The present invention describes methods of performing rapid nucleic acid detection using a flow through process. The methods comprise single-step signal amplification and/or a one-step hybridization protocol. Using the flow through hybridization process, the present invention provides a more efficient, faster and less expensive genotyping method. This invention further provides a Single Nucleotide Polymorphism (SNP)-based DNA fingerprinting method for rapid and accurate genotyping, identification as well as DNA analyses of genetic materials from human beings and other different organisms. In addition this invention also discloses devices for rapid and sensitive analysis of target analysts.