DNA sequencing by sequential addition/incorporation of non 3’capped and fluorescently labeled nucleotides. Each incorporation of individual nucleotides (A, or T or G or C) are separated by a wash. After all incorporation using all four bases, the substrate is imaged then the dyes are cleaved, and the following cycle of incorporations, washes, imaging and cleave is resumed.

DNA sequencing by sequential addition/incorporation of non 3’capped and fluorescently labeled nucleotides. Each incorporation of individual nucleotides (A, or T or G or C) are separated by a wash. After all incorporation using all four bases, the substrate is imaged then the dyes are cleaved, and the following cycle of incorporations, washes, imaging and cleave is resumed.

An instrument is provided that can monitor nucleic acid sequence amplification reactions, for example, PCR amplification of DNA and DNA fragments. The instrument includes a multi-notch filter disposed along one or both of an excitation beam path and an emission beam path. Methods are also provided for monitoring nucleic acid sequence amplifications using an instrument that includes a multi-notch filter disposed along a beam path.

Apparatus and method for detecting analyte in a reaction mixture comprising an internal control. The invention is illustrated using amplification and detection of nucleic acids, where the amplification reaction comprises an exogenous internal control. Magnitude of the detection signal serves as the variable for identifying invalid trials, identifying valid trials that are negative for analyte, and identifying trials that are positive for analyte. Detection of a signal indicating probe hybridization can be used for assigning the presence or absence of analyte nucleic acid in validated reactions using only a single detectable label, and without distinguishing the proportion of signal contributed by internal control probe binding, and analyte probe binding.

Apparatus and method for detecting analyte in a reaction mixture comprising an internal control. The invention is illustrated using amplification and detection of nucleic acids, where the amplification reaction comprises an exogenous internal control. Magnitude of the detection signal serves as the variable for identifying invalid trials, identifying valid trials that are negative for analyte, and identifying trials that are positive for analyte. Detection of a signal indicating probe hybridization can be used for assigning the presence or absence of analyte nucleic acid in validated reactions using only a single detectable label, and without distinguishing the proportion of signal contributed by internal control probe binding, and analyte probe binding.

This invention provides a method of quantifying chimeric DNA in a cell-free DNA sample.

This invention provides a method of quantifying chimeric DNA in a cell-free DNA sample.

Provided herein are methods for determining the presence of a mutant of target polynucleotides in a sample solution by contacting the sample solution and a reference solution containing the target nucleotide with identical probe sets and then comparing the hybridization intensities of corresponding probes of the probe sets. The probes provide a varying complementarity to the target sequence so that a range of hybridization intensities for the hybridization between the target polynucleotide and the probes is covered.

Provided herein are methods for determining the presence of a mutant of target polynucleotides in a sample solution by contacting the sample solution and a reference solution containing the target nucleotide with identical probe sets and then comparing the hybridization intensities of corresponding probes of the probe sets. The probes provide a varying complementarity to the target sequence so that a range of hybridization intensities for the hybridization between the target polynucleotide and the probes is covered.

According to the present teachings, methods and compositions are provided that utilize at least one reference dye of formula (I): ##STR00001##
In some embodiments, a method comprises measuring a detection signal of a reporter dye and at least one reference dye of formula (I). In some embodiments, a composition comprises a reference dye of formula (1), a buffer, a selection of nucleotides and a protein.