Abstract: The present invention provides a process for the sulfurization of phosphorus-containing compounds. More particularly, the process involves contacting the compound to be sulfurized with a sulfur transfer reagent as defined hereinbefore in a solvent or a mixture of solvents.

Abstract: The purpose of the invention is to develop a silyl linker that can be efficiently introduced on a solid-phase support used for the synthesis of nucleic acid oligomers such as DNA. The present invention relates to a silyl linker for use in the solid-phase synthesis of nucleic acid, comprised of a compound of the general formula or its ester or salt: H—(R1)Si(R2)-(C6H4)—CONH-(A)-COOH??(I) wherein each of R1 and R2 is an alkyl or aryl group, and (A) represents a spacer moiety; a 3?-end nucleoside unit having said compound linked via an oxygen atom to the 3-position of a sugar of the nucleoside or its derivative, a solid-phase support having the 3?-end nucleoside unit, and a method for synthesis of nucleic acid oligomer with the use of said solid-phase support.

Abstract: A method of producing a polydeoxyribonucleotide molecule by reverse transcriptase polymerase chain reaction wherein the polydeoxyribonucleotide molecule has a length of greater than 5,000 base-pairs is disclosed. The method involves combining two reverse transcriptases followed by two protocols of polymerase chain reaction. This method enable the amplification of large DNAs, such as viruses, from a sample while preserving genetic diversity of the large DNA.

Abstract: The present invention provides compounds having a chelating moiety and an oligonucleotide sequence wherein the oligonucleotide includes one or more modified nucleobases, such as hydroxynucleobases. The disclosed compounds are suitable for antisense therapy. The chelating moiety can be complexed to an ion of a lanthanide metal. These compounds are efficient translation inhibitors of nucleic acids and have increased binding affinity for target nucleic acids. The invention also includes compositions and methods of using these compositions as antisense therapy.

Abstract: The invention relates to a novel strategy for the synthesis of Locked Nucleic Acid derivatives, such as ?-L-oxy-LNA, amino-LNA, ?-L-amino-LNA, thio-LNA, ?-L-thio-LNA, seleno-LNA and methylene LNA, which provides scalable high yielding reactions utilising intermediates that also can produce other LNA analogues such as oxy-LNA. Also, the compounds of the formula X are important intermediates that may be reacted with varieties of nucleophiles leading to a wide variety of LNA analogues.

Abstract: Oligonucleotide analogues are provided that incorporate 5-aza-cytosine in the oligonucleotide sequence, e.g., in the form of 5-aza-2?-deoxycytidine (decitabine) or 5-aza-cytidine. In particular, oligonucleotide analogues rich in decitabine-deoxyguanosine islets (DpG and GpD) are provided to target the CpG islets in the human genome, especially in the promoter regions of genes susceptible to aberrant hypermethylation. Such analogues can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position. Methods for synthesizing these oligonucleotide analogues and for modulating nucleic acid methylation are provided. Also provided are phosphoramidite building blocks for synthesizing the oligonucleotide analogues, methods for synthesizing, formulating and administering these compounds or compositions to treat conditions, such as cancer and hematological disorders.

Abstract: The present invention relates to methods for treating cancers by manipulating a target gene expression by up-regulation, silencing and/or down-regulation of the gene, such as EGFR-RP, TRA1, MFGE8, TNFSF13 and ZFP236, respectively. The methods are useful in treating cancers and/or inhibiting tumor growth by enhancing expression of a gene that is validated as a target such as ICT1030, for protein, peptide drug and gene therapy modalities; or by RNA interference to silence and/or down-regulate targets such as ICT1024, ICT1025 and ICT1031 and ICB1003 that are validated for antibody, small molecule and other inhibitor drug modalities.

Abstract: The present invention features novel compositions, linkers, derivatized solid supports, and methods for the efficient solid phase synthesis of oligonucleotides, including RNA, DNA, RNA-DNA chimeras, and analogs thereof.

Abstract: The invention provides methods of diagnosing diseases and conditions associated with PKC?, methods for identifying compounds that can be used to treat or to prevent such diseases and conditions, and methods of using these compounds to treat or to prevent such diseases and conditions. Also provided in the invention are animal model systems that can be used in screening methods.

Abstract: Methods and compositions for synthesizing polymers, such as nucleic acids, are provided. Aspects of the invention include methods in which lipids and monomeric precursors, e.g., mononucleotides, of the desired polymeric products are combined to produce a reaction mixture. The reaction mixture is then subjected to one or more steps of drying and rehydrating to produce a desired polymeric product, e.g., nucleic acid. Also provided are the polymeric products themselves, e.g., nucleic acid products, as well as systems and kits for practicing embodiments of the invention.

Abstract: The invention provides nucleotide analogs and methods of using them in sequencing reactions.

Abstract: This invention relates to the use of tumor-derived or associated extracellular ribonucleic acid (RNA) found circulating in the plasma or serum fraction of blood for the detection, monitoring, or evaluation of cancer or premalignant conditions. Specifically, this invention enables the extraction of circulating RNA from plasma or serum and utilizes nucleic acid amplification assays for the identification, detection, inference, monitoring, or evaluation of any neoplasm, benign, premalignant, or malignant, in humans or other animals, which might be associated with that RNA. Further, this invention allows the qualitative or quantitative detection of tumor-derived or associated extracellular RNA circulating in the plasma or serum of humans or animals with or without any prior knowledge of the presence of cancer or premalignant tissue.

Abstract: The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.

Abstract: This invention provides methods for detecting the presence of malignant or premalignant cells, or trophoblastic cells in a human wherein the malignant, premalignant or trophoblastic cells express 5T4. The methods of the invention detect 5T4 RNA in blood, blood plasma, serum, and other bodily fluids. The inventive methods are useful for detection, diagnosis, monitoring, treatment, or evaluation of neoplastic disease, and for the detection and evaluation of placental tissue in pregnant women.

Abstract: This disclosure provides novel reversibly terminated ribonucleotides which can be used as a reagent for DNA sequencing reactions. Methods of sequencing nucleic acids using the disclosed nucleotides are also provided.

Abstract: A process of manufacturing oligonucleotides includes a 5?-deblocking step in which the 5-blocking group is removed with dichloroacetic acid that is essentially free of chloral. The process is useful for making oligonucleotides that are substantially free of chloral adducts.

Abstract: The current invention restates substituted indole nucleosides as both terminal as well as internal building blocks of labeled oligonucleotide probes for the detection, analysis and quantitation of nucleic acids. The substituent comprises a linker and a detectable group or a linker and a reactive group for post synthesis coupling. These modified nucleosides grant access to a wide application area. These new substituted indole nucleosides can be used as labeling reagents for the facile preparation of e.g. optimized hybridization probes, Taqman-probes, or molecular beacon probes.

Abstract: The current invention restates substituted nitroindole nucleosides as both terminal as well as internal building blocks of labeled oligonucleotide probes for the detection, analysis and quantitation of nucleic acids. The substituent comprises a linker and a detectable group or a linker and a reactive group for post synthesis coupling. These modified nucleosides grant access to a wide application area. These new substituted nitroindole nucleosides can be used as labeling reagents for the facile preparation of, e.g., optimized hybridization probes, simple probes, TAQMAN-probes or molecular beacon probes.

Abstract: Highly functionalized, porous organosilica particles and methods of their synthesis are described that employ high amounts of functional silane such as 3-mercaptopropyl trimethoxysilane. Silane particle diameters are controlled from less than 1 ?m to over 100 ?m. The particles have a high surface area due to their advantageous internal structures, which consist of large pores, typically up to 10 ?m that are linked by small channels of typically about 20 nm diameter. Isothiocyanate modified fluorescent dyes can enter and react with thiol groups inside the pores. The invention also provides clear silica shells of controlled thicknesses to protect fluorescent signals and provide an independent parameter for distinguishing particle types based on light scattering off different sized particles. The particles are stable and useful for many purposes, particularly for optical bar coding in combinatorial synthesis of polymers such as nucleic acid, polypeptide, and other synthesized molecules.

Abstract: The present invention provides methods of enhancing the efficacy and specificity of RNA silencing. The invention also provides compositions for mediating RNA silencing. In particular, the invention provides siRNAs, siRNA-like molecules, shRNAs, vectors and transgenes having improved specificity and efficacy in mediating silencing of a target gene. Therapeutic methods are also featured.

Abstract: A method for controlling the use of oligonucleotide sequences released from arrays, comprises synthesizing a chemical array of oligonucleotides on a substrate under conditions for producing an array of cleavable oligonucleotides that are blocked from enzymatic reactions after cleavage. Methods may also include receiving a chemical array of cleavable oligonucleotides on a substrate, and cleaving the oligonucleotides from the array, wherein the oligonucleotides are blocked from enzymatic reactions after cleavage. Arrays, populations of oligonucleotides and kits are also provided to facilitate the methods.

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: The object of the present invention is to provide a nucleoside or nucleotide having an unnatural base. The nucleoside or nucleotide of the present invention has a 5-substituted-2-oxo(1H)-pyridin-3-yl group as a base. Preferably, the 5-position of the above base is substituted with a substituent selected from the group consisting of the following: 1) a photoreactive group selected from iodine and bromine; 2) an alkenyl group, an alkynyl group or an amino group, or a derivative thereof; 3) biotin or a derivative thereof; and 4) a fluorescent molecule selected from fluorescein, 6-carboxyfluorescein, tetramethyl-6-carboxyrhodamine, and derivatives thereof.

Abstract: This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions.

Abstract: Disclosed are a method, device kit, and automated system for simple, reproducible, and high-throughput quantification of mRNA from whole blood. More particularly, the method, device, kit and automated system involve combinations of leukocyte filters attached to oligo(dT)-immobilized multi-well plates.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of CD40. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding CD40. Methods of using these compounds for modulation of CD40 expression and for treatment of diseases associated with CD40 are provided.

Abstract: Provided are a method of detecting a target substance whereby the detection sensitivity in the PALSAR method can be improved and multiple genes can be simultaneously detected, and a kit for detection. The method of detecting a target substance is a method of detecting a target substance by forming a signal probe polymer using one or more sets of paired dimer-forming probes for forming dimer probes or dimer probes, one or more kinds of crosslinking probes, and one or more kinds of assist probes, in which a dimer-forming probe includes a 5?-side region, a central region, and a 3?-side region, a crosslinking probe includes two regions, i.e.

Abstract: The present invention provides the combination of the O-2 diphenylcarbamoyl (“DPC”) and N-6 dimethylaminomethylidene (“DMF”) protecting groups for isoguanosine nucleosides that can be utilized in oligonucleotide synthesis.

Abstract: The anchoring system generally comprises a solid support and a chemical linking moiety useful for ether formation with another chemical moiety on a nucleic acid molecule. The present invention further contemplates methods for anchoring a nucleic acid molecule to a solid support via a covalent linkage. The anchoring system of the present invention is useful inter alia in construction of nucleic acid arrays, to purify nucleic acid molecules and to anchor nucleic acid molecules so that they can be used as templates for in vitro transcription and/or translation experiments and to participate in amplification reactions. The present invention is particularly adaptable for use with microspheres and the preparation of microsphere suspension arrays and optical fiber arrays. The anchoring system permits the generation of an anchored oligonucleotide for use as a universal nucleic acid conjugation substrate for any nucleic acid molecule or population of nucleic acid molecules.

Abstract: A method of making a set of labelled compounds by the use of a preferably particulate support, comprises dividing the support into lots, performing a different chemical reaction on each lot of the support, e.g. to couple a chemical moiety to that lot of the support, tagging a fraction of each lot of the support with a different label, and combining the said lots of the support. The steps are repeated several times, preferably to build up oligomer molecules carrying labels which identify the nature and position of a monomer unit of the oligomer, and which are releasable from the support. Preferred labels, which are releasable from the compounds by cleavage to provide charged groups for analysis by mass spectrometry, are groups of the trityl (trimethylphenyl) family. Also claimed are libraries of these labels and their use in assays and nucleic acid analysis methods.

Abstract: The present invention concerns modified oligonucleotides and processes for their production wherein these oligonucleotides contain at least once the structure P?N-Acc where Acc is an electron acceptor or an electron acceptor substituted with a residue R and R is any organic substituent.

Abstract: Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.

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

Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.

Abstract: The present invention relates to an automated polymer synthesis apparatus for synthesizing a polymer chain onto a solid substrates by sequentially adding polymer building blocks as well as to a method for synthesizing polymers on solid substrates by sequentially reacting polymer building blocks with reactive groups. The invention further relates to a biochip comprising a solid substrate with reactive groups where biomolecules are attached to and the remaining reactive groups are transformed into chemically inert species.

Abstract: Novel iminium-type coupling agents containing proton acceptors in their iminium moiety, which can be used beneficially as coupling agents in various chemical polypeptide and/or polynucleotide syntheses, and are particularly useful as yield enhancing and racemization suppressing coupling agents for use in peptide syntheses, are disclosed. Further disclosed are a process of preparing such iminium-type coupling agents and their use in the preparation of polypeptides and/or polynucleotides.

Abstract: An oligonucleotide array comprising an array of multiple oligonucleotides with different base sequences fixed onto known and separate positions on a support substrate, wherein said oligonucleotides are biological stress related genes or complementary sequence chains to the said genes, and the said oligonucleotides are classified according to their gene functions, wherein the fixation region on the support substrate is divided into the said classification.

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: The present invention provides selenium derivatives of nucleosides, nucleoside phosphoramidites, nucleotides, nucleotide triphosphates, oligonucleotides, polynucleotides, and larger nucleic acids and methods for their synthesis. Selenium derivatives of both ribonucleic acids and deoxyribonucleic acids, as well as methods for their synthesis, crystallization and uses in structural determinations, particularly by X-ray crystallographic techniques are disclosed. The selenium derivatives of the present invention are also useful as food supplements.

Abstract: A process for the preparation of an oligonucleotide having at least one phosphate internucleotide linkage I provided. The process comprises the steps of: a) forming a nascent oligonucleotide comprising a phosphorus (III) internucleotide linkage; and b) oxidation of the nascent oligonucleotide with aqueous iodine solution thereby to form a phosphorus (V) internucleotide linkage; wherein the oxidation is carried out in the presence of a base, the conjugate acid of said base having a pKa higher than the pKa of the conjugate acid of pyridine. Preferably the base is N-methylimidazole.

Abstract: The present invention relates to a method for synthesizing templated molecules. In one aspect of the invention, the templated molecules are linked to the template which templated the synthesis thereof. The intion allows the generation of libraries which can be screened for e.g. therapeutic activity.

Abstract: Methods for producing pathogen-inducible promoters for the expression of genes in plants are provided. The pathogen-inducible promoters are inducible by one, two, three, or more plant pathogens. Methods for producing R genes that are inducible in a plant by more than one plant pathogen are further provided.

Abstract: The use of N-formamidino-5-amino-3H-1,2,4-dithiazole-3-thiones as novel, efficient sulfur-transfer reagents is disclosed. The sulfur transfer from these reagents to compounds containing P(III) atom, triphenylphosphine, 5?-O-DMT-thymidine 2-cyanoethyl-(N,N-diisopropyl)phosphoramidite, and 5?-O-DMT-3?-O-levulinyl dithymidilyl 2-cyanoethyl phosphite, was studied in solution by 31P NMR and HPLC. The sulfur transfer from title compounds was also studied in the solid-phase synthesis of oligonucleotide phosphorothioates by phosphoramidite methods. In this application, the efficiency of the sulfur transfer reaction for 2?-deoxyoligonucleotides was better than 99.5%. The novel sulfurizing agents are synthesized, at low cost, using simple chemical methods.

Abstract: To provide an amidite for nucleic acid synthesis, which enables a protective group therein to be removed under moderate conditions and can be practically used, and a nucleic acid synthesizing method using the amidite for nucleic acid synthesis. Specifically, the present invention relates to an amidite for nucleic acid synthesis represented by General Formula (I) below, and a nucleic acid synthesizing method using the amidite for nucleic acid synthesis: where X denotes a base; Y denotes a protective group formed of any one of a 4-aminobutyric acid derivative, an o-aminomethylbenzoic acid derivative, an o-aminophenylacetic acid derivative, an o-aminoethylbenzoic acid derivative, an o-aminomethylphenylacetic acid derivative, an o-aminophenylpropionic acid derivative and a 5-aminovaleric acid derivative; and Q denotes one of a hydrogen atom and a hydroxyl group.

Abstract: Methods for the formation of sulfurized oligonucleotides are provided. The methods allow for the formation of phosphorothioate linkages in the oligonucleotides or derivatives, without the need for complex solvent mixtures and repeated washing or solvent changes. Oligonucleotides having from about 8, and up to about 50, nucleotides can be sulfurized according to the methods of the invention with higher yields than have been previously reported.

Abstract: Methods and probes are provided for the analysis of target sequences having two or more polymorphisms wherein one of the polymorphisms is to be distinguished and another polymorphism is to be masked.

Abstract: The invention pertains to different methods employing the use of a polynucleotide comprising ribose rings which carry a modification at the 2?-OH group.

Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.

Abstract: Disclosed, among other things, are primers containing certain modified nucleobases in the 3? terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof.

Abstract: The methods of the invention detect epidermal growth factor RNA, epidermal growth factor receptor RNA, her-2/neu RNA, c-myc RNA, heterogeneous nuclear ribonucleoprotein A2/B1 RNA or any combination thereof in blood plasma, serum, and other bodily fluids. The inventive methods are useful for detection, diagnosis, monitoring, treatment, or evaluation of neoplastic disease.