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High-Throughput Label-Free Detection of DNA Hybridization and Mismatch Discrimination Using Interferometric Reflectance Imaging Sensor

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Nucleic Acid Detection

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1039))

Abstract

Optical label-free biosensors have demonstrated advantages over fluorescent-based detection methods by allowing accurate quantification while also being capable of measuring dynamic bimolecular interactions. A simple, high-throughput, solid-phase, and label-free technique, interferometric reflectance imaging sensor (IRIS), can quantify the mass density of DNA with pg/mm2 sensitivity by measuring the optical path difference. We present the design of the IRIS instrument and complementary microarrays that can be used to perform a quantitative analysis of DNA microarrays. Finally, we present methods to accurately calculate the hybridization efficiency and identify SNPs from dynamic measurements, as well as supporting software algorithms needed for robust data processing.

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Acknowledgments

We thank Dr. Emre Özkumur for his contributions in developing IRIS and the presented protocol, Professor Marcella Chiari for providing her expertise in surface chemistry, Professor Mario Cabodi for his advice on flow cell design, and Alex Reddington for his help in chip fabrication.

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Authors and Affiliations

  1. Department of Biomedical Engineering, Boston University, Boston, MA, USA

    Sunmin Ahn, Xirui Zhang & M. Selim Ünlü

  2. Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA

    David S. Freedman & M. Selim Ünlü

Authors
  1. Sunmin Ahn
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  2. David S. Freedman
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  3. Xirui Zhang
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  4. M. Selim Ünlü
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Editor information

Editors and Affiliations

  1. University of Central Florida Department of Chemistry, Orlando, Florida, USA

    Dmitry M. Kolpashchikov

  2. University of Central Florida Department of Chemistry, Orlando, Florida, USA

    Yulia V. Gerasimova

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© 2013 Springer Science+Business Media, New York

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Ahn, S., Freedman, D.S., Zhang, X., Ünlü, M.S. (2013). High-Throughput Label-Free Detection of DNA Hybridization and Mismatch Discrimination Using Interferometric Reflectance Imaging Sensor. In: Kolpashchikov, D., Gerasimova, Y. (eds) Nucleic Acid Detection. Methods in Molecular Biology, vol 1039. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-535-4_16

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  • DOI: https://doi.org/10.1007/978-1-62703-535-4_16

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-534-7

  • Online ISBN: 978-1-62703-535-4

  • eBook Packages: Springer Protocols

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