Abstract: The present invention encompasses methods for producing a modified polynucleotide sequence that comprises a (e.g., one or more) phosphorothiolate linkage, methods for determining a polynucleotide sequence comprising a (e.g., one or more) phosphorothiolate linkage, and methods for separating forward and reverse extension products that comprise a (e.g., one or more) phosphorothiolate linkage. The invention also encompasses kits for producing and/or determining the sequence of a modified polynucleotide that comprises a (e.g., one or more) phosphorothiolate linkage.

Abstract: The present invention concerns an isolated siRNA of from about 5 to about 20 nucleotides that mediates RNA interference. Also disclosed are methods of reducing expression of a target gene in a cell comprising obtaining at least one siRNA of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 basepairs in length; and delivering the siRNA into the cell. The siRNAs can be chemically synthesized RNA or an analog of a naturally occurring RNA.

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

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: A camera alignment system that can enable alignment in at least one of three planes and about an axis of at least one of the planes. An alignment mount can mate to a camera and lens. The alignment mount can comprise a mechanism to adjust the camera relative to the lens to that an image plane of the camera aligns with an image plane of the lens in a predetermined orientation. One predetermined orientation can be that the image plane of the camera being parallel to the image plane of the lens.

Abstract: 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.

Abstract: 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.

Abstract: The invention discloses a system and methods for quantitating the presence of nucleic acid sequences by evaluation of amplification data generated using real-time PCR. In one aspect, the methods may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction. The methodology used in the analysis may be readily automated such that subjective user interpretation of the data is substantially reduced or eliminated.

Abstract: Systems and methods are provided that can include a storage and retrieval robot operating under program control to extract a selective number of support beads from a storage or retainment region, for dispensing to titer wells or other vessels for assays and other purposes. According to various embodiments, the storage and retrieval robot can position a capture device over any one or more storage wells containing oligonucleotide or other material support beads, and withdraw or extract those support beads into a collection tube under vacuum pressure or other force. According to various embodiments, a selected number of support beads can be extracted, using a linear motor piston to limit available space for support bead insertion. According to various embodiments, the collected support beads can be dispensed into one or more destination tubes, wells, or other containers, surfaces, vessels, receptacles or mixture containment region, for use in assays or other purposes.

Abstract: The present invention provides novel, water-soluble, red-emitting fluorescent rhodamine dyes and red-emitting fluorescent energy-transfer dye pairs, as well as labeled conjugates comprising the same and methods for their use. The dyes, energy-transfer dye pairs and labeled conjugates are useful in a variety of aqueous-based applications, particularly in assays involving staining of cells, protein binding, and/or analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing.

Abstract: Improved ball mill disruption techniques. In different embodiments, disrupting particles that are not substantially spherical are used. In other embodiments, roughened disrupting particles are used. In other embodiments, larger disrupting particles are used. In each instance, improved disruption can be achieved.

Abstract: 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.

Abstract: A method for selectively recovering nucleic acid from a first cell type in a sample containing cells of at least a first cell type and a second cell type, and a cell suspension medium comprising extracellular impurities, is provided. The method entails combining the sample with particles responsive to a magnetic field in a vessel, the magnetic particles having the ability to sequester the cells from the cell suspension medium upon application of a magnetic field; exposing the vessel to a magnetic field for a time sufficient to cause sequestration of the cells by the particles; removing the impurities-containing cell suspension medium from the vessel while retaining the cells; lysing selectively cells of the first cell type; and isolating the nucleic acid from the lysed cells. Methods for recovering nucleic acid from the second cell type are also provided.

Abstract: 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.

Abstract: 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.

Abstract: A microfluidic manipulation system is provided that includes a blade for manipulating deformable material and at least one movable support that is capable of moving the blade into contact with a microfluidic device including a deformable feature. When the microfluidic device is operatively held by a holder, a movable support can position the distal end of the blade relative to the microfluidic device and move the contact tip surface of the blade such that it deforms the deformable feature.

Abstract: Ligation-enhanced nucleic acid detection assay embodiments for detection of RNA or DNA are described. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection. The assay embodiments are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. Very little background amplification is observed and as few as 1000 copies of target nucleic acid can be detected. Method embodiments are particularly adept for detection of RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. Heavily degraded and cross-linked nucleic acids of compromised samples, in which classic quantitative real time PCR assays typically fail to adequately amplify signal, can be reliably detected and quantified.

Abstract: An apparatus and methods are provided for heating and sensing the temperature of a chemical reaction chamber without direct physical contact between a heating device and the reaction chamber, or between a temperature sensor and the reaction chamber. A plurality of chemical reaction chambers can simultaneously or sequentially be heated independently and monitored separately.