{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T21:25:39Z","timestamp":1761427539792,"version":"build-2065373602"},"reference-count":33,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2011,6,9]],"date-time":"2011-06-09T00:00:00Z","timestamp":1307577600000},"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 use of quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET) offer several advantages for the development of multiplexed solid-phase QD-FRET nucleic acid hybridization assays. Designs for multiplexing have been demonstrated, but important challenges remain in the optimization of these systems. In this work, we identify several strategies based on the design of interfacial chemistry for improving sensitivity, obtaining lower limits of detection (LOD) and enabling the regeneration and reuse of solid-phase QD-FRET hybridization assays. FRET-sensitized emission from acceptor dyes associated with hybridization events at immobilized QD donors provides the analytical signal in these assays. The minimization of active sensing area reduces background from QD donor PL and allows the resolution of smaller amounts of acceptor emission, thus lowering the LOD. The association of multiple acceptor dyes with each hybridization event can enhance FRET efficiency, thereby improving sensitivity. Many previous studies have used interfacial protein layers to generate selectivity; however, transient destabilization of these layers is shown to prevent efficient regeneration. To this end, we report a protein-free interfacial chemistry and demonstrate the specific detection of as little as 2 pmol of target, as well as an improved capacity for regeneration.<\/jats:p>","DOI":"10.3390\/s110606214","type":"journal-article","created":{"date-parts":[[2011,6,9]],"date-time":"2011-06-09T15:42:46Z","timestamp":1307634166000},"page":"6214-6236","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Interfacial Chemistry and the Design of Solid-Phase Nucleic Acid Hybridization Assays Using Immobilized Quantum Dots as Donors in Fluorescence Resonance Energy Transfer"],"prefix":"10.3390","volume":"11","author":[{"given":"W. Russ","family":"Algar","sequence":"first","affiliation":[{"name":"Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. North, Mississauga, ON L5L 1C6, Canada"}]},{"given":"Ulrich J.","family":"Krull","sequence":"additional","affiliation":[{"name":"Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. North, Mississauga, ON L5L 1C6, Canada"}]}],"member":"1968","published-online":{"date-parts":[[2011,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1126\/science.281.5385.2013","article-title":"Semiconductor Nanocrystals as Fluorescent Biological Labels","volume":"281","author":"Bruchez","year":"2008","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1126\/science.281.5385.2016","article-title":"Quantum Dot Bioconjugates for Ultrasensitive Nonisotopic Detection","volume":"281","author":"Chan","year":"1998","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/nmat1390","article-title":"Quantum Dot Bioconjugates for Imaging, Labelling and Sensing","volume":"4","author":"Medintz","year":"2005","journal-title":"Nat. Mater"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1126\/science.1104274","article-title":"Quantum Dots for Live Cells, in vivo Imaging, and Diagnostics","volume":"307","author":"Michalet","year":"2005","journal-title":"Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.aca.2010.05.026","article-title":"Beyond Labels: A Review of the Application of Quantum Dots as Integrated Components of Assays, Bioprobes, and Biosensors Utilizing Optical Transduction","volume":"673","author":"Algar","year":"2010","journal-title":"Anal. Chim. Acta"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1007\/s00216-007-1703-3","article-title":"Quantum Dots as Donors in Fluorescence Resonance Energy Transfer for the Bioanalysis of Nucleic Acids, Proteins, and Other Biological Molecules","volume":"391","author":"Algar","year":"2008","journal-title":"Anal. Bioanal. Chem"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1039\/B813919A","article-title":"Quantum Dot-Based Resonance Energy Transfer and Its Growing Application in Biology","volume":"11","author":"Medintz","year":"2009","journal-title":"Phys. Chem. Chem. Phys"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2439","DOI":"10.1007\/s00216-010-3837-y","article-title":"New Opportunities in Multiplexed Optical Bioanalyses Using Quantum Dots and Donor-Acceptor Interactions","volume":"398","author":"Algar","year":"2010","journal-title":"Anal. Bioanal. Chem"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"7602","DOI":"10.1002\/anie.200800169","article-title":"Semiconductor Quantum Dots for Bioanalysis","volume":"47","author":"Gill","year":"2008","journal-title":"Angew. Chem. Int. Ed"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"5514","DOI":"10.1021\/la703812t","article-title":"Multidentate Surface Ligand Exchange for the Immobilization of CdSe\/ZnS Quantum Dots and Surface Quantum Dot-Oligonucleotide Conjugates","volume":"24","author":"Algar","year":"2008","journal-title":"Langmuir"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"4113","DOI":"10.1021\/ac900421p","article-title":"Toward A Multiplexed Solid-Phase Nucleic Acid Hybridization Assay Using Quantum Dots as Donors in Fluorescence Resonance Energy Transfer","volume":"81","author":"Algar","year":"2009","journal-title":"Anal. Chem"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1021\/ac902221d","article-title":"Multiplexed Interfacial Transduction of Nucleic Acid Hybridization Using a Single Color of Immobilized Quantum Dot Donor and Two Acceptors in Fluorescence Resonance Energy Transfer","volume":"82","author":"Algar","year":"2010","journal-title":"Anal. Chem"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"6041","DOI":"10.1021\/la903751m","article-title":"Developing Mixed Films of Immobilized Oligonucleotides and Quantum Dots for the Multiplexed Detection of Nucleic Acid Hybridization Using a Combination of Fluorescence Resonance Energy Transfer and Direct Excitation of Fluorescence","volume":"26","author":"Algar","year":"2010","journal-title":"Langmuir"},{"key":"ref_14","first-page":"1241-XX09-04","article-title":"FRET-Based Solid-Phase Three-Color and Four-Color Hybridization Assays Using Mixed Films of Quantum Dots and Oligonucleotides","volume":"1241E","author":"Algar","year":"2010","journal-title":"Mater Res Soc Symp Proc"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1021\/la803082f","article-title":"Interfacial Transduction of Nucleic Acid Hybridization Using Immobilized Quantum Dots as Donors in Fluorescence Resonance Energy Transfer","volume":"25","author":"Algar","year":"2009","journal-title":"Langmuir"},{"key":"ref_16","first-page":"79090C:1","article-title":"Immobilization of CdSe\/ZnS Quantum Dots on Glass Beads for the Detection of Nucleic Acid Hybridization Using Fluorescence Resonance Energy Transfer","volume":"7909","author":"Algar","year":"2011","journal-title":"Proc SPIE"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4000","DOI":"10.1021\/ac050236r","article-title":"Electrokinetically Based Approach for Single-Nucleotide Polymorphism Discrimination Using a Microfluidic Device","volume":"77","author":"Erickson","year":"2005","journal-title":"Anal. Chem"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4939","DOI":"10.1021\/ac9709763","article-title":"Surface Plasmon Resonance Imaging Measurements of DNA Hybridization Adsorption and Streptavidin\/DNA Multilayer Formation at Chemically Modified Gold Surfaces","volume":"69","author":"Jordan","year":"1997","journal-title":"Anal. Chem"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.bios.2005.01.006","article-title":"Comparison of Surface Plasmon Resonance Spectroscopy and Quartz Crystal Microbalance Techniques for Studying DNA Assembly and Hybridization","volume":"21","author":"Su","year":"2005","journal-title":"Biosens. 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Acids Res"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1007\/BF02716841","article-title":"Influence of Formamide on the Thermal Stability of DNA","volume":"6","author":"Sadhu","year":"1984","journal-title":"J. Biosci"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4984","DOI":"10.1021\/la991508m","article-title":"Effects of Oligonucleotide Immobilization Density on Selectivity of Quantitative Transduction of Hybridization of Immobilized DNA","volume":"16","author":"Watterson","year":"2000","journal-title":"Langmuir"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.aca.2009.12.001","article-title":"A Mixed Film Composed of Oligonucleotides and Poly(2-hydroxyethyl methacrylate) Brushes to Enhance Selectivity for Detection of Single Nucleotide Polymorphisms","volume":"661","author":"Wong","year":"2010","journal-title":"Anal. Chim. Acta"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1093\/nar\/24.11.2095","article-title":"Thermodynamic Effects of Formamide on DNA Stability","volume":"24","author":"Blake","year":"1996","journal-title":"Nucl. Acids Res"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2706","DOI":"10.1529\/biophysj.107.119271","article-title":"Quantitative Determination of Size and Shape of Surface-Bound DNA Using an Acoustic Wave Sensor","volume":"94","author":"Tsortos","year":"2008","journal-title":"Biophys. J"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"8633","DOI":"10.1103\/PhysRevB.54.8633","article-title":"Long-Range Resonance Energy Transfer of Electronic Excitations in Close-Packed CdSe Quantum-Dot Solids","volume":"54","author":"Kagan","year":"1996","journal-title":"Phys. Rev. B"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"11346","DOI":"10.1021\/la062217y","article-title":"Adsorption and Hybridization of Oligonucleotides on Mercaptoacetic Acid-Capped CdSe\/ZnS Quantum Dots and Quantum Dot-Oligonucleotide Conjugates","volume":"22","author":"Algar","year":"2006","journal-title":"Langmuir"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"73860J","DOI":"10.1117\/12.840545","article-title":"Development of Methods to Study the Conformational Dynamics of Quantum Dot-Oligonucleotide Conjugates by Single Molecule Spectroscopy","volume":"7386","author":"Algar","year":"2009","journal-title":"Proc. SPIE"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"16860","DOI":"10.1021\/jp062279x","article-title":"Luminescent Properties of Water-Soluble Denatured Bovine Serum Albumin-Coated CdTe Quantum Dots","volume":"110","author":"Wang","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/nmat961","article-title":"Self-Assembled Nanoscale Biosensors Based on Quantum Dot FRET Donors","volume":"2","author":"Medintz","year":"2003","journal-title":"Nat. Mater"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"5142","DOI":"10.1073\/pnas.0930122100","article-title":"The Molecular Basis for the Chemical Denaturation of Proteins by Urea","volume":"100","author":"Bennion","year":"2003","journal-title":"Proc. Natl. Acad. Sci. 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