Abstract: The present teachings disclose methods for evaluation of sequence information to characterize putative heterozygous indel mutations. The mutation analysis methods utilize sequence and trace information to identify mixed-base presence resulting from allelic differences. These methods may be applied to identify and resolve single nucleotide polymorphisms, insertions, deletions, and other mutational events.

Abstract: The present invention relates generally to nucleobase polymer functionalizing reagents, to mobility-modified sequence-specific nucleobase polymers, to compositions comprising a plurality of mobility-modified sequence-specific nucleobase polymers, and to the use of such polymers and compositions in a variety of assays, such as, for example, for the detection of a plurality of selected nucleotide sequences within one or more target nucleic acids. The mobility-modifying polymers of the present invention include phosphoramidite reagents which can be joined to other mobility-modifying monomers and to sequence-specific oligonucleobase polymers via uncharged phosphate triester linkages. Addition of the mobility-modifying phosphoramidite reagents of the present invention to oligonucleobase polymers results in unexpectedly large effects the mobility of those modified oligonucleobase polymers, especially upon capillary electrophoresis in non-sieving media.

Abstract: The present teachings relate to DNA polymerases that have an F667Y mutation as defined with respect to Taq DNA polymerase and exhibit reduced discrimination against labeled nucleotides into polynucleotides. The teachings also include kits comprising the subject DNA polymerases and numerous methods of using the subject DNA polymerases, including uses for chain termination sequencing and PCR. The present teachings relate to DNA polymerases that have an F667Y mutation as defined with respect to Taq DNA polymerase and exhibit reduced discrimination against labeled nucleotides into polynucleotides. The teachings also include kits comprising the subject DNA polymerases and numerous methods of using the subject DNA polymerases, including uses for chain termination sequencing and PCR.

Abstract: Disclosed herein a reversible terminator nucleotides and methods of use.

Abstract: The invention is directed to a method and device for simultaneously testing a sample for the presence, presence, and/or amounts of one or more of a plurality of selected analytes. The invention includes, in one aspect, device for detecting or quantitating a plurality of different analytes in a liquid sample. Each chamber may include analyte-specific reagent effective to react with a selected analyte that may be present in the sample, and detection means for detecting the signal. Also disclosed are methods utilizing the device.

Abstract: A vortex mixer and method for forming an emulsion wherein the mixer is adapted to form an emulsion with a desired droplet size and having a desired volume. The vortex mixer provides improved uniformity in emulsion preparation and may be used to create multiple emulsions simultaneously.

Abstract: Biological reagent carrier devices and methods are disclosed, which employ RFID techniques to associate information with biological reagents.

Abstract: A method for calibrating temperature can include cycling temperatures of a set of wells, wherein each well of the set comprises a sample with a spectrally distinguishable species. The method can further include measuring a signal from the spectrally distinguishable species for each well at a temperature during a first temperature cycle, and calibrating the temperatures for measuring the signal from each well during subsequent temperature cycles.

Abstract: Assemblies comprising nanoparticles and chemiluminescent substrates such as dioxetanes are provided. The assemblies can be used in assays to detect the presence and/or amount of a single analyte or multiple analytes in a sample. Methods of making the assemblies are also described.

Abstract: A thermal cycling device for thermally cycling samples of biological material contained in a microcard having a top and bottom surface. The thermal cycling device can include a sample block having an upper surface configured for engaging the bottom surface of a microcard, a vacuum device, and a temperature control system operatively connected with the sample block. The upper surface of the sample block may include a plurality of channels, the channels defining spaces between the sample block and the bottom surface of a microcard that may be positioned thereon. The vacuum device may be in fluid communication with the sample block for drawing gas out of the spaces defined by the channels in the sample block. The vacuum device may be configured for substantially maintaining a vacuum between the sample block and microcard so that a retention force is imparted on the microcard to urge the microcard toward the sample block.

Abstract: Disclosed are systems and methods for identifying and quantitating the presence of one or more DNA species in a sample population through PCR amplification. DNA species quantitation includes a determination of a threshold fluorescence value used in the assessment of the PCR amplification reaction. Various embodiments of the present invention incorporate an enhancement function useful in selecting appropriate threshold fluorescence values and facilitate the determination of DNA concentrations by quantitative PCR based methodologies.

Abstract: Disclosed are systems and methods for identifying and quantitating the presence of one or more DNA species in a sample population through PCR amplification. DNA species quantitation includes a determination of a threshold fluorescence value used in the assessment of the PCR amplification reaction. Various embodiments of the present invention incorporate an enhancement function useful in selecting appropriate threshold fluorescence values and facilitate the determination of DNA concentrations by quantitative PCR based methodologies.

Abstract: The present invention relates to the enrichment of specific target sequences. Enrichment can be achieved through the formation of a heteroduplex that includes the specific target sequence and then the specific cleavage of the heteroduplex. A binding moiety is then added to the cleaved heteroduplex, allowing for the subsequent manipulation of the specific target sequence in the heteroduplex.

Abstract: The present invention is a method for performing a mass spectrometric analysis of analytes in a complex mixture. In particular, samples containing unknown analytes are analyzed by MS/MS to identify portions of a molecule of interest that has been labeled with a selected isotope. Ionization and detection identify a characteristic isotope shift in real time based on a selective precursor ion scan that in turn identifies precursor masses that also contain the isotopic shift. From the precursor ion scan, precursor masses are identified for further mass spectrometric analyses. The method of the invention is preferably performed in real time such that the precursor ion scan simultaneously identifies target precursor ions and identifies precursor masses for further analyses.

Abstract: Disclosed are systems and methods for identifying and quantitating the presence of one or more DNA species in a sample population through PCR amplification. DNA species quantitation includes a determination of a threshold fluorescence value used in the assessment of the PCR amplification reaction. Various embodiments of the present invention incorporate an enhancement function useful in selecting appropriate threshold fluorescence values and facilitate the determination of DNA concentrations by quantitative PCR based methodologies.

Abstract: An injection system including a first electrical circuit for concentration of an analyte and a second electrical circuit for injection of the concentrated analyte into an electrophoretic device is described, as well as methods of using the injection system.

Abstract: Microfluidic devices, assemblies, and systems are provided, as are methods of manipulating micro-sized samples of fluids. Microfluidic devices having a plurality of specialized processing features are also provided.

Abstract: Methods and systems for processing signals to minimize the effects of dye crosstalk. Deconvolution of multiplexed dye signals can include corrections for residual error determined from experimental measurements. Residual error corrections can account for reaction or assay specific factors and modify the subsequent filtering of signals. Correction values can be determined for specific dye-probe conjugates to minimize dye crosstalk and may be combined with residual error correction to further minimize errors in spectral deconvolution. Apparatus, systems, and computer-readable media can process signals and modify filters based on values obtained using the methods.

Abstract: The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.

Abstract: Dibenzorhodamine compounds having the structure are disclosed, including nitrogen- and aryl-substituted forms thereof. In addition, two intermediates useful for synthesizing such compounds are disclosed, a first intermediate having the structure including nitrogen- and aryl-substituted forms thereof, and a second intermediate having the structure including nitrogen- and aryl-substituted forms thereof, wherein substituents at positions C-14 to C18 taken separately are selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, carboxylic acid, sulfonic acid, —CH2OH, alkoxy, phenoxy, linking group, and substituted forms thereof. The invention further includes energy transfer dyes comprising the dibenzorhodamine compounds, nucleosides labeled with the dibenzorhodamine compounds, and nucleic acid analysis methods employing the dibenzorhodamine compounds.