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A Comparison of Hybridization Efficiency between Flat Glass and Channel Glass Solid Supports

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Abstract

Two different solid supports, channel glass and flat glass, were compared for their affect on the sensitivity and efficiency of DNA hybridization reactions. Both solid supports were tested using a set of arrayed, synthetic oligonucleotides that are designed to detect short insertion/deletion polymorphisms (SIDPs). A total of 13 different human SIDPs were chosen for analysis. Capture probes, designed for this test set, were covalently immobilized on substrates. Hybridization efficiency was assessed using fluorescently labeled stacking probes which were preannealed to the target and then hybridized to the support-bound oligonucleotide array; the hybridization pattern was detected by fluorescence imaging. It was found that structural features of nucleic acid capture probes tethered to a solid support and the molecular basis of their interaction with targets in solution have direct implications on the hybridization process. Our results demonstrate that channel glass has a number of practical advantages over flat glass including higher sensitivity and a faster hybridization rate.

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Acknowledgements

Financial support for this work was provided by PROMEP/103.5/03/1130, Fondo Sectorial Área de Ciencia Básica SEP-CONACYT 2004-C01-46537 and by NIH grant R01 HL62681-01.

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Authors and Affiliations

  1. Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Abasolo 600 Pachuca de Soto, Hidalgo, 42000, Mexico

    Gabriel Betanzos-Cabrera

  2. Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA

    Brent W. Harker

  3. Biosciences Division, Oak Ridge National Laboratory, Building 4500-S, MS 6123, Bethel Valley Road, PO Box 2008, Oak Ridge, TN, 37831, USA

    Mitchel J. Doktycz & Kenneth L. Beattie

  4. Center for Medical Genetics, Marshfield Medical Research Foundation, Marshfield, WI, USA

    James L. Weber

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  1. Gabriel Betanzos-Cabrera
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  2. Brent W. Harker
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  3. Mitchel J. Doktycz
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  4. James L. Weber
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  5. Kenneth L. Beattie
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Correspondence to Gabriel Betanzos-Cabrera.

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Betanzos-Cabrera, G., Harker, B.W., Doktycz, M.J. et al. A Comparison of Hybridization Efficiency between Flat Glass and Channel Glass Solid Supports. Mol Biotechnol 38, 71–80 (2008). https://doi.org/10.1007/s12033-007-9001-z

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