Abstract: An automated process performed in an analyzer for detecting the presence of a target nucleic acid in a sample. The process includes separating the target nucleic acid from other material present in the sample, performing an amplification reaction to produce an amplification product indicative of the presence of the target nucleic acid in the sample, and detecting the amplification product. The amplification reaction can be performed in an open receptacle vessel, such as a test tube.

Abstract: The present invention is directed to novel and improved methods for humanizing rabbit heavy and light variable regions. The resulting humanized rabbit heavy and light chains and antibodies and antibody fragments containing are well suited for use in immunotherapy and immunodiagnosis as they retain the antigen binding affinity of the parent antibody and based on their very high level of sequence identity to human antibody sequences should be essentially non-immunogenic in humans. The invention exemplifies the protocol for the manufacture of therapeutic humanized anti-human TNF-alpha and anti-human IL-6 antibodies.

Abstract: A process for producing a functional molecule includes a forming step which forms a modified nucleotide n-mer (where, n represents an integer) containing a modified nucleoside prepared by introducing a substituent into a nucleoside composing a nucleic acid; and a producing step which produces a modified oligonucleotide sequence by randomly polymerizing the modified nucleotide n-mer. A preferable embodiment thereof includes a selecting step which selects a sequence having an affinity to a target from the modified oligonucleotide sequence, a determining step which amplifies the selected modified oligonucleotide sequence and determines the base sequence thereof, and a translating step which translates the sequence of the modified oligonucleotide sequence on the basis of a relation table prepared by relating at least one of 4n kinds of nucleotide n-mers, which are presented in the relation table prepared by the one-to-one combination of 4 kinds of nucleosides, to a modified nucleotide n-mer.

Abstract: A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.

Abstract: The present invention relates to solid supports functionalized with phosphorus-containing dendrimers, to a process for preparing them, to their use for preparing biochips and to the uses of these biochips, in particular for immobilizing molecules of interest, especially biological molecules of interest such as nucleic acids, polypeptides, lipids and proteins.

Abstract: This disclosure relates to nucleic acid constructs modified to have a reduced net anionic charge. In some aspects the constructs comprise phosphodiester and/or phosphothioate protecting groups. The disclosure also provide methods of making and using such constructs.

Abstract: The present invention provides antibodies comprising an antigen recognition domain that specifically binds to a metal chelate: mutant antibodies comprising a reactive site not present in the wild-type of the antibody, wherein the reactive site is in a position proximate to or within the antigen recognition domain; and methods of using such antibodies to diagnose and treat disease.

Abstract: The objective of the invention is to provide nucleic acid derivatives with designated compounds introduced specifically into the base of nucleic acids. A DNA or RNA, or a nucleic acid molecular weight marker, wherein a designated compound (R), which is selected from any one of dyes, fluorescent dyes, RI labeled substances, and compounds capable of linking specifically to other compounds, is introduced at the N?3 position of a thymine base or uracil base in which (R?) at Position 1 is other than hydrogen atom.

Abstract: The present invention provides multisignal labeling reagents and these are useful in a number of biochemical applications, including the manufacture of biomolecular probes and their use in detecting or amplifying analyte-specific moieties.

Abstract: Compounds having structure (1) wherein R1 is —H a protecting group, a linker or a binding partner; and R2 and R34 are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.

Abstract: The method of differentiating beer yeast of the invention is a method which comprises a first step of synthesizing a primer capable of amplifying the linker portion between a base sequence (A) and a base sequence (B) in a novel gene (C) which has the base sequence (B) comprising a portion of yeast chromosome IX linked downstream from the base sequence (A) comprising a portion of the N-terminal end of yeast gene Lg-FLO1, and which includes the base sequences listed as SEQ. ID. Nos. 1-6 of the Sequence Listing; a second step of carrying out a PCR (Polymerase Chain Reaction) using the primer synthesized in the first step and DNA separated from a yeast specimen; and a third step of differentiating whether the yeast is bottom-fermenting yeast or wild yeast, based on the PCR amplification product obtained from the second step.

Abstract: The present invention provides novel, water-soluble, red-emitting fluorescent rhodamine dyes and red-emitting fluorescent energy-transfer dye pairs, as well as labeled conjugates comprising the same and methods for their use. The dyes, energy-transfer dye pairs and labeled conjugates are useful in a variety of aqueous-based applications, particularly in assays involving staining of cells, protein binding, and/or analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing.

Abstract: Oligonucleotides comprising one or more 4?-thioarabinonucleotides are described, as well as uses thereof for applications such as antisense- and RNAi-based gene silencing. 4?-thioarabinose-based phosphoramidite and H-phosphonate compounds are also described, as well as uses thereof for the synthesis of oligonucleotides comprising one or more 4?-thioarabinonucleotides.

Abstract: The invention relates to detectable labels useful for detection of nucleotide sequences. Specifically, the invention relates to labeled-imidazole-PEG compounds, such as nucleosides, nucleotides, and nucleic acids incorporating such compounds, and methods utilizing such compounds. The invention further relates to kits comprising labeled imidazole-PEG compounds.

Abstract: To provide an excellent amidite for synthesizing modified nucleic acid, which enables a protective group therein to be removed under a moderate condition, thereby stably producing a hydroxyl group-containing modified nucleic acid, and a method for synthesizing modified nucleic acid using the amidite. Specifically, an amidite for synthesizing modified nucleic acid, expressed by General Formula (I): where X represents a base, Y represents a substituent, Z represents a protective group for protecting a hydroxyl group in the substituent, and Q represents one of a hydrogen atom, a hydroxyl group and a hydroxyl group protected by a protective group, wherein the protective group can be removed in an aprotic solvent, and when the protective group is removed, the hydroxyl group emerges in the substituent, and a method for synthesizing modified nucleic acid using the amidite.

Abstract: This application describes methods and compositions for detecting and treating HLTF-associated neoplasia. Differential methylation of the HLTF nucleotide sequences has been observed in HLTF-associated neoplasia such as colon neoplasia.

Abstract: Double-stranded RNA of about 19 to about 25 nucleotides in length capable of regulating gene expression by RNA interference is provided. Such double-stranded RNA are particularly useful for treating disease or conditions associated with a target mRNA or gene. Methods of manufacture and methods of use of the double-stranded RNA are also provided.

Abstract: The present invention provides improved methods for generating fluorescent aptamer polynucleotides, novel polynucleotides, and methods for use thereof.

Abstract: The present invention provides a thionucleoside-S-nitrosyl derivative of the following Formula I or a salt thereof: [wherein R1 represents ribose, 2-deoxyribose or a derivative of either, and R2 represents a hydrogen atom, an amino group, a hydroxyl group, a halogen atom, a R3-oxy group or a R3-amino group (wherein R3 represents an optionally substituted C1-15 alkyl group or an optionally substituted C1-15 acyl group)].

Abstract: The present invention provides a method of synthesizing phosphoramidite linkers that are useful for the production of synthesizing two or more oligonucleotides in tandem. The inventive linker has the following desirable properties: (i) enhanced stability to alkali conditions versus the linkers previously published, (ii) cleaves to produce 5? and 3? ends that are fully biologically compatible, (iii) cleaves completely under conditions that are already used in cleavage/deprotection processes so it is fully compatible with conditions that are common in laboratories and does not require additives that necessitate further purification after cleavage, (iv) integrates easily onto commercially available synthesizers because it is compatible with standard coupling chemistry, and (v) is compatible with DNA, RNA, forward, reverse, and LNA, synthesis chemistries. In addition, the inventive linkers may be coupled to a solid support. Thus, the inventive linkers provide a significant advancement in the state of the art.

Abstract: Bulk negative refractive index materials (NIM) or left-handed metamaterials (LHM) as an amorphous and isotropic solid material consisting of mutually electrically insulated synthetic rings or pucks smaller than the wavelength of visible light. Each ring or puck contains a nanometer sized metallized nucleic acid ring containing one or more non-metallized segments. The bulk material can be formed as a plurality of individual pucks randomly oriented, or as multiple rings stacked together in an axial direction whose axes may be randomly oriented.

Abstract: Universal supports for oligonucleotide synthesis include a support material represented by the following formula: In this formula, substituent A is selected from H, alkyl, aryl, or a polymeric or silica base material; substituent B is selected from acyl, aroyl, or a polymeric or silica base material; and substituent C is selected from a dimethoxytrityl group or a protecting group removable under acidic or neutral conditions. For the supports, one of substituents A or B constitutes the polymeric or silica base material. In use, an oligonucleotide is attached to the support at substituent C.

Abstract: The present invention provides a series of artificial CpG-containing single-stranded oligodeoxynucleotides (ODNs), each of which is consisted of single-stranded oligodeoxynucleotide DNA molecule containing one or more CpG(s), wherein said ODNs can stimulate human peripheral blood mononuclear cell (PBMC) to produce antiviral substances. These ODNs can protect the cells against the attack from virus, wherein said virus is preferably selected from the group consisted of influenza virus and single-stranded positive strand RNA virus such as SARS virus, hepatitis C virus, dengue virus and Japanese encephalitis virus. Moreover, the antiviral use of artificial CpG ODNs and its use for treating and preventing viral infection are also provided.

Abstract: A method for simplification of a microbial genome or microbial nucleic acid comprising treating microbial genome or nucleic acid with an agent that modifies cytosine to form derivative microbial nucleic acid and amplifying the derivative microbial nucleic acid to produce a simplified form of the microbial genome or nucleic acid.

Abstract: Immunostimulatory agents, including nucleic acids having one or more than one locked nucleic acid (LNA) nucleosides are provided. The nucleic acids may further comprise CpG motifs. The nucleic acids may be double stranded, and may comprise dsRNA.

Abstract: Methods for synthesizing a collection of partially identical polynucleotides are disclosed.

Abstract: The invention relates to methods of using fragmented RNA, such as RNA obtained from archived fixed paraffin-embedded tissue material (FPET RNA) or other clinically biopsied tissue specimens for universal gene expression profiling.

Abstract: The invention generally relates to a complex mixture of oligonucleotide primers and/or probes. Another aspect of the invention includes a method of selective priming of a target nucleic acid.

Abstract: The present invention relates to a method of producing single-stranded nucleic acid molecules from oligo- or polynucleotides wherein each of said oligo- or polynucleotides has a predefined 5? or 3? terminus, comprising the steps of (a) annealing an adaptor oligonucleotide simultaneously or step by step to (aa) a first oligo- or polynucleotide; and (ab) a second oligo- or polynucleotide wherein the 5?-terminus of said adaptor oligonucleotide is complementary in sequence to the 5? terminus of said first oligo- or polynucleotide and the 3?terminus of said adaptor molecule is complementary in sequence to the 3? terminus of said second oligo- or polynucleotide; and optionally (a?) simultaneously with or subsequently to step (a) annealing at least one further adaptor oligonucleotide to free termini of said first or second oligonucleotides and to free termini of further oligo- or polynucleotides; (b) optionally filling in gaps between the neighbouring ends of said oligo- or polynucleotides; (c) ligating said oligo-

Abstract: The present invention provides methods and compositions for performing nucleic acid mediated chemistry in a variety of organic solvents. A variety of nucleic acid mediated chemical reactions may be efficiently carried out in organic solvents.

Abstract: This invention relates to agents and conjugates that can be used to detect and isolate target components from complex mixtures such as nucleic acids from biological samples, cells from bodily fluids, and nascent proteins from translation reactions. Agents comprise a detectable moiety bound to a photoreactive moiety. Conjugates comprise agents coupled to substrates by covalent bounds which can be selectively cleaved with the administration of electromagnetic radiation. Targets substances labeled with detectable molecules can be easily identified and separated from a heterologous mixture of substances. Exposure of the conjugate to radiation releases the target in a functional form and completely unaltered. Using photocleavable molecular precursors as the conjugates, label can be incorporated into macromolecules, the nascent macromolecules isolated and the label completely removed.

Abstract: The invention provides a highly efficient, rapid, and cost effective method of linking nucleic acid components in a predetermined order to produce a nucleic acid multicomponent construct. The invention further provides nucleic acid components, each nucleic acid component comprising a double stranded nucleic acid molecule having at least one single stranded 5? or 3? terminal sequence, the terminal sequence having sufficient complementarity to either a terminal sequence in a separate nucleic acid component or to a sequence in a linking nucleic acid molecule so as to allow for specific annealing of complementary sequences and linkage of the components in a predetermined order. Kits containing reagents required to practice the method of the invention are also provided.

Abstract: This invention relates to a process for stereoselectively preparing a nucleoside of the following formula: wherein R3, R4, and B are defined herein. The process includes reacting a furanose compound with a nucleobase in the presence of a halide salt. Also disclosed is another process for stereoselectively synthesizing an intermediate that can be used to make the starting compound in the first-mentioned process.

Abstract: The present invention relates in one aspect to a method for determining the cell culture history of a cell unit labelled with more than one type of tag comprising the steps of: (a) measuring one or more parameters of each tag that is used to label the cell unit; (b) identifying each tag in the cell unit; and (c) correlating the identity of each tag to the identity of the cell unit and/or the specific cell culture conditions to which the cell unit has been exposed.

Abstract: The present invention relates to expression cassettes comprising transcription regulating sequences with constitutive expression profiles in plants obtainable from Arabidopsis thaliana genes At5g17920, At3g03780, At2g01100, At2g34770, At5g61560, At4g00830, At3g10220, At4g38520, At3g1111, At2g47170, At1g64090, At5g60690, At1g76350, At1g7650, At1g31930, At5g18230, At1g20970, or At4g35620.

Abstract: Polynucleotides having in excess of 1,000 nucleotides can be prepared using a solid phase synthesis technique. A feature of the technique is the use of a reusable solid support that contains covalently bound oligonucleotide. This covalently bound oligonucleotide is annealed to a bridge oligonucleotide, where the bridge is also annealed to a first oligonucleotide that forms a portion of the target polynucleotide. After the target polynucleotide is synthesized, it can be removed from the solid support under denaturing conditions, and the solid support re-used to prepare additional target polynucleotides. The yield of the target polynucleotide increases when shearing force is applied to the solid support that is linked to the growing oligonucleotide. This shearing force is thought to extend the growing end of the oligonucleotide away from contact with other oligonucleotide bound to the solid support and make that end more accessible to annealing with solution oligonucleotide.

Abstract: The invention provides a method for stably cross-linking a first nucleic acid sequence selected for being stably cross-linked in the presence of a second nucleic acid sequence selected for not being stably cross-linked in a nucleic acid molecule. The method comprises providing a nucleic acid sequence that is complementary to the first nucleic acid sequence; hybridizing the first nucleic acid sequence to its complementary sequence; and stably cross-linking the first nucleic acid sequence to the complementary sequence.

Abstract: The present invention relates to a copolymer termed a ladder copolymer because it has two backbones that serve as legs/sides of a ladder structure. These two backbones, one of which is a nucleic acid or nucleic acid-like polymer, are linked together as the legs/sides of a ladder are linked together by the rungs.

Abstract: The invention relates to the field of bioinformatics and in particular of biomolecular computing (‘DNA computing’). “Computational genes” comprising nucleic acids are provided which, via autonomous spontaneous self-assembly, can be produced in vivo by means of a biomolecular finite automaton.

Abstract: The invention relates to a method and apparatus for the fragmentation of large molecules, especially biopolymers. The invention consists in reacting analyte ions with excited or radical neutral particles, whereby, at least in the case of bombardment of analyte ions with helium atoms from an FAB generator, a new type of fragmentation occurs which strongly resembles fragmentation by electron capture (ECD). The reactions may be performed in magnetic ion traps (ion cyclotron resonance cells, ICR), in RF ion traps according to Wolfgang Paul, in RF ion guides, or in free beams of analyte ions or neutral particles.

Abstract: The invention provides nucleotide analogs for use in sequencing nucleic acid molecules.

Abstract: Oliognucleotide primers are provided that are specific for nucleic acid characteristic of certain beta-lactamases. The primers can be employed in methods to identify nucleic acid characteristic of family-specific beta-lactamase enzymes in samples, and particularly, in clinical isolates of Gram-negative bacteria.

Abstract: Conventional techniques for preparing a chimera gene having an inverted repeat sequence of a target sequence suffer from complications since a target sequence is inserted into 2 sites on a vector in sense and antisense orientations, and restriction enzyme recognition sequences must be independently provided at an insertion site of a vector and both ends of the target sequence. In this invention, a cassette construct comprising an arbitrary adaptor sequence and an inverted adaptor sequence separated by an arbitrary spacer sequence or a plasmid vector comprising such cassette construct incorporated therein is prepared, a target sequence is ligated to either or both ends of the cassette construct, or a target sequence is inserted into one end of the cassette construct on the plasmid vector, followed by PCR. Thus, a chimera gene having an inverted repeat sequence is prepared.

Abstract: A method for preparing a crosslinked polymer coated controlled porosity glass (CPG) particle is provided. The method involves mixing CPG particles in a solution comprising polyvinylbenzylchloride and a first solvent at a temperature below 10° C. A second solvent is added and a crosslinking agent is added to the mixture. The first solvent is removed rapidly within 1½ hours of addition of the crosslinking agent. The crosslinking reaction is permitted to proceed and the mixture is then cooled and treated to remove any remaining solvent. The resulting coated CPG particles are washed and dried. Also provided a polymer coated CPG particles using for loading ligand thereon.

Abstract: Novel compounds are provided which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar—C(R1)(R2)—O—C(O)-wherein: Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative thereof; R1 and R2 are independently H, optionally substituted alkyl, alkenyl or alkynyl, optionally substituted aryl or optionally substituted heteroaromatic, or a vinylogous derivative of the foregoing; and X is a leaving group, a chemical fragment linked to Ar—C(R1)(R2)—O—C(O)— via a heteroatom, or a solid support; provided that when Ar is 1-pyrenyl and R1 and R2 are H, X is not linked to Ar—C(R1)(R2)—O—C(O)— via a nitrogen atom.

Abstract: The embodiments of the present invention are directed to discrete, cis-acting regulatory elements that include a barrier element, an insulating element, a silencing element, and matrix attachment regions (“MARs”). Additional embodiments of the present invention are directed to nucleic acid molecules that are useful for facilitating stable transgene expression within a chromatin environment. Additional embodiments of the present invention are directed to recombinant expression vectors including nucleic acid molecules of the present invention that can be incorporated into artificial chromosomes, eukaryotic cell-lines, non-human transgenic animals, and transgenic plants, to improve recombinant protein production in a broad range of eukaryotic hosts, and pharmaceutical compositions including nucleic acid molecules of the present invention that are also useful for gene therapy in the treatment of various genetic diseases.

Abstract: The present invention provides compositions and methods for detecting incorporation of a labeled nucleotide triphosphate onto the growing end of a primer nucleic acid molecule. The method is used, for example, to genotype and sequence a nucleic acid. In a preferred embodiment, the method described herein detects individual NTP molecules.

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: Based at least in part on an understanding of the mechanisms by which small RNAs (e.g., naturally-occurring miRNAs) mediate RNA silencing in plants, rules have been established for determining, for example, the degree of complementarity required between an RNAi-mediating agent and its target, i.e., whether mismatches are tolerated, the number of mismatches tolerated, the effect of the position of the mismatches, etc. Such rules are useful, in particular, in the design of improved RNAi-mediating agents which allow for more exact control of the efficacy of RNA silencing.

Abstract: This invention relates to a new method of synthesis of biologically active substances of determined structure directly in the cells of living organisms containing specific RNA or DNA molecules of determined sequence. The method is based on the hybridization of two or more oligomers bound with biologically inactive precursors of biologically active substances to specific RNA or DNA in vivo in the cells of living organisms. After hybridization of the oligomers to RNA or DNA the biologically inactive precursors bound to the 5? and/or 3? ends of the oligomers can interact with each other to make biologically active form of the substances. This changing of properties is due to chemical reactions which bind the biologically inactive precursors through a chemical bond into a biologically active form of the whole compound.