{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T20:27:28Z","timestamp":1768076848044,"version":"3.49.0"},"reference-count":31,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2010,8,5]],"date-time":"2010-08-05T00:00:00Z","timestamp":1280966400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Sensors"],"abstract":"<jats:p>The CombiMatrix microarray with 12,544 electrodes supports in situ electrochemical synthesis of user-defined DNA probes. As an alternative, we immobilized commercially synthesized DNA probes on individual electrodes coated with electropolymerized polypyrrole (Ppy). Hybridization was measured using a biotinylated target oligonucleotide and either Cy5-streptavidin and fluorescence detection or horseradish peroxidase-streptavidin and enzyme-enhanced electrochemical detection. Detection efficiencies were optimized by varying the deposition of the Ppy, the terminal groups on the DNA probes, and other factors that impacted fluorescence quenching and electrical conductivity. Optimized results were compared against those obtained using a microarray with the same DNA sequences synthesized in situ. Immobilized probes produced higher fluorescence signals, possibly by providing a greater stand off between the Cy5 on the target oligonucleotide and the quenching effects of the Ppy and the platinum electrode.<\/jats:p>","DOI":"10.3390\/s100807371","type":"journal-article","created":{"date-parts":[[2010,8,5]],"date-time":"2010-08-05T10:48:37Z","timestamp":1281005317000},"page":"7371-7385","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Use of a Multiplexed CMOS Microarray to Optimize and Compare Oligonucleotide Binding to DNA Probes Synthesized or Immobilized on Individual Electrodes"],"prefix":"10.3390","volume":"10","author":[{"given":"Karl","family":"Maurer","sequence":"first","affiliation":[{"name":"CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite #202, Mukilteo WA 98275, USA"}]},{"given":"Nina","family":"Yazvenko","sequence":"additional","affiliation":[{"name":"CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite #202, Mukilteo WA 98275, USA"}]},{"given":"Jodi","family":"Wilmoth","sequence":"additional","affiliation":[{"name":"CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite #202, Mukilteo WA 98275, USA"}]},{"given":"John","family":"Cooper","sequence":"additional","affiliation":[{"name":"CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite #202, Mukilteo WA 98275, USA"}]},{"given":"Wanda","family":"Lyon","sequence":"additional","affiliation":[{"name":"AFRL\/RHPB, Wright Patterson AFB, 2729 R Street, Area B B837, Dayton, OH 45433, USA"}]},{"given":"David","family":"Danley","sequence":"additional","affiliation":[{"name":"CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite #202, Mukilteo WA 98275, USA"}]}],"member":"1968","published-online":{"date-parts":[[2010,8,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1371\/journal.pone.0000034","article-title":"Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays","volume":"1","author":"Maurer","year":"2006","journal-title":"PLoS One"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.jbbm.2004.01.011","article-title":"Immunoassays and sequence-specific DNA detection on a microchip using enzyme amplified electrochemical detection","volume":"59","author":"Dill","year":"2004","journal-title":"J Biochem. Biophys. Methods"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1982","DOI":"10.1002\/elan.200603603","article-title":"Electrochemical detection of short dna oligomer hybridization using the combimatrix electrasense microarray reader","volume":"18","author":"Roth","year":"2006","journal-title":"Electroanalysis"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1016\/j.bios.2006.06.024","article-title":"CombiMatrix oligonucleotide arrays: genotyping and gene expression assays employing electrochemical detection","volume":"22","author":"Ghindilis","year":"2007","journal-title":"Biosens. Bioelectron"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1021\/ol052891r","article-title":"Building addressable libraries: Site selective coumarin synthesis and the \u201creal-time\u201d signaling of antibody-coumarin binding","volume":"8","author":"Tesfu","year":"2006","journal-title":"Org. Lett"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1021\/bc800025z","article-title":"Moving known libraries to an addressable array: A site-selective hetero-Michael reaction","volume":"19","author":"Stuart","year":"2008","journal-title":"Bioconjug. Chem"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"16020","DOI":"10.1021\/ja067194o","article-title":"Building addressable libraries: The use of a mass spectrometry cleavable linker for monitoring reactions on a microelectrode array","volume":"128","author":"Chen","year":"2006","journal-title":"J. Am. Chem. Soc"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"9781","DOI":"10.1371\/journal.pone.0009781","article-title":"Targeted deposition of antibodies on a multiplex CMOS microarray and optimization of a sensitive immunoassay using electrochemical detection","volume":"5","author":"Cooper","year":"2010","journal-title":"PLoS One"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3351","DOI":"10.3390\/s100403351","article-title":"Multiplexed electrochemical detection of yersinia pestis and staphylococcal enterotoxin b using an antibody microarray","volume":"10","author":"Wojciechowski","year":"2010","journal-title":"Sensors"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1021\/ma00081a024","article-title":"Kinetics of DNA binding to electrically conducting polypyrrole films","volume":"27","author":"Minehan","year":"1994","journal-title":"Macromolecules"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3285","DOI":"10.1021\/ac049580z","article-title":"Electrochemical sensors","volume":"76","author":"Bakker","year":"2004","journal-title":"Anal. Chem"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1002\/elan.200603855","article-title":"Label-free impedance biosensors: opportunities and challenges","volume":"19","author":"Daniels","year":"2007","journal-title":"Electroanalysis"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"118","DOI":"10.3390\/s8010118","article-title":"Electrochemical sensors based on organic conjugated polymers","volume":"8","author":"Rahman","year":"2008","journal-title":"Sensors"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2132","DOI":"10.1016\/j.biomaterials.2008.12.065","article-title":"Conducting polymers for electrochemical DNA sensing","volume":"30","author":"Peng","year":"2009","journal-title":"Biomaterials"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2478\/s11696-008-0083-2","article-title":"Polymer interfaces used in electrochemical DNA-based biosensors","volume":"63","author":"Galandoava","year":"2009","journal-title":"Chem. Pap"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3183","DOI":"10.1016\/j.bios.2009.01.045","article-title":"The physicochemical aspects of DNA sensing using electrochemical methods","volume":"24","author":"Wildgoose","year":"2009","journal-title":"Biosens. Bioelectron"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"9513","DOI":"10.3390\/s91209513","article-title":"DNA Hybridization sensors based on electrochemical impedance spectroscopy as a detection tool","volume":"9","author":"Park","year":"2009","journal-title":"Sensors"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2915","DOI":"10.1093\/nar\/22.15.2915","article-title":"Preparation of a DNA matrix via an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing a pyrrole group","volume":"22","author":"Livache","year":"1994","journal-title":"Nucleic. Acid. Res"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1006\/abio.1997.2462","article-title":"Polypyrrole DNA chip on a silicon device: example of hepatitis C virus genotyping","volume":"255","author":"Livache","year":"1998","journal-title":"Anal. Biochem"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/S0925-4005(99)00287-7","article-title":"Biochips on CMOS: An active matrix address array for DNA analysis","volume":"61","author":"Caillat","year":"1999","journal-title":"Sens. Actuat. B: Chem"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/S1246-7820(01)00141-0","article-title":"DNA chips: A new tool for genetic analysis and diagnostics","volume":"8","author":"Cuzin","year":"2001","journal-title":"Transfus. Clin. Biol"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1016\/S0731-7085(03)00176-6","article-title":"Polypyrrole based DNA hybridization assays: study of label free detection processes versus fluorescence on microchips","volume":"32","author":"Livache","year":"2003","journal-title":"J. Pharm. Biomed. Anal"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1081\/MA-100108381","article-title":"DNA binding to electropolymerized polypyrrole: The dependence on film characteristics","volume":"38","author":"Minehan","year":"2001","journal-title":"J. Macromol. Sci. Part A: Pure Appl. Chem"},{"key":"ref_24","first-page":"303","article-title":"Characterization of DNA immobilized on electrochemically prepared conducting polypyrrole-polyvinyl sulfonate films","volume":"96","author":"Gambhir","year":"2001","journal-title":"Appl. Biochem. Biotechnol"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1163\/156856299X00919","article-title":"Development and analytical characterization of cysteine-grafted polypyrrole films electrosynthesized on Pt- and Ti-substrates as precursors of bioactive interfaces","volume":"10","author":"Sabbatini","year":"1999","journal-title":"J. Biomater. Sci. Polym. Ed"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3275","DOI":"10.1016\/j.bios.2009.04.023","article-title":"Potentiometric monitoring DNA hybridization","volume":"24","author":"Zhou","year":"2009","journal-title":"Biosens. Bioelectron"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.bios.2007.06.013","article-title":"Conducting polymer based fluorescence quenching as a new approach to increase the selectivity of immunosensors","volume":"23","author":"Ramanavicius","year":"2007","journal-title":"Biosen. Bioelectron"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2342","DOI":"10.1021\/cm011681f","article-title":"Conjugated polymers as efficient fluorescence quenchers and their applications for bioassays","volume":"14","author":"Song","year":"2002","journal-title":"Chem. Mater"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1002\/(SICI)1097-4628(19970418)64:3<519::AID-APP8>3.0.CO;2-N","article-title":"Structural and mechanical degradation of polypyrrole films due to aqueous media and heat treatment and the subsequent redoping characteristics","volume":"64","author":"Neoh","year":"1997","journal-title":"J. Appl. Polym. Sci"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S0008-6223(00)00098-1","article-title":"Electric conductivity changes of polypyrrole and polythiophene films with heat-treatment","volume":"39","author":"Ando","year":"2001","journal-title":"Carbon"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/nnano.2008.4","article-title":"Conductivity of a single DNA duplex bridging a carbon nanotube gap","volume":"3","author":"Guo","year":"2008","journal-title":"Nat Nano"}],"container-title":["Sensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8220\/10\/8\/7371\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T22:03:05Z","timestamp":1760220185000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8220\/10\/8\/7371"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,5]]},"references-count":31,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2010,8]]}},"alternative-id":["s100807371"],"URL":"https:\/\/doi.org\/10.3390\/s100807371","relation":{},"ISSN":["1424-8220"],"issn-type":[{"value":"1424-8220","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,8,5]]}}}