>7</month><year>2011</year></pub-date><volume>6</volume><issue>7</issue><elocation-id>e22177</elocation-id><history><date date-type="received"><day>21</day><month>12</month><year>2010</year></date><date date-type="accepted"><day>17</day><month>6</month><year>2011</year></date></history><permissions><copyright-statement>Agbavwe, Somoza.</copyright-statement><copyright-year>2011</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><abstract><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></abstract><counts><page-count count="10"></page-count></counts></article-meta></front></pmc><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. Somoza</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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