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

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 polymor...

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Bibliographic Details
Published in:Molecular biotechnology 2008-01, Vol.38 (1), p.71-80
Main Authors: Betanzos-Cabrera, Gabriel, Harker, Brent W., Doktycz, Mitchel J., Weber, James L., Beattie, Kenneth L.
Format: Article
Language:English
Subjects:
Base Sequence
Biochemistry
Biological and medical sciences
Biological Techniques
Biophysics
Biotechnology
Cell Biology
Chemistry
Chemistry and Materials Science
DNA - genetics
DNA - isolation & purification
DNA Probes - genetics
Fluorescent Dyes
Fundamental and applied biological sciences. Psychology
Glass
Human Genetics
Humans
Hybridization
Materials science
Molecular Sequence Data
Nucleic Acid Hybridization - methods
Nucleic acids
Oligonucleotide Array Sequence Analysis - methods
Polymerase Chain Reaction
Polymorphism
Polymorphism, Genetic
Probes
Protein Science
Thermodynamics
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Summary: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.
ISSN:1073-6085
1559-0305
DOI:10.1007/s12033-007-9001-z