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Two procedures, multibase and multiprimer, have been developed for single nucleotide extension of primers immobilized within polyacrylamide gel pads on a microchip. In the multibase assay, a primer is next to a polymorphic nucleotide; the nucleotide is identified by the specificity with which the primer incorporates fluorescently labeled dideoxyribo-nucleoside triphosphates. In the multiprimer assay, several primers containing different 3'-terminal nucleotides overlapping the variable nucleotide in DNA are used. The polymorphic nucleotide is identified according to the primer that is extended. The methods were compared for diagnosis of beta-thalassemia mutations. Isothermal amplification of the fluorescent signal was achieved by performing both assays at elevated temperature. Anthrax toxin genes were identified in a model system using this amplification method.

Polymorphism analysis and gene detection by minisequencing on an array of gel-immobilized primers