title: Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip.
abstract: We describe a method for the discrimination of short tandem repeat (STR) alleles based on active microarray hybridization. An essential factor in this method is electronic hybridization of the target DNA, at high stringency, in <5 min. High stringency is critical to avoid slippage of hybrids along repeat tracts at allele-specific test sites in the array. These conditions are attainable only with hybridization kinetics realized by electronic concentration of DNA. A sandwich hybrid is assembled, in which proper base stacking of juxtaposed terminal nucleotides results in a thermodynamically favored complex. The increased stability of this complex relative to non-stacked termini and/or base pair mismatches is used to determine the identification of STR alleles. This method is capable of simultaneous and precise identification of alleles containing different numbers of repeats, as well as mutations within these repeats. Given the throughput capabilities of microarrays our system has the potential to enhance the use of microsatellites in forensic criminology, diagnostics and genetic mapping.
authors.affiliation: Nanogen Inc., 10398 Pacific Center Court, San Diego, CA 92121, USA.
authors.forename: R
authors.initials: R
authors.lastname: Radtkey
authors.forename: L
authors.initials: L
authors.lastname: Feng
authors.forename: M
authors.initials: M
authors.lastname: Muralhidar
authors.forename: M
authors.initials: M
authors.lastname: Duhon
authors.forename: D
authors.initials: D
authors.lastname: Canter
authors.forename: D
authors.initials: D
authors.lastname: DiPierro
authors.forename: S
authors.initials: S
authors.lastname: Fallon
authors.forename: E
authors.initials: E
authors.lastname: Tu
authors.forename: K
authors.initials: K
authors.lastname: McElfresh
authors.forename: M
authors.initials: M
authors.lastname: Nerenberg
authors.forename: R
authors.initials: R
authors.lastname: Sosnowski
mesh_terms: D000483:Alleles; D004247:DNA / Q000032:analysis* / Q000737:chemistry; D004563:Electrochemistry; D005069:Evaluation Studies as Topic; D014644:Genetic Variation; D006801:Humans; D007453:Iodide Peroxidase / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D016186:Receptor, Macrophage Colony-Stimulating Factor / Q000235:genetics; D020080:Tandem Repeat Sequences / Q000235:genetics*; D014446:Tyrosine 3-Monooxygenase / Q000235:genetics
chemical_list: D004247:DNA; D007453:Iodide Peroxidase; D014446:Tyrosine 3-Monooxygenase; D016186:Receptor, Macrophage Colony-Stimulating Factor