Abstract: A method for depositing samples, in which at least one sample (10) is arranged on a substrate (30), comprises the following steps: positioning a sample dispenser (20) above the substrate (30), and actuating the sample dispenser (20) so that the sample (10) is moved from the sample dispenser (20) along a trajectory (11) to a predefined deposition position (32) on the substrate (30), wherein at least part of the trajectory (11) is shielded against electrical interference fields. Also described is a substrate (30) for receiving samples (10), comprising a substrate body (31), on the surface of which at least one deposition position (32) is provided, and a shielding electrode (40), which is designed so as to electrostatically shield the space above the at least one deposition position (32) against electrical interference fields.

Abstract: Versatile, efficient cell assays which can be prepared with use of nanolithography and can be used to test nanomaterials, pharmaceuticals, toxins, and the like. For example, a method comprising: depositing at least one first composition comprising at least one cell adhesion material on at least one substrate to form a pattern which forms an interior space on the substrate within the pattern, depositing in the interior space on the substrate at least one second composition, different from the first, comprising at least one material adapted to affect or potentially affect cell function. Tip-based deposition and direct-write methods can be used for deposition at nanoscale and sub-cellular resolutions. Nanoscopic and atomic force microscope tips can be used. Multiplexing can be carried out.

Abstract: A carbon nanotube array is provided. The carbon nanotube array includes at least two isotope-doped carbon nanotube sub-arrays. Each isotope-doped carbon nanotube sub-array includes a plurality of carbon nanotubes. The carbon nanotubes in different isotope-doped carbon nanotube sub-array are composed of different kinds of carbon isotopes. The present disclosure also provides a method for making the carbon nanotube arrays.

Abstract: Method of processing a biological sample to yield nucleic acid appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The invented method advantageously can improve detection of some target nucleic acids without substantially compromising detectability of others. The method is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions.

Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.

Abstract: The present invention relates to a sample arraying/assembling device, its method, and an apparatus using a sample assembly, and has an object of providing a sample arraying/assembling device which is adapted to various microplates, and is capable of efficiently and quickly arraying and assembling various samples; its method; and an apparatus using a sample assembly. The present invention includes: a distributing section which is capable of holding respective solutions containing samples to be distributed, and which has a plurality of holding ends arranged in a predetermined matrix; and a wound body which has a plane surface wound with a slender foundation member on which samples are to be distributed at distribution intervals of column or line of the matrix, which is arranged in parallel at the winding intervals of the line or column on the plane surface, so that the respective holding ends can come into contact therewith.

Abstract: The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.

Abstract: Described herein are compositions, kits and methods for diagnosing and tracking the progression of AMD in a subject by detecting the presence or absence of particular lipid metabolism markers associated with AMD. Predictive computer models of disease risk are also disclosed.

Abstract: An apparatus and system for stirring liquid inside a flow cell. In one implementation, the apparatus includes a rotatable disc configured to receive liquid at a top side of the disc and distribute the liquid substantially evenly around a periphery of the flow cell. The disc has a triangular cross sectional area. The apparatus may further include a set of fins attached to a bottom side of the disc, wherein the set of fins is configured to draw the liquid from the periphery of the flow cell into the center of the flow cell.

Abstract: The present invention is directed to carbohydrate microarray and conjugated nanoparticles methods of making the same.

Abstract: The subject matter relates to relates to a one-bead-one-sequence composition, a library of tagged chemicals comprising a plurality of one-bead-one-sequence compositions, a method for identifying a candidate molecule from a library of tagged chemicals, and a composition produced by a process, all as described herein.

Abstract: The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing.

Abstract: Methods and devices use in two-color measurement systems. The methods and devices include methods of making corrections, methods of calculating correction factors, fluorescence scanners, and microarray chips. The said methods and devices enable a user to correct fluorescence intensities for errors caused by the occurrence of FRET and /or cross-talk when two fluorophores are used in two-color fluorescence arrays.

Abstract: This invention relates to a method for the fabrication of photonic biosensor arrays and applications of arrays produced by the method in the biomedical field.

Abstract: The present invention relates to novel methods for the quantitative detection of molecules in an array. In particular, the present invention relates to methods and apparatuses for producing a frameless array. In another embodiment, the present invention relates to a composition comprising nitrocellulose that is useful of producing a frameless array. In another embodiment, the present invention relates to a method for detecting a molecular interaction. In yet another embodiment, the present invention relates to kits useful for practicing the methods and apparatuses of the present invention. The present invention provides improved methods and apparatuses for the high throughput analysis of molecular interactions and quantitative detection.

Abstract: Disclosed herein is a multiplex microarray having serially attached non-functionalized biomolecules attached to a polymer coating covering each electrode of an array of electrodes for assays and a method of making the multiplex microarray. The method comprises serially blocking the electrodes of the microarray with a blocking protein, electropolymerizing pyrrole or a functionalized pyrrole on the electrodes where the biomolecule is not present during polymerization, exposing the microarray to a biomolecular solution containing a non-functionalized biomolecule for attachment to the polymer coating, and then repeating the steps to form the multiplex microarray.

Abstract: The present invention provides materials and methods for the utilization of the specific interaction of replication termination sequences with their binding proteins in molecular biology applications.

Abstract: The present invention relates to a molecularly imprinted polymer and a method of producing the same using complementary oligo- and/or polynucleotides.

Abstract: The present invention describes microfluidics being employed to achieve multiplex surface functionalization of nanosensor chips by selectively delivering probe molecules to individual nanosensors in an array, and microfluidics being employed to achieve delivery of a solution containing multiple analytes over individual nanosensors in an array, where each nanosensor was previously configured with a specific capture molecule.

Abstract: The present invention relates to a formulations and methods for coupling a reactant (or probe precursor) to a functionalized surface for purposes of forming an arrayed sensor. This method includes the steps of: providing a surface having a reactive functional group; and introducing onto the surface, at a plurality of discrete locations, two or more compositions of the invention, which include a different reactant (probe precursor) and a non-nucleophilic additive, wherein such introduction is carried out under conditions effective to allow for covalent binding of the reactant to the surface via the reactive functional group. This results in a probe-functionalized array that substantially overcomes the problem of surface morphological anomalies on the array surface. Use of the resulting arrays in various detection systems is also encompassed.

Abstract: Substrates are provided for use in the detection, identification and analysis of biologic or chemical samples that are labeled with a fluorescent label, in which the plane of maximum fluorescence is displaced from a reflective substrate surface so that the intensity maximum of the standing wave interference pattern of incident and reflected probe radiation is enhanced. The format of the substrates includes substantially planar surfaces as well as substrates with introduced variations to the substrate surface, e.g., depressions, wells, pedestals and the like, disposed in arrays or other similar structures such that one or more fluorophore-comprising objects can be attached thereto.

Abstract: A photolabile compound, an oligomer probe array, and a substrate for oligomer probe array comprising the same, and a manufacturing method of the same are disclosed.

Abstract: An antibody-fragment-immobilizing substrate includes a substrate and at least one set of antibody fragments, wherein antibody fragments of each set include at least two types of separate antibody fragments, the at least two types of separate antibody fragments include at least one type of labeled antibody fragment having a labeled site labeled with a luminescent substance and at least one type of acceptor antibody fragment having an acceptor site for accepting emission from the labeled antibody fragment, and the at least one type of labeled antibody fragment and the at least one type of acceptor antibody fragment are capable of cooperatively recognizing one type of antigen in combination and are independently immobilized on the substrate in a positional relationship that allows each of the antibody fragments in one set to bind to the same antigen.

Abstract: An apparatus for applying a solution to be used for manufacturing DNA chips is provided in a holding member with a sensor for monitoring a substrate temperature, a temperature adjusting section for controlling the substrate temperature, and a control section for feeding back a control temperature, by using the monitored temperature, to the temperature adjusting section for controlling the substrate temperature, wherein the substrate temperature is controlled to such a level as will accelerate the reaction between the substrate and probes in the sample solution.

Abstract: Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Abstract: A system for performing quality control for nucleic acid sample sequencing is disclosed. The system comprises a set of solid supports, each solid support having attached thereto a plurality of nucleic acid sequences, wherein the set comprises plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived, and the nucleic acids sequences are designed such that the nucleic acid sequences produce a predefined pattern of detectable signals during a sequencing run. A method of preparing a quality control for performing nucleic acid sample sequencing, a method of validating a nucleic acid sequencing instrument during a nucleic acid sequencing experiment, and a method of processing nucleic acid sequencing data during a nucleic acid sequencing experiment are also disclosed.

Abstract: The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of DNA with a gene array.

Abstract: Methods for optically trapping and manipulating micro- and nano-sized particles by using light to induce localized surface plasmon resonance on metallic surface of a substrate. The method includes the steps of contacting a substrate with a medium having particles suspended therein; focusing a beam of coherent light onto the substrate such that the beam induces surface plasmon resonance; and trapping at least one of the suspended particles using a light induced dielectrophoresis force generated by the surface plasmon resonance.

Abstract: Elongated molecules are stretched across a substrate by controlled fluid flow.

Abstract: An apparatus for use in fabricating structures and depositing materials from tips to surfaces for patterning in direct-write mode, providing ability to travel macroscopic distances and yet provide for nanoscale patterning. Useful in small scale fabrication and nanolithography. The instrument can be compact and used on a laboratory bench or desktop. An apparatus comprising: at least one multi-axis assembly comprising a plurality of nanopositioning stages, at least one pen assembly, wherein the pen assembly and the multi-axis assembly are adapted for delivery of material from the pen assembly to a substrate which is positioned by the multi-axis assembly, at least one viewing assembly, at least one controller. Nanopositioning by piezoelectric methods and devices and motors is particularly useful. The apparatus can include integrated environmental chambers and housings, as well as ink reservoirs for materials to be delivered. The viewing assembly can be a microscope with a long working distance.

Abstract: A substrate comprising a microporous microstructure, an interlayer over at least a portion of the microstructure and a functional layer attached to the interlayer, the functional layer having functional sites with a density of at least 50 nanomoles/cm2.

Abstract: Holding device for the arrangement of at least one optical component in front of a laser light source of a laser unit, including a first holding part to which at least one optical component is attached, the holding device furthermore including a second holding part which is attached to one part of the laser unit, and the first holding part being attached to the second holding part. Furthermore this invention relates to an arrangement with such a holding device and a process for producing this arrangement.

Abstract: The present invention provides methods of synthesizing libraries of molecules comprising a functional moiety which is operatively linked to an encoding oligonucleotide, wherein the encoding oligonucleotide comprises a capping sequence containing degenerate nucleotides.

Abstract: The invention relates to the field of molecular recognition or detection of discontinuous or conformational binding sites or epitopes corresponding to a binding molecule, in particular, in relation to protein-protein, protein-nucleic acid, nucleic acid-nucleic acid or biomolecule-ligand interactions. The invention provides a synthetic molecular library allowing testing for, identification, characterization or detection of a discontinuous binding site capable of interacting with a binding molecule, the library having been provided with a plurality of test entities, each test entity comprising at least one first segment spotted next to a second segment, each segment having the capacity of being a potential single part of a discontinuous binding site.

Abstract: Novel processes are disclosed for forming an array of polymers by functionalizing the surface of particles by methods that include covalently attaching a functionalized silicon compound. Substrates such as microparticles having functionalized silicon compounds attached thereto are produced by introducing at least one carboxyl group directly by silanating a carboxylated silane compound to the surface of a microparticle. In a further aspect of the invention, the silane compound is a dipodal carboxylated silane.

Abstract: Disclosed is a method for immobilizing a target protein to the surface of silicon oxide-containing substance such as glass without modifying the surface of silicon oxide-containing substance by using a protein binding strongly to silicon oxide-containing substance. A protein capable binding strongly to silicon oxide-containing substance such as glass has been found, and thus a target protein can be directly bound and immobilized to the surface of silicon oxide-containing substance via the found protein. In addition, a fusion protein of the found protein and a target protein can be bound and immobilized to silicon oxide-containing substance.

Abstract: A method is described for the detection of the degree of methylation of a specific cytosine in the sequence context 5?-CpG-3? of a genomic DNA sample. In the first step, the genomic DNA is chemically treated in such a way that the cytosine bases are converted to uracil, but not the 5-methylcytosine bases. Then segments of the genomic DNA which contain the said specific cytosine are amplified, whereby the amplified products are given a detectable label and in the following steps the extent of hybridization of the amplified products on two classes of oligonucleotides is determined by detection of the label of the amplified products, and a conclusion is made on the extent of methylation of said specific cytosine in the genomic DNA sample from the ratio of the labels detected on the two classes of oligonucleotides as a consequence of the hybridization.

Abstract: The present invention relates to the use of mass spectrometry to analyze arrays. The present invention provides methods for characterizing solutions comprising one or more proteins using arrays and mass spectrometry. The arrays of the present invention are coated with porous gold and utilize hydrophobic and hydrophilic self-assembled monolayers.

Abstract: Provided are a gold-silver alloy nanoparticle chip, a method of fabricating the same and a method of detecting microorganisms using the same. The gold-silver alloy nanoparticle chip includes a hydrophilized glass substrate, a self-assembled monolayer formed on the glass substrate, and gold-silver alloy nanoparticles fixed on the self-assembled monolayer. The gold-silver alloy nanoparticle chip having such a structure enables microorganisms in a water purifier and tap water to be readily detected and enables detection efficiency to be enhanced.

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: The present teachings provide a fluid processing device adapted to produce different oligomers in a plurality of respective reaction sites. The fluid processing device can comprise a first manifold for delivering reactants to the plurality of reaction sites, and a second manifold for removing waste from, and optionally delivering wash fluid to, the plurality of reaction sites. Surface tension control valves can be disposed in fluid communication with the first manifold and can selectively allow reactants and/or fluids into the reaction sites. A method of making oligonucleotides is also provided.

Abstract: A polymer synthesis apparatus (20) for building a polymer chain including a head assembly (21) having an array of nozzles (22) with each nozzle coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) for deposition of the liquid reagent (24) into selected reaction wells (26). A sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein. A gas inlet (70) into the common chamber (31), upstream from the nozzles (22), and a gas outlet (71) out of the common chamber (31), downstream from the nozzles (22), sweeps the common chamber (31) of toxic fumes emitted by the reagents.

Abstract: A novel encoding system, compositions for use therein and methods for determining the source, location and/or identity of a particular item or component of interest is provided. In particular, the present invention utilizes a collection of one or more sizes of populations of semiconductor nanocrystals having characteristic spectral emissions, to “track” the source or location of an item of interest or to identify a particular item of interest. The semiconductor nanocrystals used in the inventive compositions can be selected to emit a desired wavelength to produce a characteristic spectral emission in narrow spectral widths, and with a symmetric, nearly Gaussian line shape, by changing the composition and size of the semiconductor nanocrystal. Additionally, the intensity of the emission at a particular characteristic wavelength can also be varied, thus enabling the use of binary or higher order encoding schemes.

Abstract: The present invention provides diverse chemical libraries bound to small particle with paramagnetic properties. Typically, the chemical structures comprise a plurality of different chemical moieties, the particles are paramagnetic and have a diameter between about 100 nm and about 10 microns, the chemical structures bound to each particular particle have substantially the same structure and the combinatorial library comprises at least 100,000 different chemical structures.

Abstract: The present invention can provide a novel saccharide primer, which makes it possible to efficiently synthesize a sugar chain, and a method for using the primer. According to the present invention, the saccharide primer of the present invention is a saccharide primer having an alkenyl chain that has one or more double bonds in a position other than the alkyl chain terminal, and represented by the following general formula (I): Lac-O-Ck:m(n) ??General formula (I) In the general formula (I), Ck represents an alkenyl chain, m represents a total number of double bonds, and n represents a position of the double bond in the alkenyl chain. Here, k is preferably an integer in the range of 8 to 14, and particularly 12 or 13. In addition, when m is 1, n is an integer satisfying 1?n?k?2; and when m satisfies 2?m?k?1, n is a plurality of integers satisfying 1?n?k?1.

Abstract: Three-dimensional cellular arrays, methods of making three-dimensional cellular arrays, and methods of identifying agents using the arrays are disclosed.

Abstract: Combinations, called matrices with memories, of matrix materials with remotely addressable or remotely programmable recording devices that contain at least one data storage unit are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluophors or other luminescent moieties to produce luminescing matrices with memories. The data storage units are non-volatile antifuse memories or volatile memories, such as EEPROMS, DRAMS or flash memory. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided.

Abstract: Embodiments of the invention are directed to a one-bead-two-compound method for the creation of encoded cyclic peptoid libraries. This scheme is useful for the creation of cyclic peptoid microarrays since only the cyclic peptoid, not the linear encoding molecule, contains an attachment residue and thus can be spotted onto an activated substrate.

Abstract: 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)m, where Y is a transition metal, magnesium or aluminum, L is oxygen, sulfur, selenium or an amine, and “Pol” represents a passivating agent such as a polyethylene glycol, a hydrocarbon, or a fluorocarbon. The resulting modified surface can be further reacted with a passivating agent having a phosphate functional group or a polyvalent reagent comprising a passivating moiety and a plurality of functional groups that are reactive with or that form complexes with Y. The passivating agent can also include a functional group such as biotin to provide surfaces with a desired functionality. The passivated surfaces exhibit minimal binding to bio-molecules and can be used in single-molecule detection schemes.

Abstract: Improved compositions, methods, apparatus, and kits for high-throughput nucleic acid amplification, detection and sequencing are disclosed. A nucleic acid cluster having an identifiable center is produced by generating on a solid support an immobilized nucleic acid complement from a template, one of which comprises a detectable label; and amplifying the complement and the template to obtain a nucleic acid cluster on the support, the cluster having a substantially central location marked by the detectable label and a surrounding region comprising immobilized copies. Also disclosed are nucleotide sequence determination in nucleic acid clusters so produced, center position annotation in the clusters, assignment of sequence information to overlapping clusters, and related compositions and methods.