Abstract: An apparatus is disclosed for use in solid-phase chemical synthesis procedures. The apparatus allows the separation of a cleaved product from the solid-phase used to make the product, and subsequent removal of the solid-phase from the apparatus. The apparatus allows the cleaved product to be concentrated within the apparatus without transfer to another device.

Abstract: The invention teaches the use of an addressable nanoscale device to create a programmable substrate useful in selectively attracting proteins, nucleating protein crystals and growing protein crystals of a size amenable to diffraction analysis. Further taught is the use of nanoscale assemblies to create charge patterns, where such charge patterns are useful in purifying, nucleating or crystallizing protein molecules. Charge extension moieties, including water, are taught. The invention provides rapid and efficient identification, purification and detection of proteins and protein-related complexes.

Abstract: Methods and devices are disclosed for microarray analysis. In one embodiment a method is disclosed for processing a non-standard size slide having an array of chemical compounds attached to a surface of the slide. A sample is exposed to the surface of the non-standard size slide wherein components in the sample bind to the chemical compounds on the surface of the slide. The sample and the slide are incubated under conditions for carrying out the binding reactions, and the surface of the non-standard size slide is examined for the results of the binding reactions. Prior to the exposing step or the incubating step or the examining step, the non-standard size slide is placed into a slide holder comprising a slide-holding section a slide-holding section adapted to dispose the non-standard size slide to a processing instrument in a manner similar to that for a standard size slide. The non-standard size slide may also include an identifier such as a bar code.

Abstract: The present invention relates to methods of immobilizing membrane-associated molecules within a sol-gel matrix. The membrane-associated molecule is embedded in the bilayer of a liposome. The molecule-liposome assembly remains functionally intact when it is immobilized within a protein and membrane-compatible sol-gel derived from polyol silane precursors or sodium silicate. The activity and stability of the entrapped membrane-associated molecule was significantly improved in macroporous silica.

Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.

Abstract: Modified surfaces, substrates, and methods of producing and using such substrates and surfaces are provided. The substrates and surfaces provide either non-reactive surfaces or low density reactive groups, preferably on an otherwise non-reactive surface, for use in different applications including single molecule analyses.

Abstract: The present invention relates to a method and to a microarray for detecting herpesviruses. The invention provides new primers and oligonucleotides for detecting herpesviruses, in particular herpesviruses selected from the group comprising HSV-1, HSV-2, CMV, EBV, VZV, HHV-6A, HHV-6B and HHV-7. By using the method of the invention several different herpesviruses can be detected simultaneously from the same biological sample.

Abstract: Methods, systems and substrates for providing molecules of interest in selected regions of substrates for use in analytical operations. Methods employ mechanical methods of applying force for the removal of molecules of interest from other than the desired locations on a substrate.

Abstract: This invention provides a new generalized method for screening, identifying, selecting and designing symmetry-based compounds useful for blocking pores or prepores formed by pathogenic agents including bacteria, viruses, fungi, parasites, and other proteins capable of forming pores on cellular membranes as a step in the pathogenic mechanism of the agent. Also provided are pharmaceutical compositions, filtering devices, and treatment methods useful for preventing, delaying, or otherwise altering the pathogenesis of the pore-forming pathogenic agents.

Abstract: Disclosed are efficient methods for loading amino derivatives onto trityl chloride resins and for cleaving chemically modified amino derivatives from trityl chloride resins. Methods for making a library of discrete chemically modified amino derivatives also disclosed.

Abstract: Methods and apparatuses for generating microscopic patterns of macromolecules such as proteins on a solid surface are described. Pulsed laser light is used to alter surface portions of a solid surface substrate in a predetermined pattern, by removing macromolecules from surface portions of the substrate where the light is focused. The same wavelength light at lower intensity can be used to visualize the removal by its reflection from the specimen surface along the path to the detector. Select macromolecules introduced to the substrate selectively adhere to select surface portions, thereby depositing macromolecules in the predetermined pattern on the solid surface.

Abstract: The invention relates to a method of preparing a library of template polynucleotides with uniform sequence representation and to use of a library of templates prepared using this method for solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends, which contains even representation of all the fragments present in a starting sample of nucleic acid before fragmentation. The invention is especially applicable to the preparation of short insert libraries, where the sample fragments are less than 150 base pairs in length.

Abstract: A nanoparticle probe is attached to a substrate to capture targets. The nanoparticle probe includes a specific binding agent that specifically binds to a target biomolecule. The biomolecule can be associated with a cell, for example expressed on the cell's surface, such that the cell is bound to the probe immobilized on the substrate. The nanoparticle probes can be applied to the substrate in a layer, for example in the form of a spot, and multiple spots can be applied to the substrate to form patterns or arrays of the spots on the substrate. The nanoparticle probe presents a binding surface on which oriented specific binding agents (such as antibodies or nucleic acids) can be attached. In particular examples the nanoparticle is spaced slightly from the substrate, for example by a linker, to provide a probe with improved contact with a liquid in which target biomolecules or cells are suspended.

Abstract: The invention provides a microarray and methods for producing a protein microarray. The array comprises multiple nucleic acid molecules immobilized on a substrate, each comprising (i) a protein-binding domain and (ii) a nucleic acid sequence encoding a fusion protein comprising a polypeptide of interest and a DNA-binding protein that binds the protein-binding domain, and one or more fusion proteins produced from the multiple nucleic acid molecules. Each fusion protein is immobilized on the substrate via binding to a nucleic acid sequence comprising the protein-binding domain present on the nucleic acid molecule from which the fusion protein is produced or on the substrate. The invention also provides a method of analyzing protein interactions with, for example, other proteins, lipids and drugs.

Abstract: The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are constructs that include pairs of target sequences which are separated by a known distance in the polynucleotide from which they are derived.

Abstract: The present invention relates to arrays of biochemical and/or biofunctional elements such as nucleic acids (oligonucleotides, for example) or other biomolecules on a carrier surface and methods of producing such arrays using photoactivation of predetermined areas for synthesis using an illumination matrix that is computer-controlled to generate an exposure pattern. This exposure pattern can be adjusted and monitored by computer using a light sensor matrix, for example a CCD matrix, to allow precise, controlled illumination of specific regions and therefore attachment of array building blocks to those specific regions. The methods and compositions of the invention permit spatially resolved photochemical synthesis of polymer probes on a carrier.

Abstract: The present invention relates to devices for the simultaneous performance of microarray experiments for detecting specific interactions between probe and target molecules in a microtiter plate as well as to methods for manufacturing such devices. Furthermore, the present invention relates to the use of such devices in a method for qualitatively and/or quantitatively detecting specific interactions between probe and target molecules.

Abstract: The present invention provides a hybridization method suited for using a signal probe. An array of the present invention comprises: a substrate; a nucleic acid probe that is fixed to the substrate and is hybridized with a sample to have a signal change; and at least one cavity that is filled with a specific liquid containing the sample and causing the hybridization of the nucleic acid probe with the sample. The array in this arrangement effectively enhances the reproducibility and the efficiency of hybridization with the signal probe.

Abstract: The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are constructs that include pairs of target sequences which are separated by a known distance in the polynucleotide from which they are derived.

Abstract: The present invention provides a substrate, system and method for synthesizing chain molecules in parallel using light-directed chemistry by imaging a selected pattern of light onto a dense array of microwells extending into a substrate surface, wherein the microwells are packed with high-surface-area carrier particles on which the chain molecules are grown in a series of sequential photoinitiated chemical steps.

Abstract: A nucleic acid probe for classification of pathogenic bacterial species is capable of collectively detecting bacterial strains of the same species and differentially detecting them from other bacterial species. Any one of the base sequences of SEQ ID NOS. 87 to 89 and complementary or modified sequences thereof or a combination of at least two of them is used for detecting the gene of an infectious disease pathogenic bacterium.

Abstract: The present invention relates to automated methods, systems, and apparatuses for protein separation and analysis. In particular, the present invention provides an automated system for the separation, identification, and characterization of protein samples. The present invention thus provides improved methods for the separation and analysis of samples containing a plurality of proteins (e.g., cells).

Abstract: Chemically modified nucleic acid sequences of genomic DNA, oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA. In addition, a method for ascertaining genetic and/or epigenetic parameters of genes for the characterization, classification, differentiation, grading, staging, treatment and diagnosis of oligodendrogliomas, astrocytomas and oligoastrocytomas.

Abstract: The present invention lies in developing a novel method for the preparation of oligonucleotide microarrays obviating the drawbacks to an extent, such as time consuming complex chemical reactions, preparation of modified supports/oligomer modifying reagents, use of activating/condensing reagent, low signal to noise ratio, poor immobilization and hybridization efficiencies, etc. Further, the prepared arrays can be used to detect single or multiple nucleotide mismatches using hybridization assay.

Abstract: A composition containing a photoacid generator monomer and surfactant, and a method for synthesizing a compound on a substrate using the composition are provided. The method includes bonding a layer of first molecules having an acid labile protecting group to a solid substrate; coating a layer of the photoacid generator monomer composition according to the present invention on the layer of first molecules; exposing the composition layer to light and then heat-treating to remove the acid labile protecting group from the first molecules corresponding to the exposed portion; washing and removing the composition layer from the exposed and unexposed portions; and bonding second molecules to the exposed first molecules.

Abstract: A DNA probe synthesis system may include a target holder for holding a target chip, an ejector array chip, a wash and dry station, and conveyance means for moving the target holder and the chip between the ejector array chip and the wash and dry station. The ejector array chip may include ejectors, reservoirs for containing DNA bases, and microchannels all on the same substrate. The ejectors may be Self Focusing Acoustic Transducers (SFATs).

Abstract: A microarray disc characterized in that a substrate is provided with a pregroove and a thin film with an excellent adherence to a probe DNA or protein is disposed at least on the pregroove, and that a liquid drop containing the probe DNA or protein is arranged on a convex part or concave part of the pregroove so that the liquid drop expands in the tangential direction of the pregroove due to the surface tension of the liquid drop and/or in the instance of concave part, due to the restriction by the concave groove wall with any expansion in the direction perpendicular to the groove, and that in the above condition, the probe DNA or protein is immobilized on the substrate.

Abstract: A combinatorial library of solid-state fluorescent dyes is prepared by reacting an aldehyde with a solid-supported pyridinium salt having a linker.

Abstract: Methods and compositions provide biological microarrays with enhanced fluorescent and luminescent signals by providing refraction index variations within a porous composition used to prepare the microarrays.

Abstract: An efficient molecular evolution system was obtained by combining two novel approaches in the field, intramolecular acyl migration for DCL generation and boronic acid as a selector. 1,4-Di-O-benzoyl chiro-inositol in acetonitrile with DBU as a base generated a reversible equilibrium of 9 regioisomers. Only 3,4-di-O-benzoyl chiro-inositol, containing two sets of cis-diols, is most favored toward binding with phenyl boronic acid, and its percentage of the DCL composition was amplified by up to 82%.

Abstract: The present invention relates to methods for the site-specific synthesis of biopolymers such as nucleic acids or peptides and their respective derivatives on solid supports, wherein the local discrimination of the synthesis is performed by using masks that guide aqueous activating reagents for cleaving off protecting groups to predetermined regions on the support.

Abstract: The invention relates to methods and materials involved in diagnosing SLE. More particularly, the invention relates to methods and materials involved in diagnosing SLE, diagnosing severe SLE, and assessing a mammal's susceptibility to develop severe SLE. For example, the invention provides nucleic acid arrays that can be used to diagnose SLE in a mammal. Such arrays can allow clinicians to diagnose SLE based on a simultaneous determination of the expression levels of many genes that are differentially expressed in SLE patients as compared to healthy controls.

Abstract: According to some embodiments of the invention, provided herein is a microarray comprising a substrate; a plurality of probe cells formed in the substrate, wherein at least one probe cell includes a linker; and a probe cell separation area. In addition, in some embodiments, the microarray may include a molecular probe coupled to the linker. Related methods are also described herein.