Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization

The physical–chemical properties of the surface of DNA microarrays and biosensors play a fundamental role in their performance, affecting the signal’s amplitude and the strength and kinetics of binding. We studied how the interaction parameters vary for hybridization of complementary 23-<i>mer...

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Autores principales:	Luka Vanjur, Thomas Carzaniga, Luca Casiraghi, Giuliano Zanchetta, Francesco Damin, Laura Sola, Marcella Chiari, Marco Buscaglia
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	DNA hybridization label-free detection DNA hybridization kinetics copolymers Organic chemistry QD241-441
Acceso en línea:	https://doaj.org/article/34f8ec51b01446df835f4298147330bf
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spelling	oai:doaj.org-article:34f8ec51b01446df835f4298147330bf2021-11-25T18:48:06ZCopolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization10.3390/polym132238972073-4360https://doaj.org/article/34f8ec51b01446df835f4298147330bf2021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4360/13/22/3897https://doaj.org/toc/2073-4360The physical–chemical properties of the surface of DNA microarrays and biosensors play a fundamental role in their performance, affecting the signal’s amplitude and the strength and kinetics of binding. We studied how the interaction parameters vary for hybridization of complementary 23-<i>mer</i> DNA, when the probe strands are immobilized on different copolymers, which coat the surface of an optical, label-free biosensor. Copolymers of <i>N</i>, <i>N</i>-dimethylacrylamide bringing either a different type or density of sites for covalent immobilization of DNA probes, or different backbone charges, were used to functionalize the surface of a Reflective Phantom Interface multispot biosensor made of a glass prism with a silicon dioxide antireflective layer. By analyzing the kinetic hybridization curves at different probe surface densities and target concentrations in solution, we found that all the tested coatings displayed a common association kinetics of about 9 × 10<sup>4</sup> M<sup>−1</sup>·s<sup>−1</sup> at small probe density, decreasing by one order of magnitude close to the surface saturation of probes. In contrast, both the yield of hybridization and the dissociation kinetics, and hence the equilibrium constant, depend on the type of copolymer coating. Nearly doubled signal amplitudes, although equilibrium dissociation constant was as large as 4 nM, were obtained by immobilizing the probe via click chemistry, whereas amine-based immobilization combined with passivation with diamine carrying positive charges granted much slower dissociation kinetics, yielding an equilibrium dissociation constant as low as 0.5 nM. These results offer quantitative criteria for an optimal selection of surface copolymer coatings, depending on the application.Luka VanjurThomas CarzanigaLuca CasiraghiGiuliano ZanchettaFrancesco DaminLaura SolaMarcella ChiariMarco BuscagliaMDPI AGarticleDNA hybridizationlabel-free detectionDNA hybridization kineticscopolymersOrganic chemistryQD241-441ENPolymers, Vol 13, Iss 3897, p 3897 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA hybridization label-free detection DNA hybridization kinetics copolymers Organic chemistry QD241-441
spellingShingle	DNA hybridization label-free detection DNA hybridization kinetics copolymers Organic chemistry QD241-441 Luka Vanjur Thomas Carzaniga Luca Casiraghi Giuliano Zanchetta Francesco Damin Laura Sola Marcella Chiari Marco Buscaglia Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization
description	The physical–chemical properties of the surface of DNA microarrays and biosensors play a fundamental role in their performance, affecting the signal’s amplitude and the strength and kinetics of binding. We studied how the interaction parameters vary for hybridization of complementary 23-<i>mer</i> DNA, when the probe strands are immobilized on different copolymers, which coat the surface of an optical, label-free biosensor. Copolymers of <i>N</i>, <i>N</i>-dimethylacrylamide bringing either a different type or density of sites for covalent immobilization of DNA probes, or different backbone charges, were used to functionalize the surface of a Reflective Phantom Interface multispot biosensor made of a glass prism with a silicon dioxide antireflective layer. By analyzing the kinetic hybridization curves at different probe surface densities and target concentrations in solution, we found that all the tested coatings displayed a common association kinetics of about 9 × 10<sup>4</sup> M<sup>−1</sup>·s<sup>−1</sup> at small probe density, decreasing by one order of magnitude close to the surface saturation of probes. In contrast, both the yield of hybridization and the dissociation kinetics, and hence the equilibrium constant, depend on the type of copolymer coating. Nearly doubled signal amplitudes, although equilibrium dissociation constant was as large as 4 nM, were obtained by immobilizing the probe via click chemistry, whereas amine-based immobilization combined with passivation with diamine carrying positive charges granted much slower dissociation kinetics, yielding an equilibrium dissociation constant as low as 0.5 nM. These results offer quantitative criteria for an optimal selection of surface copolymer coatings, depending on the application.
format	article
author	Luka Vanjur Thomas Carzaniga Luca Casiraghi Giuliano Zanchetta Francesco Damin Laura Sola Marcella Chiari Marco Buscaglia
author_facet	Luka Vanjur Thomas Carzaniga Luca Casiraghi Giuliano Zanchetta Francesco Damin Laura Sola Marcella Chiari Marco Buscaglia
author_sort	Luka Vanjur
title	Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization
title_short	Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization
title_full	Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization
title_fullStr	Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization
title_full_unstemmed	Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization
title_sort	copolymer coatings for dna biosensors: effect of charges and immobilization chemistries on yield, strength and kinetics of hybridization
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/34f8ec51b01446df835f4298147330bf
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Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization

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