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Open AccessArticle

A Reliable, Label Free Quality Control Method for the Production of DNA Microarrays with Clinical Applications

1
Photonics Center, Department of Electrical Engineering, Boston University, Boston, MA 02215, USA
2
Istituto di Scienze e Tecnologie Chimiche “G. Natta” SCITEC- Consiglio Nazionale delle Ricerche, 20131 Milano, Italy
*
Authors to whom correspondence should be addressed.
Polymers 2021, 13(3), 340; https://doi.org/10.3390/polym13030340
Received: 17 December 2020 / Revised: 15 January 2021 / Accepted: 18 January 2021 / Published: 21 January 2021
(This article belongs to the Special Issue Functional Polymers for Biosensing Applications)
The manufacture of a very high-quality microarray support is essential for the adoption of this assay format in clinical routine. In fact, poorly surface-bound probes can affect the diagnostic sensitivity or, in worst cases, lead to false negative results. Here we report on a reliable and easy quality control method for the evaluation of spotted probe properties in a microarray test, based on the Interferometric Reflectance Imaging Sensor (IRIS) system, a high-resolution label free technique able to evaluate the variation of the mass bound to a surface. In particular, we demonstrated that the IRIS analysis of microarray chips immediately after probe immobilization can detect the absence of probes, which recognizably causes a lack of signal when performing a test, with clinical relevance, using fluorescence detection. Moreover, the use of the IRIS technique allowed also to determine the optimal concentration of the probe, that has to be immobilized on the surface, to maximize the target recognition, thus the signal, but to avoid crowding effects. Finally, through this preliminary quality inspection it is possible to highlight differences in the immobilization chemistries. In particular, we have compared NHS ester versus click chemistry reactions using two different surface coatings, demonstrating that, in the diagnostic case used as an example (colorectal cancer) a higher probe density does not reflect a higher binding signal, probably because of a crowding effect. View Full-Text
Keywords: DNA microarray; spotting optimization; label-free detection DNA microarray; spotting optimization; label-free detection
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MDPI and ACS Style

Chiodi, E.; Damin, F.; Sola, L.; Ferraro, L.; Brambilla, D.; Ünlü, M.S.; Chiari, M. A Reliable, Label Free Quality Control Method for the Production of DNA Microarrays with Clinical Applications. Polymers 2021, 13, 340. https://doi.org/10.3390/polym13030340

AMA Style

Chiodi E, Damin F, Sola L, Ferraro L, Brambilla D, Ünlü MS, Chiari M. A Reliable, Label Free Quality Control Method for the Production of DNA Microarrays with Clinical Applications. Polymers. 2021; 13(3):340. https://doi.org/10.3390/polym13030340

Chicago/Turabian Style

Chiodi, Elisa; Damin, Francesco; Sola, Laura; Ferraro, Lucia; Brambilla, Dario; Ünlü, M. S.; Chiari, Marcella. 2021. "A Reliable, Label Free Quality Control Method for the Production of DNA Microarrays with Clinical Applications" Polymers 13, no. 3: 340. https://doi.org/10.3390/polym13030340

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Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

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