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APPLIED BIOSYSTEMS, LLC

APPLIED BIOSYSTEMS, LLC Patent applications
Patent application numberTitlePublished
20120122217METHODS AND COMPOSITIONS FOR REDUCING TARGET GENE EXPRESSION USING COCKTAILS OF siRNAS OR CONSTRUCTS EXPRESSING siRNAS - The present invention concerns methods and compositions involving the production or generation of siRNA mixtures or pools capable of triggering RNA-mediated interference (RNAi) in a cell. Compositions of the invention include kits that include reagents for producing or generating siRNA pools. The present invention further concerns methods using polypeptides with RNase III activity for generating siRNA mixtures or pools that effect RNAi, including the generation of a number of RNA molecules to the same target gene.05-17-2012
20120055793Emulsions of Ionic Liquids - The present teachings provide emulsions using ionic liquids for separation of biomolecules and related methods, compositions, and devices.03-08-2012
20120015832METHODS, PANELS OF IDENTIFICATION MARKERS, AND KITS FOR IDENTIFYING FORENSIC SAMPLES - Methods for identifying forensic samples using panels of markers and gene expression profiling, including without limitation, mRNA profiling, miRNA profiling, or both, are disclosed. Panels of markers for identifying certain tissue samples and certain body fluid samples are also disclosed. Kits for expediting performance of certain of the disclosed methods are provided.01-19-2012
20120015370MULTIPLEX COMPOSITIONS AND METHODS FOR QUANTIFICATION OF HUMAN NUCLEAR DNA AND HUMAN MALE DNA AND DETECTION OF PCR INHIBITORS - The invention relates to a method for simultaneous quantification of human nuclear DNA and human male DNA in a biological sample while also detecting the presence of PCR inhibitors in a single reaction. The multiplex quantification method also provides a ratio of human nuclear and male DNA present in a biological sample. Such sample characterization is useful for achieving efficient and accurate results in downstream molecular techniques such as genotyping.01-19-2012
20110318811COMPOSITIONS AND METHODS OF USING A SYNTHETIC DNASE I - Compositions and method for making and using a synthetic bovine DNase I are disclosed. More particularly, the sbDNase I of the present invention is a versatile enzyme that cleaves DNA nonspecifically to release 5′-phosphorylated nucleotides. The sbDNase I molecules of the present invention find particular use in a wide range of molecular biology applications, including: degradation of contaminating DNA after RNA isolation; RNA clean-up prior to, or in conjunction with, RT-PCR after in vitro transcription; identification of protein binding sequences on DNA (DNase I footprinting); prevention of clumping when handling cultured cells; tissue dissociation and creation of fragmented DNA for in vitro recombination reactions.12-29-2011
20110311979METHOD FOR DETECTING THE PRESENCE OF A SINGLE TARGET NUCLEIC ACID IN A SAMPLE - A miniaturized assembly is provided whereby a fluid sample can be divided into a plurality of sample portions in retaining wells and the sample fluid can be displaced from open ends of the wells while simultaneously being sealed in the wells. A method of dividing a fluid sample using the assembly is also provided.12-22-2011
20110287436Detection Of Analytes And Nucleic Acids - Methods of detecting at least one analyte and at least one nucleic acid in a sample are provided. Reagents for carrying out the methods are also provided.11-24-2011
20110278474Axial Illumination for Capillary Electrophoresis - System and method for fluorescent light excitation and detection from samples to enhance the numerical aperture and/or reduce the cross-talk of the fluorescent light.11-17-2011
20110262898Compositions, Methods, and Kits for Amplifying Nucleic Acids - The present teachings are directed to compositions, methods, and kits for amplifying target nucleic acids while reducing non-specific fluorescence and undesired amplification products, sometimes referred to as secondary amplification products or spurious side-products. The enzyme inhibitors disclosed herein comprise a nucleotide sequence and at least one quencher. Complexes comprising an enzyme inhibitor associated with an enzyme, wherein at least one enzymatic activity of the enzyme is inhibited, are also provided. Methods for amplifying a target nucleic acid while reducing undesired amplification products are disclosed, as are methods for reducing non-specific fluorescence. Kits for expediting the performance of certain disclosed methods are also provided.10-27-2011
20110257046Emulsion PCR And Amplicon Capture - Compositions and methods of use are disclosed for clonally amplifying target polynucleotide sequences in solution and attaching the amplicons to a surface by activation of a masked binding moiety.10-20-2011
20110251083Multiplexed Amplification of Short Nucleic Acids - The present teachings provide methods, compositions, and kits for reverse transcribing and amplifying small nucleic acids such as micro RNAs. High levels of multiplexing are provided by the use of a zip-coded stem-loop reverse transcription primer, along with a PCR-based pre-amplification reaction that comprises a zip-coded forward primer. Detector probes in downstream decoding PCRs can take advantage of the zip-code introduced by the stem-loop reverse transcription primer. In some embodiments, further amplification is achieved by cycling the reverse transcription reaction. The present teachings also provide compositions and kits useful for performing the reverse transcription and amplification reactions described herein.10-13-2011
20110250402LOCALIZATION OF NEAR-FIELD RESONANCES IN BOWTIE ANTENNAE: INFLUENCE OF ADHESION LAYERS - A plasmonic nanostructure for enhanced light excitation is disclosed. The plasmonic nanostructure includes a substrate, an adhesion layer disposed on top of the substrate, a surface plasmon resonance layer, and a cavity that extends into the surface plasmon resonance layer. The surface plasmon resonance layer is configured to concentrate an applied plasmon field to a bottom portion of the cavity.10-13-2011
20110223680Microfluidic Device and Material Manipulating Method Using Same - Microfluidic devices for manipulating relatively dense materials, such as colloidal rod particles, are provided. Microfluidic devices for separating a denser first material from a less-dense second material are provided. Methods of manipulating a relatively dense first material, for example, colloidal rod particles, and separating the first material from a less-dense second material, are provided. Methods of marking samples or sample components with relatively dense materials, are also provided.09-15-2011
20110186432BUFFERS FOR ELECTROPHORESIS AND USE THEREOF - Various embodiments provide, for example, buffer compositions and/or sieving formulations useful in connection with electrophoresis instruments, such as capillary electrophoresis (CE) devices. In various embodiments, a buffer composition can include Bis-Tris, TAPS and/or TAPSO, and, optionally, a chelating agent, such as EDTA. Methods of separating samples containing bio-molecules, such as DNA or RNA, are also described.08-04-2011
20110174623Concentration and Purification of Analytes Using Electric Fields - Embodiments of a device and method are described which provide for concentration and purification of analytes, e.g., polynucleotides, in channel devices using AC and DC electric fields.07-21-2011
20110159305Intermediates And Methods For Forming Passivated Surfaces On Oxide Layers And Articles Produced Thereby - Intermediates and methods for forming passivated surfaces on oxide layers and articles produced thereby are described. Hydroxyl or hydroxide groups on the oxide surfaces are reacted with a metal reagent of the formula Y(L-Pol)06-30-2011
20110143343Methods and Kits for Methylation Detection - Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.06-16-2011
20110123985COLUMN ENRICHMENT OF PCR BEADS COMPRISING TETHERED AMPLICONS - An enrichment module and method are provided for enriching a population of templated beads and separating them from non-templated beads. The method can include hybridizing a templated bead with an enrichment bead to form a complex, trapping the complex in a filtration medium, washing non-templated beads through the filtration medium while retaining the complex, and then eluting the templated bead from the complex. The module can include a column for enrichment and filtration material exhibiting desired size-exclusion properties.05-26-2011
20110115633METHODS AND SYSTEMS FOR USING RFID IN BIOLOGICAL FIELD - Biological reagent carrier devices and methods are disclosed, which employ RFID techniques to associate information with biological reagents.05-19-2011
20110096620DEVICES, SYSTEMS, AND METHODS FOR PREPARING EMULSIONS - 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.04-28-2011
20110046359REVERSIBLE TERMINATOR NUCLEOTIDES AND METHODS OF USE - Disclosed herein a reversible terminator nucleotides and methods of use.02-24-2011
20110003277Dioxetane-Nanoparticle Assemblies For Energy Transfer Detection Systems, Methods Of Making The Assemblies, And Methods Of Using The Assemblies in Bioassays - 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.01-06-2011
20100311176METHOD OF MASS ANALYSIS OF TARGET MOLECULES IN COMPLEX MIXTURES - 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.12-09-2010
20100300879DUAL ELECTRODE INJECTION OF ANALYTE INTO A CAPILLARY ELECTROPHORETIC DEVICE - 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.12-02-2010
20100298172MICROFLUIDIC SIZE-EXCLUSION DEVICES, SYSTEMS, AND METHODS - 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.11-25-2010
20100292457Dye-labeled ribonucleotide triphosphates - 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.11-18-2010
20100279305COMPOSITIONS, METHODS, AND KITS FOR DETECTING RIBONUCLEIC ACID - Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.11-04-2010
20100266177SIGNAL PROCESSING BY ITERATIVE DECONVOLUTION OF TIME SERIES DATA - A signal processing method is provided and involves iteratively deconvoluting at least one digital signal data set with respect to time. A signal processor is also provided that can perform a signal processing method for iteratively deconvoluting at least one digital signal data set. Also provided is an instruction set readable by a machine, tangibly embodying a program of instructions executable by a machine to perform a signal processing method of iteratively deconvoluting at least one digital signal data set. Also provided is a data set readable by a machine, tangibly embodying a data set computed by a signal processing method for iteratively deconvoluting at least one digital signal data set.10-21-2010
20100262379Sequencing System With Memory - The present teachings provide a device including a memory. According to various embodiments, the memory is readable, writable, and rewritable. The present teachings further provide processing stations, e.g., for carrying out electrophoresis, per, genetic analysis, sample preparation, and/or sample cleanup, etc., that are capable of reading from and/or writing/rewriting to such memory.10-14-2010
20100261230SYSTEM COMPRISING DUAL-SIDED THERMAL CYCLER AND EMULSION PCR IN POUCH - A system and method are provided for large volume sample amplification adaptable for use with conventional PCR-based reactions as well as emulsion-based PCR reactions. A sample is retained in a pouch or flexible bag which permits bulk PCR amplification with efficient heat-transfer properties. For applications involving emulsion-based PCR amplification, the system and method provide improved uniformity in emulsion amplification and can be used to amplify large or small volume emulsions rapidly and reproducibly.10-14-2010
20100261229SYSTEM AND METHOD FOR PREPARING AND USING BULK EMULSION - An emulsion generation apparatus and method for forming an emulsion are provided wherein a customized impeller design is adapted to form an emulsion with a desired droplet size that defines a desired volume. The emulsion generation apparatus provides improved uniformity in emulsion preparation and may be used to create large or small volume emulsions rapidly and reproducibly. A system and method are also provided for large volume sample amplification adaptable for use with conventional PCR-based reactions as well as emulsion-based PCR reactions and other reactions. For applications involving emulsion-based PCR amplification, the system and method provide improved uniformity in emulsion amplification and can be used to amplify large or small volume emulsions rapidly and reproducibly.10-14-2010
20100233763DUAL-SIDED THERMAL CYCLER - A device, system, and method are provided for thermally treating a fluid processing device. According to various embodiments, a system is provided that can include a thermal device and a fluid processing device holder. The thermal device can include a first block having a thermal conductivity greater than 0.5 Watt per centimeter Kelvin (W/cm·K), a second block having a thermal conductivity greater than 0.5 W/cm·K, and a heat-pump device disposed between the first block and the second block. The heat-pump device can transfer thermal energy from at least one of the first block and the second block to the other of the first block and the second block. The fluid processing device holder can hold a fluid processing device in a heat-transfer position with respect to the first block and the second block. The fluid processing device can be a microfluidic device.09-16-2010
20100222414SiRNA Sequence-Independent Modification Formats for Reducing Off-Target Phenotypic Effects in RNAi, and Stabilized Forms Thereof - Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.09-02-2010
20100221790Analyzing Messenger RNA and Micro RNA in the Same Reaction Mixture - The present teachings provide methods, compositions, and kits for performing primer extension reactions on at least two target polynucleotides in the same reaction mixture. In some embodiments, a reverse transcription reaction is performed on a first target polynucleotide with a hot start primer comprising a self-complementary stem and a loop, and extension products form at high temperatures but extension products form less so at low temperatures since the self-complementary stem of the hot start primer prevents hybridization of the target specific region to the target. However, non-hot start primers with free target specific regions can hybridize to their corresponding targets at the low temperature and extension can happen at the low temperature.09-02-2010
20100216146Methods and Kits for Hybridizing Multiple PNA Probe Panels to Nucleic Acid Samples - Described herein are methods and kits that employ multiple probe sets in combination with sequential steps of hybridization analysis for multiplex analysis and/or detection of nucleic acids having one or more distinguishable target sequences.08-26-2010
20100203545Two-color Real-time/End-point Quantitation of MicroRNAs (miRNAs) - The present invention is directed to methods, reagents, kits, and compositions for detecting target polynucleotide sequences, especially small target polynucleotides such as miRNAs, between two samples. A pair of linker probes can be employed in two different reactions to query a particular species of target polynucleotide. A pair of detector probes, a single forward primer specific for the target polynucleotide, and a reverse primer can be employed in an amplification reaction to query the difference in expression level of the target polynucleotide between the two samples. In some embodiments a plurality of small miRNAs are queried with a plurality of linker probes. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.08-12-2010
20100196887COMPOSITIONS AND METHODS FOR MULTIPLEX ANALYSIS OF POLYNUCLEOTIDES - Provided herein are compositions and methods for the multiplex analysis and/or detection of polynucleotides having one or more distinguishable target sequences. The methods employ signal-quencher probe pairs having specific relative differential thermal melting temperatures that permit the detection of one or more target sequences on one or more polynucleotides.08-05-2010
20100184159Compositions, Methods, and Kits for Selective Amplification of Nucleic Acids - The current teachings are directed to compositions, methods, and kits for selectively amplifying and for detecting target sequences. In some embodiments, a circularizable probe and/or a probe pair are disclosed for selectively amplifying target sequences. Methods for selectively amplifying target sequences are also disclosed, as are methods for detecting selectively amplified target sequences. Certain embodiments of the disclosed methods comprise a circularizable probe, a probe pair, comprising a first probe and a second probe, or both. In certain embodiments, a multiplicity of different circularizable probes, a multiplicity of different probe sets, or a multiplicity of different circularizable probes and a multiplicity of different probe sets are provided to selectively amplify or to detect a multiplicity of different target sequences, typically in a multiplex reaction. According to certain disclosed methods, surrogates of the target sequences are selectively amplified, including without limitation ligated probes, first amplification products, second amplification products, or combinations thereof. In some embodiments, selectively amplified target sequences or their surrogates are detected, directly or indirectly, indicating the presence of the corresponding target sequence. Kits to facilitate the performance of the disclosed methods are also provided.07-22-2010
20100178691Systems, Methods, and Apparatus for Single Molecule Sequencing - An embodiment generally relates to a system for analysis of an analyte. The system can include a transparent substrate. The system also includes an excitation light source configured to induce an evanescent wave excitation of a fluorescently labeled molecule near the access to the transparent substrate and a detector for detecting the fluorescently labeled molecule.07-15-2010
20100129802Method of Sequencing a Genome - A method and computer-program product for sequencing nucleic acid sequences using restriction fragment maps derived from end-sequenced nucleotide fragments. The initial nucleotide sequence can be processed to form a shot-gun-data set. The present teachings employ a technique called Restriction Site Shotgun Sequencing (RSSS.) It can reduce the amount of overlap required between fragment ends while still producing a good assembly. A decrease in overlap can be achieved by using additional information in the fragments to assist in determining that two fragments overlap.05-27-2010
20100126254Method for Screening Urine for Organic Acids - The present teachings relate to systems and screening methods for measuring organic acids in urine samples.05-27-2010
20100112708Methods and Mixtures Pertaining to Analyte Determination Using Electrophilic Labeling Reagents - This invention pertains to methods, mixtures, kits and/or compositions for the determination of analytes by mass analysis using unique labeling reagents or sets of unique labeling reagents. The labeling reagents can be isomeric or isobaric and can be used to produce mixtures suitable for multiplex analysis of the labeled analytes.05-06-2010
20100112683Thermal Cycler for Automatic Performance of the Polymerase Chain Reaction with Close Temperature Control - A thermal cycler for automatic performance of the polymerase chain reaction is provided. The thermal cycler comprises a heater control that provides close temperature control of the reaction. 05-06-2010
20100105040MICROFLUIDIC SYSTEMS INCLUDING POROUS POLYMER ELECTRODES - Microfluidic devices that incorporate a porous polymer electrode assemblies, including microfluidic device useful for detection of nucleic acids, as well as methods of using the microfluidic devices.04-29-2010
20100103416DNA Sequencing System - An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector.04-29-2010
20100096548SPECTRAL CALIBRATION OF FLUORESCENT POLYNUCLEOTIDE SEPARATION APPARATUS - The invention relates to methods, compositions, and systems for calibrating a fluorescent polynucleotide separation apparatus. One aspect of the invention is multiple color calibration standards and their use. A multiple color calibration standard is a mixture of at least two polynucleotides of different length, wherein each of the polynucleotides is labeled with a spectrally distinct fluorescent dye. Another aspect of the invention is to produce total emission temporal profiles of multiple color calibration standards for use in calibrating fluorescent polynucleotide separation apparatus. The peaks corresponding to the fluorescently labeled polynucleotides in the total emission temporal profile may be detected using a peak detector that is driven by changes in the slopes of the total emission temporal profile. Calibration of fluorescent polynucleotide separation apparatus, with various embodiments of the methods of the invention, includes the step of identification of the labeled polynucleotides of the multiple color calibration standards. The process of spectral calibration of a fluorescent polynucleotide separation apparatus using a multiple color calibration standard may include the step of the estimating (extracting) of the dyes' reference spectra, using information from the peak detection process performed on the total emission temporal profile. Other aspects of the invention include systems for separating and detecting fluorescently labeled polynucleotides, wherein the system is designed for spectral calibration in accordance with the subject calibration methods employing multiple color calibration standards. Another aspect of the invention is methods and compositions for detecting the flow of electrical current through a separation channel of a fluorescent polynucleotide separation apparatus. These methods and compositions employ monitoring dyes. Monitoring dyes are fluorescent dyes that are spectrally distinct from the dye on the polynucleotide intended to convey genetic information, e.g., fluorescent polynucleotide sequencing reaction products.04-22-2010
20100092867Porous Polymer Electrodes - Porous polymer electrode assemblies are useful in the detection or quantification of a variety of analytes. By preparing a porous monolith, and applying a conductive polymer to the monolith, a porous matrix is prepared that combines favorable conductive properties, by virtue of the presence of the conductive polymer, with the porous character of the underlying monolith. The resulting porous electrode can be used for qualitative or quantitative analysis, and the capture and/or release of selected charged materials, such as nucleic acids. The pores of the electrode matrix may also be filled with nonconductive material, yielding electrodes having a plurality of discrete conductive surfaces.04-15-2010
20100022022FLUOROGENIC HOMOGENEOUS BINDING ASSAY METHODS AND COMPOSITIONS - Disclosed are binding substrate compositions, methods and kits useful for, among other things, detecting and/or characterizing binding interactions between molecules of interest.01-28-2010
20100022001Cationic Liposomes And Method of Use - Highly efficient cationic liposomes are provided as a system for the delivery to cells of agents or compounds, such as, compounds capable of silencing a target protein and enzyme substrates. The cationic liposomes can be used in methods of detecting the inhibition activity or apparent activity of a target protein in a cell, and methods of identifying a protein associated with a pathway, such as, a signal transduction pathway in a cell.01-28-2010
20090325277Thermal Device, System, and Method, for Fluid Processing Device - A device, system, and method are provided for thermally treating a fluid processing device. According to various embodiments, a system is provided that can include a thermal device and a fluid processing device holder. The thermal device can include a first block having a thermal conductivity greater than 0.5 Watt per centimeter Kelvin (W/cm·K), a second block having a thermal conductivity greater than 0.5 W/cm·K, and a heat-pump device disposed between the first block and the second block. The heat-pump device can transfer thermal energy from at least one of the first block and the second block to the other of the first block and the second block. The fluid processing device holder can hold a fluid processing device in a heat-transfer position with respect to the first block and the second block. The fluid processing device can be a microfluidic device.12-31-2009
20090275117SLIP COVER FOR HEATED PLATEN ASSEMBLY - A heated platen assembly for use in a biological testing device is disclosed having a heated platen defining a plurality of optical openings configured to permit radiation to pass through the heated platen, a light transmissive slip cover configured to cover at least one of the plurality of optical openings, and means for retaining the slip cover over the at least one of the plurality of optical openings.11-05-2009
20090141272Optical instrument comprising multi-notch beam splitter - 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.06-04-2009

Patent applications by APPLIED BIOSYSTEMS, LLC