Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.

Abstract: Nanowire-channel metal oxide semiconductor field effect transistors (MOSFETs) and techniques for the fabrication thereof are provided. In one aspect, a MOSFET includes a nanowire channel; a fully silicided gate surrounding the nanowire channel; and a raised source and drain connected by the nanowire channel. A method of fabricating a MOSFET is also provided.

Abstract: The present invention provides methods of making a population of nucleic acid molecules, wherein each nucleic acid molecule comprises a predetermined nucleic acid sequence, each of said methods comprising the steps of: (a) synthesizing, on a substrate, a population of nucleic acid molecules wherein: i) each synthesized nucleic acid molecule comprises a predetermined nucleic acid sequence; and ii) each synthesized nucleic acid molecule is localized to a defined area of said substrate; (b) harvesting said population of synthesized nucleic acid molecules from said substrate to yield harvested nucleic acid molecules; and (c) introducing said harvested nucleic acid molecules into vector molecules.

Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

Abstract: The present invention relates to cationic lipids capable of forming complexes with nucleic acids and the use thereof for the transfection of eukaryotic cells. The cationic lipids according to the invention have general formulas (I) and (Ia): (see formulas (I) and (Ia), wherein E is a heteroaryl; R1 and R2 are selected from H, —R7—NH2, alkyl; R7 is selected from alkyl, alkenyl, aryl, (C1-C20) alkyl-aryl-(C0-C20) alkyl; R3 and R4 are selected from: H, —R8—SH, R8—NH—NH2/—R8—CO—R9 or —R8—NH2; R8 is selected from: alkyl, alkenyl, aryl, (C1-C20) alkyl-aryl-(C0-C20) alkyl; R9 is selected from: H, alkyl; R5 and R6 are selected from: H, alkyl, alkenyl, aryl, (C1-C20) alkyl-aryl.

Abstract: A DNA chip includes a substrate, at least one first electrode and at least one second electrode on the substrate, the first electrode and the second electrode being opposite to and separated from each other, multiple oligonucleotide probes, one end of the oligonucleotide probes being immobilized on the first electrode, and a charge-carrier transport layer on the second electrode, the charge-carrier layer contacting an other end of the oligonucleotide probes.

Abstract: Disclosed herein is a method of orienting a carbon nanotube comprising functionalizing a nucleic acid or a carbon nanotube with a plurality of functional groups to form either a functionalized nucleic acid or a functionalized carbon nanotube; disposing a nucleic acid on a functionalized carbon nanotube or a functionalized nucleic acid on a carbon nanotube or a functionalized nucleic acid on a functionalized carbon nanotube to form a nucleic acid-carbon nanotube molecular composite; adsorbing the nucleic acid-carbon nanotube molecular composite upon a substrate; the substrate comprising a plurality of material phases, at least one of which the nucleic acid-carbon nanotube molecular composite has an affinity for; and orienting the nucleic acid-carbon nanotube molecular composite so that it contacts two or more identical material phases.

Abstract: Gene expression profiling and hierarchal clustering analysis readily distinguish normal ovarian epithelial cells from primary ovarian serous papillary carcinomas. Laminin, tumor-associated calcium signal transducer 1 and 2 (TROP-1/Ep-CAM; TROP-2), claudin 3, claudin 4, ladinin 1, S100A2, SERPIN2 (PAI-2), CD24, lipocalin 2, osteopontin, kallikrein 6 (protease M), kallikrein 10, matriptase and stratifin were found among the most highly overexpressed genes in ovarian serous papillary carcinomas, whereas transforming growth factor beta receptor III, platelet-derived growth factor receptor alpha, SEMACAP3, ras homolog gene family, member I (ARHI), thrombospondin 2 and disabled-2/differentially expressed in ovarian carcinoma 2 (Dab2/DOC2) were significantly down-regulated. Therapeutic strategy targeting TROP-1/Ep-CAM by monoclonal chimeric/humanized antibodies may be beneficial in patients harboring chemotherapy-resistant ovarian serous papillary carcinomas.

Abstract: The present invention is a method to assist in the identification of single nucleotide polymorphisms (SNP) from microarray hybridization data. Data from hybridization protocols run on microarrays often have variations in the data resulting from variations in hybridization conditions and efficiencies and variations in optical intensities. An algorithm is described to screen the results to identify those data points most likely to be real SNPs as opposed to variations in the hybridization or sensing data.

Abstract: The present invention provides a microarray for multiple sample analysis that does not require an alignment of well walls with corresponding probe sets. Methods for building and using such a microarray are also within the scope of the present invention.

Abstract: This invention involves the nano-structured support used for separation or/and analysis, especially the chip substrate, ELISA plate substrate, planar chromatography strip and chromatography gel. Besides, it involves the functionalized nano-structured support of high sensibility for separation or/and analysis, especially the analysis-chip, ELISA plate, planar chromatography reagent strip and chromatography gel. In addition, this invention also involves the nano-structured marking system for analysis. Moreover, it concerns the test kit; especially the chip kit, ELISA kit, and planar chromatography kit. What's more, this invention involves the preparing methods and the applications of all those mentioned above, especially the chip analysis, analyses with ELISA plate, planar chromatography strip and chromatography separation.

Abstract: A universal linker structure is provided, in which a functional group and activating leaving group are placed on a tether, allowing the placement of an electrophile at the end of any nucleic acid sequence. The electrophile on the tether can react with a second nucleic acid carrying a nucleophile when the two nucleic acids are hybridized near one another, resulting in release of the leaving group, and creation of a functional change. The linker can be designed to destabilize the ligation product without slowing the rate of reaction. This lowers product inhibition, and the target DNA or RNA can become a catalyst for isothermally generating multiple signals for detection. This enhanced signal is demonstrated in solution experiments and in solid supported assays. The universal linkers of the present invention are simple and inexpensive to prepare, and can be appended to any polynucleotide in automated steps on a standard DNA synthesizer.

Abstract: New modifiers were synthesized for incorporation of a methacrylic function in 3?-, 5?- and internal positions of oligonucleotides during solid phase synthesis. A modifier was used for synthesis of 5?-methacrylated oligonucleotides for preparation of microarrays by a co-polymerization method.

Abstract: A PNA zip-code chip in which PNA zip-code probes are immobilized on a substrate at high density using an epoxy compound as a linker, and method for fabricating such PNA chip. The use of PNA provides the chip with superior properties to DNA chips, allowing precise diagnosis of congenital diseases or base mutations with much higher sensitivity than is achievable with a DNA chip. The use of the PNA zip-code chip enables diagnosis of gene mutations in a simple manner, using only hybridization reaction, without the difficulties associated with processes in which probes must be immobilized directly on a substrate every time the target gene changes.

Abstract: Two dimensional polynucleic acid arrays are assembled from robust nucleic acid motifs as polygonal units. The polygonal units in an array have edges composed of nucleic acid multi-crossover domains and are joined together by double cohesion of adjacent polygonal units. A subset of polygonal units in the array have a nanoparticle or pendant molecule attached to an end of one edge of each polygonal unit within this subset.

Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.

Abstract: Provided is a method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, the method including: obtaining a biological sample from a lung cancer patient; measuring an expression level of at least one marker gene from the biological sample, the marker gene being selected from the group consisting of marker genes of Table 1, 2 or 3, to obtain data for the expression level of the marker gene; and determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group.

Abstract: Biosensors and methods to determine the activity of any and all nucleic acid binding factors, proteins, cellular events, nucleic acid binding protein coregulators, or fragments thereof, based upon the stabilization of the interaction of two nucleic acid components, which together comprise a complete nucleic acid binding element, by the binding of a nucleic acid binding factor are provided. Preferably, a fluorescence donor is attached to a nucleic acid comprising one portion or component of a complete nucleic acid binding element and a fluorescence acceptor is attached to a nucleic acid comprising the other portion or component of the same complete binding element. Alternatively, a solid substrate is attached to a nucleic acid comprising one portion of a binding element and a detectable label is attached to a nucleic acid comprising the other portion of the same binding element.

Abstract: A method by which silicon nanostructures may be selectively coated with molecules or biomolecules using an electrochemical process. This chemical process may be employed as a method for coating many different nanostructures within a circuit, each with a different molecular or biomolecular material. The density of devices within a circuit of devices that can be coated with different molecules is limited only by the ability to electronically address each device separately. This invention has applications toward the fabrication of molecular electronic circuitry and toward the fabrication of nanoelectronic molecular sensor arrays.

Abstract: Functionalized fluorescent nanocrystal compositions and methods for making and using these compositions are disclosed. The compositions are fluorescent nanocrystals coated with at least one material. The coating material has chemical compounds or ligands with functional groups or moieties with conjugated electrons and moieties for imparting solubility to coated fluorescent nanocrystals in aqueous solutions. The coating material provides for functionalized fluorescent nanocrystal compositions which are water soluble, chemically stable, and emit light with a high quantum yield and/or luminescence efficiency when excited with light. The coating material may also have chemical compounds or ligands with moieties for bonding to target molecules and cells as well as moieties for cross-linking the coating.

Abstract: The present invention relates to biochips, in particular nucleotide chips, which contain hyphen-specific proteins coding nucleotides, protein chips which contain hyphen-specific proteins, and antibody chips which contain antibodies directed against these hyphen-specific proteins, diagnostic compositions which contain these nucleotide, protein, or antibody chips, processes for the location and identification of substances which are therapeutically effective against diseases caused by types of Candida and processes for the diagnosis of a disease caused by Candida.