Abstract: A nanostructure array is disclosed. The nanostructure array comprises a plurality of elongated organic nanostructures arranged generally perpendicularly to a plane.

Abstract: The invention features methods of making devices, or “platens”, having a high-density array of through-holes, as well as methods of cleaning and refurbishing the surfaces of the platens. The invention further features methods of making high-density arrays of chemical, biochemical, and biological compounds, having many advantages over conventional, lower-density arrays. The invention includes methods by which many physical, chemical or biological transformations can be implemented in serial or in parallel within each addressable through-hole of the devices. Additionally, the invention includes methods of analyzing the contents of the array, including assaying of physical properties of the samples.

Abstract: The invention utilizes clinical features of diseases with a genetic background to define logical panels of diseases which have shared signs or symptoms. The invention includes methods for collecting data for use in determining a cause or risk factor for disease and includes micro arrays for use in detecting mutations associated with the diseases set forth in the panel.

Abstract: The present invention relates to methods for identifying compounds capable of modulating a cellular response. The methods involve attaching living cells to solid supports comprising a library of test compounds. Test compounds modulating a cellular response, for example via a cell surface molecule may be identified by selecting solid supports comprising cells, wherein the cellular response of interest has been modulated. The cellular response may for example be changes in signal transduction pathways modulated by a cell surface molecule.

Abstract: The present invention provides methods and systems for discretized, combinatorial processing of regions of a substrate such as for the discovery, implementation, optimization, and qualification of new materials, processes, and process sequence integration schemes used in integrated circuit fabrication. A substrate having an array of differentially processed regions thereon is processed by delivering materials to or modifying regions of the substrate.

Abstract: A carrier pre-encoded with information sufficient to distinguish it from a heterogeneous population of carriers is disclosed on which a compound can be synthesised. The carrier has two attributes integrally associated therewith, which attributes are detectable and/or quantifiable during synthesis of the compound and which define a code identifying the carrier before, during and after said synthesis, with the proviso that one of said attributes is other than shape, or surface deformation(s) of the carrier. The invention also encompasses a plurality of carriers that are pre-encoded as above and a method of synthesising and deconvoluting a combinatorial library using such carriers.

Abstract: The present invention relates to expression vector comprising (a) a promoter region comprising a non-inducible constitutively active ribosomal protein gene promoter, (b) an operably linked reporter or gene sequence, and (c) a 3? untranslated region (3? UTR), which are suitable means for an selective assessment of post-transcriptional regulation, post-transcriptional control elements and factors as well as for identifying compounds that effect post-transcription. The present invention furthermore relates to arrays, expression vector libraries and cell lines containing the expression vector(s). The present invention furthermore relates to a method and kit for identifying compounds that affect post-transcriptional regulation of reporter(s) or gene(s), that utilize the expression vector(s).

Abstract: The present invention relates to novel nucleic acid ligands or aptamers that bind to and inhibit the activation of the ?-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) subtype of ionotropic glutamate receptors. Also disclosed is a novel combination of technologies, i.e., SELEX and laser pulse photolysis for the selection and screening of aptamers that inhibit receptor function and are useful therefore, in the treatment of diseases associated with excessive activation of ionotropic glutamate receptors.

Abstract: Disclosed herein is a stamping apparatus for biochips and a method of operating the stamping apparatus. The apparatus includes a table, a first chip table, a second chip table, a stamping unit and a control unit. The first chip table is provided on the table. A first biochip is seated onto the first ship table. A second biochip is seated onto the second chip table. The stamping unit is mounted to the table and operates the second chip table such that a surface of a junction of the second biochip seated on the second chip table is joined to a surface of a junction of the first biochip seated on the first chip table. The control unit controls operation of the first chip table or the second chip table.

Abstract: The present invention provides methods and systems for discretized, combinatorial processing of regions of a substrate such as for the discovery, implementation, optimization, and qualification of new materials, processes, and process sequence integration schemes used in integrated circuit fabrication. A substrate having an array of differentially processed regions thereon is processed by delivering materials to or modifying regions of the substrate.

Abstract: A protein scaffold based on a consensus sequence of fibronectin type III (FN3) proteins, such as the tenth FN3 repeat from human fibronectin (human Tenascin), including isolated nucleic acids that encode a protein scaffold, vectors, host cells, and methods of making and using thereof, exhibit enhanced thermal and chemical stability while presenting six modifiable loop domains which can be engineered to form a binding partner capable of binding to a target for applications in diagnostic and/or therapeutic compositions, methods and devices.

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 provides a ligand-nucleic acid nanostructure that promotes cell-cell interaction. Specially, the invention provides a ligand-nucleic acid nanostructure for treating tumor in a mammal. The methods of using and making the composition comprising a ligand-nucleic acid nanostructure are also provided.

Abstract: The present invention provides methods for synthesizing arrays of polymers. The polymers are synthesized from monomers through a series of synthesis steps at chemically-modified electrodes by the action of an electrochemically generated reagent (EGR) at subsets of the electrodes. These subsets of electrodes vary with each step. Crosstalk of the EGR between electrodes is prevented by the production of a scavenging agent, which neutralizes the EGR, at those electrodes where the EGR is not produced. The scavenging agent acts as a “virtual cap” to prevent mis-incorporation of monomers and other anomalies in the polymers.

Abstract: The present invention is directed methods for collecting and storing samples compatible for high throughput automation. The present invention is also directed to a device comprising: (a) a plate containing multiple wells, and (b) multiple rubber covers; wherein each rubber cover is (i) an integral part of the device, (ii) is on top of each well and individually seal each well, and (iii) has a pierceable area in the center of the cover. The device is suitable for collecting, storing, transporting, and tracking samples compatible for high throughput downstream automated processing.

Abstract: The present invention provides novel algorithms for designing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. Such oligonucleotides are particularly useful as primers for reverse transcription. The invention also provides compositions containing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts.

Abstract: Methods for labeling a substrate using a hetero-Diels-Alder reaction are disclosed. The hetero-Diels-Alder reaction includes the reaction of an o-quinone methide (e.g., an o-naphthoquinone methide) with a polarized olefin to form a hetero-Diels-Alder adduct. The o-quinone methide or the polarized olefin can be attached to a surface of a substrate, and the other of the o-quinone methide or the polarized olefin can include a detectable label. The o-quinone methide can conveniently be generated by irradiation of a precursor compound, preferably in an aqueous solution, suspension, or dispersion.

Abstract: The system relates to filed-programmable lab-on-chip (FPLOC) microfluidic operations, fabrications, and programming based on Microelectrode Array Architecture are disclosed herein. The FPLOC device by employing the microelectrode array architecture may include the following: (a) a bottom plate comprising an array of multiple microelectrodes disposed on a top surface of a substrate covered by a dielectric layer; wherein each of the microelectrode is coupled to at least one grounding elements of a grounding mechanism, wherein a hydrophobic layer is disposed on the top of the dielectric layer and the grounding elements to make hydrophobic surfaces with the droplets; (b) a field programmability mechanism for programming a group of configured-electrodes to generate microfluidic components and layouts with selected shapes and sizes; and, (c) a FPLOC functional block, comprising: (i) I/O ports; (ii) a sample preparation unit; (iii) a droplet manipulation unit; (iv) a detection unit; and (iv) a system control unit.

Abstract: Libraries of nanoparticles comprising therapeutic agents and/or imaging agents are disclosed, as well as methods of making, customizing, and using such libraries of nanoparticles.

Abstract: A microarray package device and a method of manufacturing the same. An effective microarray analyzing reaction is performed by using the microarray package device that provides structural stability and reliable experimental results.

Abstract: A method of forming a solid-phase support, the method including the steps of providing a substrate having a reaction vessel, dispensing a particle in the reaction vessel, and permanently bonding the particle in the substrate within the reaction vessel. The particle may include a microbead. The particle may include controlled pore glass. A method of synthesis is also disclosed that includes including the steps of providing a solid-phase support including a particle embedded to the substrate adjacent a surface of substrate, the particle being functionalized to covalently attach an intermediate compound of a synthetic reaction, dispensing a liquid including a reagent to the solid-phase support to effect the synthetic reaction, and removing the liquid from the solid-phase support by centrifugation, whereby the intermediate compound remains attached to the substrate by the particle.

Abstract: Flow-through assay reaction chamber (6) of cassette has back and forth liquid mixing in narrow gap (G) over array of capture agent (S), with net flow advance to waste confinement (19), produced by reversible pumps (3 or 12), operable with rolling diaphragm action with at least limited elastic recovery that advance sample or buffer liquids through conditioning paths (4A, 8, 8?, 9, 14, 15, 15?) before reaching the reaction chamber (6). A single pump produces accurate flow control, liquid conditioning, e.g., liquefying dry reagent from internal surfaces of flow-dividing material (14a, 15A, 15A?, e.g. open cell foam or frit), heating (4A), and air bubble removal (8, 8?, 9), as well as replenishment of reagent while accomplishing mixing within the flow-through reaction chamber (6). Lower viscosity buffer liquid is arranged to propel higher viscosity reagent, the flow-dividing storage material preserving reagent concentration.

Abstract: The invention provides a diverse population of uniquely labeled probes, containing about thirty or more target specific nucleic acid probes each attached to a unique label bound to a nucleic acid. Also provided is a method of producing a population of uniquely labeled nucleic acid probes. The method consists of (a) synthesizing a population of target specific nucleic acid probes each having a different specifier; (b) synthesizing a corresponding population of anti-genedigits each having a unique label, the population having a diversity sufficient to uniquely hybridize to genedigits within the specifiers, and (c) hybridizing the populations of target nucleic acid probes to the anti-genedigits, to produce a population in which each of the target specific probes is uniquely labeled. Also provided is a method of detecting a nucleic acid analyte.

Abstract: Libraries of nucleic acids encoding chimeric binding polypeptides based on plant scaffold polypeptide sequences. Also described are methods for generating the libraries.

Abstract: The invention provides particle compositions having applications in nucleic acid analysis. Nucleic acid polymer particles of the invention allow polynucleotides to be attached throughout their volumes for higher loading capacities than those achievable solely with surface attachment. In one aspect, nucleic acid polymer particles of the invention comprise polyacrylamide particles with uniform size distributions having low coefficients of variations, which result in reduced particle-to-particle variation in analytical assays. Such particle compositions are used in various amplification reactions to make amplicon libraries from nucleic acid fragment libraries.

Abstract: Nature evolves biological molecules such as proteins through iterated rounds of diversification, selection, and amplification. The present invention provides methods, compositions, and systems for synthesizing, selecting, amplifying, and evolving non-natural molecules based on nucleic acid templates. The sequence of a nucleic acid template is used to direct the synthesis of non-natural molecules such as unnatural polymers and small molecules. Using this method combinatorial libraries of these molecules can be prepared and screened. Upon selection of a molecule, its encoding nucleic acid template may be amplified and/or evolved to yield the same molecule or related molecules for re-screening. The inventive methods and compositions of the present invention allow for the amplification and evolution of non-natural molecules in a manner analogous to the amplification of natural biopolymer such as polynucleotides and protein.

Abstract: A microarray, a substrate for a microarray and more productive methods of fabricating the microarray and the substrate are provided. The microarray includes a substrate divided into a first region and a second region; a plurality of linkers represented by formula 1 or 2: wherein X is a site coupled to the substrate, R is a hydroxyl, aldehyde, carboxyl, amino, amide, thiol, halo, epoxy, or sulfonate group, m is an integer in the range of 3 to 16, p is an integer in the range of 1 to 30, and q is an integer in the range of 1 to 15, directly coupled to the substrate in the first region but not coupled to the substrate in the second region; and a plurality of probes coupled to the respective linkers.

Abstract: The present invention relates to systems and methods for the arrangement of droplets in pre-determined locations. Many applications require the collection of time- resolved data. Examples include the screening of cells based on their growth characteristics or the observation of enzymatic reactions. The present invention provides a tool and related techniques which addresses this need, and which can be used in many other situations. The invention provides, in one aspect, a tool that allows for stable storage and indexing of individual droplets. The invention can interface not only with microfluidic/microscale equipment, but with macroscopic equipment to allow for the easy injection of liquids and extraction of sample droplets, etc.

Abstract: The present invention provides a method for identifying a compound of interest by screening libraries of molecules which include an encoding oligonucleotide tag.

Abstract: There is provided a biomolecule-immobilized plate having a flat part, at least a surface of the flat part comprising a polymer material, wherein the flat part has an arithmetic average roughness of 0.1 nm˜5 nm, and a portion of the flat part has functional groups. Further, the biomolecule-immobilized plate is fabricated by irradiating the flat part of the plate surface which comprises the polymer material, with an ultraviolet ray under ozone atmosphere to produce functional groups having bonding ability to the biomolecules on a portion of the flat part. Thereby, it is possible to provide a biomolecule-immobilized plate having a surface of a high degree of smoothness on which functional groups are produced, a biomolecule-immobilized plate on which biomolecules are immobilized via functional groups, and methods for fabricating these biomolecule-immobilized plates easily and inexpensively.

Abstract: A chemosensor array, a method of detecting ligands in a chemical mixture and a chemosensor system are provided. Chemosensor array designs are also provided.

Abstract: The present invention provides methods of making antibodies having the binding specificity of a reference antibody. Antibodies generated by the methods of the inventions have at least one minimal essential binding specificity determinant from a heavy chain or light chain CDR3 from the reference antibody. The method can be used, e.g., in humanization procedures. The invention also provides libraries and antibodies made in accordance with the methods.

Abstract: The invention relates to peptide conjugates including at least one turn inducer wherein the turn inducer comprises a 5-7 membered saturated or unsaturated nitrogen containing heterocyclic ring and methods of making the peptides. Libraries of these peptides, methods of making the libraries are also described and methods of screening the libraries for therapeutic activity are also described.

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: Provided are compositions and methods for preparing and identifying antibodies having CDR3s that vary in sequence and in length from very short to very long which in certain embodiments may bind to a carbohydrate moiety or the active site of an enzyme. Libraries coding for antibodies with the CDR3s are also provided. The libraries can be provided by modifying a pre-existing nucleic acid library.

Abstract: The invention relates to materials and methods for detecting interactions between lipid complexes and lipid binding agents. More specifically, the invention provides materials and methods for displaying lipid complexes, particularly those containing two or more different lipid molecules, on a hydrophobic surface so as to mimic their in vivo environment more closely than in other analytical methods. This allows more accurate detection of lipid complexes and even identification of lipid complexes which are not detected by other methods. The invention lends itself particularly well to array or microarray formats.

Abstract: Encoded bead multiplex assays for chromosomal gains and losses are provided that provide the benefits of complex, large template DNA sources, such as BAC DNA, as the probe material without bead networking or other assay performance problems. Reagents for assaying DNA are described herein which include a plurality of encoded particles having attached amplicons amplified from a template DNA sequence. Each individual attached amplicon includes a nucleic acid sequence identical to a random portion of the template DNA sequence, wherein the amplicons together represent substantially the entire template DNA and wherein the nucleic acid sequence identical to a random portion of the template DNA sequence of each individual amplicon is shorter than the entire template DNA.

Abstract: An improved process to create an arbitrarily large number of distinguishable particles allows more flexibility in experimental design and related efficiencies of scale. Novel enhanced tracers, for example, Shape Encoded Particles (SEP's) function as indicator means, such as probe-carriers in massively multiplexed assays. Shape encoded identity provides an elegantly simple tracking mechanism, whereby binding/reaction probes coupled to SEP's surfaces can be monitored, viewed, imaged or otherwise utilized leveraging off of the generation of millions of distinct, for example, approximately 100×100×10 micron squared silicon flakes fabricated using conventional MEMS techniques. Plethoric related applications, and contemplated strategies for benefiting from the novel enhanced SEP's and their respective enabling technologies are disclosed, ranging from pearl cultering seed elements to uniquely identify resulting jewelry pieces to an improved parallel stem cell differentiation screening assays.

Abstract: Disclosed herein are methods for identifying, isolating and comparing proteins and other biomolecules differing between two complex biological samples using affinity chromatography and phage display techniques.

Abstract: Subscription-based systems and methods where a provider provides one or more customers, identified as subscribers or non-subscribers, with research products and services (e.g., for industries involved in genomic and proteomic research). Initially, the provider prepares collections of clones and provides customers with access to clone collections. Individual clones in a clone collection may comprise an ORF that may be flanked by recombination sites. Further, an ORF may contain a suppressible stop codon that may be suppressed to produce a fusion protein comprising the ORF and a tag sequence. Provider may provide additional related services and/or products. The products and services offered to the customers will vary depending on their designation as either subscribers or non-subscribers.

Abstract: The present invention provides methods of synthesizing a molecule comprising a functional moiety which is operatively linked to an encoding oligonucleotide. The methods include providing an initiator compound comprising an initial functional moiety comprising n building blocks, wherein the initial functional moiety comprises at least one reactive group, and is operatively linked to an initial oligonucleotide; reacting the initiator compound with a building block comprising at least one complementary reactive group, under conditions suitable for reaction of the complementary reactive group to form a covalent bond; and reacting the initial oligonucleotide with an incoming oligonucleotide corresponding to the building block in the presence of an enzyme which catalyzes ligation of the initial oligonucleotide and the incoming oligonucleotide, under conditions suitable for ligation of the incoming oligonucleotide and the initial oligonucleotide to form an encoding oligonucleotide.

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: 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 present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.

Abstract: The present invention provides assays of nanometer-level dimension.

Abstract: The present invention relates to artificial receptors and arrays or microarrays of artificial receptors or candidate artificial receptors. Each member of the array includes a plurality of building block compounds, typically immobilized in a spot on a support. The present invention also includes the building blocks, combinations of building blocks, arrays of building blocks, and receptors constructed of these building blocks together with a support. The present invention also includes methods of making and using these arrays and receptors.

Abstract: The present invention relates to methods employing artificial receptors, such as combinatorial artificial receptor arrays. The present receptors include heterogeneous and immobilized combinations of building block molecules. In certain embodiments, combinations of 2, 3, 4, or 5 distinct building block molecules immobilized near one another on a support provide molecular structures that can be employed in the present methods. The present methods can develop artificial receptors that can then be employed to detect the receptor's ligand. The present methods can find compounds that disrupt one or more binding interactions.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Abstract: Described is a system and method for synthesizing polymeric molecules such as oligonucleotides and polypeptides. The system is capable of continuously synthesizing molecules by providing an array of reaction sites and an array of stations for carrying out synthetic manipulations. The reaction sites in the former array can be placed in a fixed order and at fixed intervals relative to each other. Similarly, the stations can be placed in a fixed order and at fixed intervals relative to each other. The two arrays can be moved relative to each other such that the stations carry out desired steps of a reaction scheme at each reaction site. The relative locations of the stations and the schedule for the relative movement can correlate with the order and duration of reaction steps in the reaction scheme such that once a reaction site has completed a cycle of interacting with the full array of stations then the reaction scheme is complete.

Abstract: Materials and methods for photodirected synthesis of oligonucleotide arrays on a solid substrate by photodirected synthesis are disclosed which employ a film formed from (i) a photoacid generator that on photolysis generates acid that is capable of directly removing the protecting group of the linker molecules or oligonucleotides and (ii) a polymer substantially lacking electronegative heteroatoms that are capable of hydrogen bonding with photogenerated acid. Methods of synthesizing an oligomer arrays are also described that use a film that restricts diffusion of reactants and products on the substrate during synthesis of the array and which includes a precursor of a deprotecting reagent. The method involves removing one or more of the non-required products of the deprotection reaction from the reactive array elements at which they are produced during the reaction, in order to displace the deprotection reaction towards completion.