Abstract: The present invention provides an array of polymers and methods of forming arrays of polymers by providing a substrate having a first layer including one or more dielectric coatings on a solid support and a second layer including a plurality of polymers disposed on the first layer. The invention also provides methods for forming an array of polymers on a substrate using light-directed synthesis by providing a substrate having a first layer including one or more dielectric coatings on a solid support, derivatizing the first layer by contacting the first layer with a silanation reagent, and a second layer disposed on said first layer wherein the second layer includes functional groups protected with a photolabile protecting group.

Abstract: Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.

Abstract: The present invention provides an array of polymers and methods of forming arrays of polymers by providing a substrate having a first layer including one or more dielectric coatings on a solid support and a second layer including a plurality of polymers disposed on the first layer. The invention also provides methods for forming an array of polymers on a substrate using light-directed synthesis by providing a substrate having a first layer including one or more dielectric coatings on a solid support, derivatizing the first layer by contacting the first layer with a silanation reagent, and a second layer disposed on said first layer wherein the second layer includes functional groups protected with a photolabile protecting group.

Abstract: Devices, systems and methods for separation of magnetic particles with either hand held devices or automated instruments. Specifically, the production of magnetic fields for the separation of the particles within containers such as microtiter plates with a magnetic field that is substantially consistent for each well. Certain embodiments produce a magnetic field that is substantially uniform across each well bottom, while other embodiments produce a magnetic field that is stronger toward the outer region of each well.

Abstract: Compositions and methods for analysis of nucleic acids are disclosed. Targets are hybridized to arrays having features that include pairs of co-localized probes within features. The probe pairs may include a first probe type that is oriented so that the 5? end is free and the 3? end is attached to the support and a second probe type that is oriented so that the 3? end is free for extension and the 5? end is attached to the support. The probes of a feature are complementary to different regions of the same target sequence so they can simultaneously hybridize to a single target with a gap or nick between. The gap may be filled by extension and ligation or ligation.

Abstract: Silanation compositions containing a mixture of two or more silanation reagents, where at least one silanation reagent includes a functional group capable of supporting polymer synthesis and at least one silanation reagent includes no functional group capable of supporting polymer synthesis are useful in modulating the active site density and hydrolytic stability of a surface. These compositions are particularly useful in silanating a surface prior to preparation of a polymer array and provide for increased hybridization results.

Abstract: A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Abstract: The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).

Abstract: Disclosed are cleaning solutions. More particularly, non-toxic solutions of base, water, alcohol and detergent, that effectively and surprisingly eliminate contaminating aliphatic acids in aqueous solutions. When present as a foam or even a contaminating film remaining on various parts and surfaces, aliphatic acid contaminants can be present a large and costly problem in manufacturing operations, cleaning tasks, personal hygiene. The need to remove such contaminants arises in a myriad environments and situations, such as during the manufacture of detergents, pharmaceuticals, consumer products, coring and core analysis, manipulation of oils, fuels, fermentation applications, manufacture of emollients, moisturizers, liquors, foods such as seafood, milk, butter and other dairy products, water processing, paper products, tissue culture, reusable clinical equipment, and the like.

Abstract: Protective groups which may be cleaved with an activatable deprotecting reagents are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments of the instant invention, the activatable deprotecting reagent is a photoacid generator and the protective groups are DMT for nucleic acids and tBOC for amino acids. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.

Abstract: Methods for detecting and optionally quantitating one or more target nucleic acids are provided, in which a surrogate nucleic acid is captured to each target nucleic acid, amplified, and detected. Compositions, kit, and systems related to the methods are also described.

Abstract: Novel methods and kits are disclosed for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences, for example, to discriminating between alleles at polymorphic positions in a genome. Complexity reduction can be accomplished by extension of a capture probes followed by amplification of the extended capture probe using common primers. The capture probes may be locus specific and allele-specific. The amplified sample may be hybridized to an array designed to interrogate the desired fragments for the presence or absence of a polymorphism. In some aspects the methods employ allele-specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele-specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele-specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity.

Abstract: The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker, i.e., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.

Abstract: Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system embodiments are provided. Embodiments are directed to concurrent detection of one or more nucleic acids and one or more proteins. Embodiments also are directed to determining the methylation state of a target sequence. Other embodiments are directed to detection of one or more proteins using DNA barcodes. Compositions, kits, and systems related to the methods are also described.

Abstract: Disclosed are methods, compositions and kits for amplifying signals for detecting the presence, quantity and/or sequence of nucleic acids and proteins, as well as methods, compositions and kits for increasing the number of such targets simultaneously detectable in a sample. Detection may be, for instance, in vivo, in cellulo or in situ. Amplification of signal is achieved by way of hybridization of nucleic acid label probe systems and structures. Increase in target multiplex capacity is achieved by way of varying the type of labels utilized in the nucleic acid label probe system.

Abstract: A system and method for forming encoded microparticles is described. One embodiment includes a method of forming an encoded microparticle, the method comprising: depositing and patterning a plurality of layers on a substrate so as to form a plurality of microparticles, each microparticle comprising a plurality of separate segments aligned along an axis and representing a code; and releasing the microparticles in order to separate the microparticles from the substrate.

Abstract: Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for allelic imbalance, imprinting and imprinting errors.

Abstract: Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes.

Abstract: The invention provides methods and components for assembly of arrays of sensors from modular units containing component sensors of the array. The methods are particularly useful for forming arrays of microarrays. The sensor modules can readily be assembled in different combinations thereby allowing many different modular sensor arrays to be assembled from the same building blocks. Such modular sensor arrays offer advantages of economies of scale for a manufacturer of the modular units and flexibility for an end user in allowing the user to customize the array of sensor according to the user's own needs from a relatively small number of sensor modules provided by the manufacturer.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.