Channel Glass-based Detection of Human Short Insertion/Deletion Polymorphisms by Tandem Hybridization

• Published in: Molecular biotechnology 2008-02, Vol.38 (2), p.145-153
• 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; Biotechnology; Cell Biology; Chemistry; Chemistry and Materials Science; Deoxyribonucleic acid; DNA; Fundamental and applied biological sciences. Psychology; Gene Deletion; Genomics; Genotype; Glass; Human Genetics; Humans; Hybridization; Molecular biology; Molecular Sequence Data; Mutagenesis, Insertional - genetics; Nucleic Acid Hybridization - methods; Polymorphism; Polymorphism, Genetic - genetics; Protein Science
• ISSN: 1073-6085; 1559-0305
• DOI: 10.1007/s12033-007-9004-9

The development and critical evaluation of new technologies for identifying genetic polymorphisms will rapidly accelerate the discovery and diagnosis of disease-related genes. We report a novel way for distinguishing a new class of human DNA polymorphisms, short insertion/deletion polymorphisms (indels). A sensor with cylindrical pores named channel glass in combination with tandem hybridization, which uses a 5′-fluorescent labeled stacking probe and microarray-based short allele-specific oligonucleotide (capture probe) was investigated. This methodology allows indels to be detected individually and rapidly with small quantities of target DNA. This establishes a reliable quantitative test. Approaches for simultaneously hybridizing different targets to arrayed probes, designed to detect various indels in parallel, were examined. Five markers were consistently detected in a single hybridization. Possible factors impeding the hybridization reaction process are discussed.