Abstract: The subject invention pertains to the rapid amplification and real-time monitoring of nucleic acid sequences at a constant temperature. Specifically, fluorescent or electroactive-labeled loop probes and primers are designed to be specific to identified regions of a target nucleic acid sequences and subsequently amplify and permit the identification of the presence of the target sequence. In this method, a DNA polymerase with no 5? to 3? exonuclease activity is added to extend the primers and probes, while a nicking endonuclease is added to specifically identify the amplified nucleic acid product and cleave the label from the loop probe-extended DNA duplex.

Abstract: The subject invention pertains to methods for the analysis of pooled samples without the need of retesting through the use of oligonucleotide hybridization and target-specific amplification reactions. Specifically, a series of identifier oligonucleotides with different sequence compositions, each corresponding to a distinct sample, are combined into the target template of interest through nucleic acid synthesis. The aforementioned products are pooled together, and the pooled samples are amplified and detected using the probe-based hybridization assay or a size separation module to identify if any of the pool of samples test positive, as well as simultaneously identifying which sample is positive for the targeted sequence.

Abstract: The subject invention pertains to the rapid amplification and real-time monitoring of nucleic acid sequences at a constant temperature. Specifically, fluorescent or electroactive-labeled loop probes and primers are designed to be specific to identified regions of a target nucleic acid sequences and subsequently amplify and permit the identification of the presence of the target sequence. In this method, a DNA polymerase with no 5? to 3? exonuclease activity is added to extend the primers and probes, while a nicking endonuclease is added to specifically identify the amplified nucleic acid product and cleave the label from the loop probe-extended DNA duplex.

Abstract: The present invention provides methods for determining a haplotype or a diplotype in a genetic sample. The method comprises the steps of contacting a probe-complex with the genetic sample, wherein the probe complex comprises at least two probes, hybridizing at least two probes to a polynucleotide sequence, each of which is specific to one of two or more genetic variants, determining the presence or absence of at least one genetic variant by detecting a signal emitted from at least one probe, wherein detection of said signal is indicative of the the presence of a genetic variant, removing or displacing at least one of said probes from said sample, and detecting a change in the signal to determine the haplotype or a diplotype in the genetic sample. Kits for use in the method of the invention are also provided.