Abstract: The present invention relates to novel bicyclic and tricyclic nucleoside and nucleotide analogues as well as to oligonucleotides comprising such elements. The nucleotide analogues, LNAs (Locked Nucleoside Analogues), are able to provide valuable improvements to oligonucleotides with respect to affinity and specificity towards complementary RNA and DNA oligomers. The novel type of LNA modified oligonucleotides, as well as the LNAs as such, are useful in a wide range of diagnostic applications as well as therapeutic applications. Among these can be mentioned antisense applications, PCR applications, strand displacement oligomers, as substrates for nucleic acid polymerases, as nucleotide based drugs, etc. The present invention also relates to such applications.

Abstract: Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are also optionally included within such template constructs. Methods are also provided for the use and preparation of these constructs as well as sequencing compositions for their application.

Abstract: Disclosed are conjugates comprising a dendrimer and a ligand, which is a functionalized congener of an agonist or antagonist of a receptor of the G-protein coupled receptor (GPCR) superfamily, for example, wherein the functionalized congener is an A1 adenosine receptor agonist having a purine nucleoside moiety and a functional group at the N6 position of the purine nucleoside moiety, wherein the functional group has the formula (I): N6H—Ar1—CH2—C(?O)NH—R1 (I), wherein Ar1 and R1 as defined herein. Also disclosed are pharmaceutical compositions, methods of treating various diseases, and a diagnostic method employing such conjugates.

Abstract: Nucleic acid aptamers are described herein which can transduce a signal into cells by crosslinking a cell surface molecule, thereby inducing of one or more biological activities by the cells; in serving as agonists.

Abstract: An oligonucleotide which comprises at least one internucleotide linkage comprising a P—S—R bond and at least two nucleosides, wherein R corresponds to the formula (I) wherein A is a geminally substituted alkylene group, preferably CH2, X and Y are independently selected from S and O, and R0 is selected from the group consisting of optionally substituted carbon bonded organic residue, such as in particular optionally substituted alkyl or aryl, SRx, ORx and NRxRy wherein Rx and/or Ry are selected from H and organic residues and at least Rx is a substituent other than H. Another object of the invention is a sulfurizing agent useful for oligonucleotide manufacture and the manufacture thereof.

Abstract: Disclosed herein are uniquely distinct nucleic acid tags and methods for their use and production. The disclosed tags do not hybridize to a genome of interest and thus can be used as labels without generating background signal associated with unintended hybridization. In one example, tag sequences are derived from a genome divergent to the genome of interest. The divergent genome provides a vast library of potential tag sequences. These potential tag sequences can be screened using a bioinformatics-based approach against the genome of interest. These potentially distinct sequences can then be synthesized and tested empirically against the genome of interest to identify those sequences that are uniquely distinct. The tags can then be produced, for example by oligonucleotide synthesis techniques.

Abstract: The invention relates to a method that can be carried out in parallel and automated for the production of any nucleic acid, comprising the following steps: a) coupling an oligonucleotide to a solid matrix b) adding an additional oligonucleotide c) ligating the oligonucleotides from steps a) and b) in one orientation d) removing excess reactants and enzymes from the reaction preparation e) cleaving the ligation product from step c) with a restriction enzyme that cleaves outside the recognition sequence, whereby cleavage occurs in the oligonucleotide from step a) or in the oligonucleotide from step b) f) separating the reaction mixture from the lengthened or shortened oligonucleotide from step a) that is obtained in step e) g) repeating steps b) to f) at least once h) successive sequence-independent linkage of the fragments obtained after performing steps a) to g) until the desired product is obtained.

Abstract: The invention relates to double-stranded RNA molecules in which each strand of said molecule possesses: (a) sufficient complementarity to a target mRNA molecule to facilitate cleavage thereof; and (b) sufficient complementarity to the other strand of the double-stranded RNA molecule so as to form a stable duplex; and in which at least one strand of said molecule possesses: (c) a seed region of complementarity to at least one seed site present in a 3? untranslated region of at least one target mRNA molecule.

Abstract: A method for detecting the presence of a target nucleotide sequence in a sample of DNA is described herein in which a test sample comprising single stranded DNA is exposed to a DNA probe and a nicking endonuclease under conditions that would permit sequence-specific hybridization of the probe to a complementary target sequence. The probe comprises a sequence complementary to the target sequence to be detected and this sequence also includes a recognition sequence for the nicking endonuclease. If the sample contains the target sequence, the probe hybridizes to the target and is cleaved by the nicking endonuclease, which leaves the target intact. Observing the presence of probe cleaved by the nicking endonuclease indicates the presence of the target nucleotide sequence in the sample of DNA.

Abstract: The invention provides method of covalently coupling two or more moieties, the method comprising: (a) providing a first moiety having covalently attached thereto (i) at least one first linker comprising a first hybridizable region and (ii) at least one first group capable of forming a covalent bond; (b) providing a second moiety having covalently attached thereto (i) at least one second linker comprising a second hybridizable region capable of hybridizing to the first hybridizable region and (ii) at least a second group capable of forming a covalent bond with the first group; (c) contacting the first and second moieties under conditions that allow the first and second hybridizable regions to hybridize and link the moieties; and (d) exposing the linked moieties to conditions that allow the formation of a covalent bond between the first and second groups.

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: Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array.

Abstract: There is provided a method for cleaving a target nucleic acid at a desired site using a metal ion or a metal ion complex as a catalyst for cleaving a nucleic acid (DNA, etc.), which has high site-selectivity, high reaction efficiency and low side-reactivity (non-specific reactivity), and is economical and convenient. The method for cleaving a target nucleic acid of the present invention comprises allowing a target nucleic acid to come into contact with a specific complex compound and a metal ion or a metal complex, or allowing a target nucleic acid to come into contact with a specific complex compound, to which a metal ion or a metal complex binds.

Abstract: The invention provides a novel method of labeling oligonucleotides, with reporter moieties, including but not limited to, quenchers, fluorophores, biotin, digoxigenin, peptides and proteins. In addition, this invention provides a method of detecting hybridization of oligonucleotides. This invention also provides novel azo quenchers having the general formula shown below. The invention further provides compositions comprising labeled oligonucleotides and solid supports. The invention also provides kits comprising at least one composition of the present invention.

Abstract: The disclosed invention pertains to improved oligonucleotide manufacturing methods, including novel support compositions that are optionally labeled, their methods of preparation and use. The compositions and methods are particularly well suited for high throughput oligonucleotide manufacturing in that the automated support recognition facilitates loading of the wells with the proper supports. In addition, the labeled supports can be used to confirm that each well of a multi-well plate, such as a 96 or 384 well plate, was properly loaded.

Abstract: Microfluidic nucleic acid hybridization systems are described that include a first reaction chamber to hold an analyte solution comprising nucleic acids, and a first mixing channel in fluid communication with the chamber. The mixing channel includes a textured surface to mix the analyte solution. The systems may also include pump coupled to the mixing channel to circulate the analyte solution through the reaction chamber and the mixing channel, and an input port in fluid communication with the mixing channel and the reaction chamber to supply the analyte solution to the microfluidic system. The input port can be closed to create a closed circulation path for the analyte solution through the reaction chamber and the mixing channel.

Abstract: A method to link a light emitting reporter to biomolecules with nucleotide oligomers is described. The light reporter particles are silylated and functionalized to produce a coated light reporter particle, prior to covalently linking the biomolecules to the light reporter particle. The light reporter particle generated by the methods of the invention can be excited by a light excitation source such as UV or IR light, and when the biomolecule is DNA, the attached DNA molecule(s) are detectable by amplification techniques such as PCR.

Abstract: The present invention relates to small-interfering RNA molecules displaying an increased thermodynamic stability at the 3? end of the antisense strand (guide strand) and the 5? end of the sense strand (passenger strand), respectively, in comparison to the base pairing in the seed region. The siRNAs of the present invention display an increased knock-down activity against targeted genes and show an improved resistance to RNAses, in particular serum RNAses. The present invention also relates to a method for the production of the siRNA molecules, a method of target-specific RNA interference making use of the improved siRNA molecules of the invention and pharmaceutical compositions containing the siRNA molecules.

Abstract: Methods and compositions are provided for producing hydrogel nucleic acid structures using photo-crosslinking. Methods of using the photo-crosslinked hydrogels for cell-free protein production, and for encapsulating and delivering compounds, are also provided.

Abstract: The invention provides analogs cyclic diguanosine monophosphate (c-di-GMP) having different substituents at the guanine C8 position.

Abstract: The invention features compounds of formula I or II: In one embodiment, the invention relates compounds and processes for conjugating ligand to oligonucleotide. The invention further relates to methods for treating various disorders and diseases such as viral infections, bacterial infections, parasitic infections, cancers, allergies, autoimmune diseases, immunodeficiencies and immunosuppression.

Abstract: A micro fluidic system includes a substrate, and, provided on said substrate, at least one flow path interconnecting with functional means in which liquid samples can be treated by desired procedures. The flow paths are laid out to form a pattern for the transport of liquid samples to and from said functional means. These flow paths comprise a plurality of micro posts protruding upwards from said substrate, the spacing between the micro posts being small enough to induce a capillary action in a liquid sample applied anywhere within any of said flow paths, so as to force said liquid to move from where said liquid sample was applied.

Abstract: The present invention provides a method for the preparation of 5-azacytidine, wherein 5-azacytidine is represented by the structure: The method involves the silylation of 5-azacytosine, followed by the coupling of silylated 5-azacytosine to a protected ?-D-ribofuranose derivative. The coupling reaction is catalyzed by trimethylsilyl trifluoromethanesulfonate (TMS-Triflate).

Abstract: Methods and apparatus relate to reduction of sequence errors generated during synthesis of nucleic acids on a microarray chip. The error reduction can include synthesis of complementary stands (to template strands), using a short universal primer complementary to the template strands and polymerase. Heteroduplex can be formed be melting and re-annealing complementary stands and template strands. The heteroduplexes containing a mismatch can be recognized and cleaved by a mismatch endonuclease. The mismatch-containing cleaved heteroduplexes can be removed from the microarray chip using a global buffer exchange. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.

Abstract: The present application provides polynucleotide structures such as nucleic acid ribbons and nucleic acid tubes, methods for making the polynucleotide structures, and methods for making two-dimensional or three-dimensional objects comprising the nucleic acid ribbons and nucleic acid tubes.

Abstract: Provided herein are signal activatable molecular constructs for enzyme-assisted delivery of molecules and related components, such as a sensor domain, compositions, methods and systems.

Abstract: The present embodiments relate to engineering imaging probes based on “triggered molecular geometry.” Upon detection of a molecular signal, nucleic acid hairpin monomers assemble an imageable molecular shape with prescribed geometry. In some embodiments the prescribed shape can be imaged directly. In some embodiments, the prescribed shape can serve as a spatial organizer or amplification scheme for other imaging entities, such as fluorophore and fluorescent proteins.

Abstract: The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).

Abstract: The present invention relates to a Drosophila in vitro system which was used to demonstrate that dsRNA is processed to RNA segments 21-23 nucleotides (nt) in length. Furthermore, when these 21-23 nt fragments are purified and added back to Drosophila extracts, they mediate RNA interference in the absence of long dsRNA. Thus, these 21-23 nt fragments are the sequence-specific mediators of RNA degradation. A molecular signal, which may be their specific length, must be present in these 21-23 nt fragments to recruit cellular factors involved in RNAi. This present invention encompasses these 21-23 nt fragments and their use for specifically inactivating gene function. The use of these fragments (or chemically synthesized oligonucleotides of the same or similar nature) enables the targeting of specific mRNAs for degradation in mammalian cells, where the use of long dsRNAs to elicit RNAi is usually not practical, presumably because of the deleterious effects of the interferon response.

Abstract: Compositions, methods and kits for detecting Group B streptococci. Particularly described are oligonucleotides that are useful as amplification primers and hybridization probes for detecting very low levels of Group B streptococci nucleic acids.

Abstract: Interfering RNA molecules are now designed and produced with specificity for multiple binding sequences present in distinct genetic contexts in one or more pre-selected target RNA molecules and are used to modulate expression of the target sequences. The multitargeting interfering RNA molecules have two strands that target multiple target sites on one or more pre-selected RNA molecules. Such a multitargeting interfering RNA approach provides a powerful tool for gene regulation.

Abstract: The synthesis of capped/tagged RNA, methods of use and kits providing same are contemplated. Tagged RNA permits isolation of RNA transcripts in vitro. The ability to isolate and purify capped RNA results in improved transcription and translation and provides a tool for identifying RNA-protein interactions. Such capped RNA finds use in therapeutic applications, diagnosis and prognosis and in the treatment of cancers and HIV.

Abstract: The present invention provides a method of producing a nucleic acid at high reaction efficiency and high reproducibility with a decreased variation in yield and purity among different reaction lots. A nucleic acid synthesis reaction is carried out on a first solid phase carrier capable of supporting nucleic acid synthesis contained in a solid phase carrier mixture comprising the first solid phase carrier and a second solid phase carrier that does not support nucleic acid synthesis.

Abstract: Strategically truncated probes specific for high-risk HPV nucleic acids, and methods for making and using the same, are disclosed herein. The disclosed probes, and methods of use thereof, permit fast and reliable detection of human papillomavirus in clinical samples without significant cross-reaction.

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: The invention provides methods and compositions for separately denaturing a probe and target in hybridization applications. The invention may, for example, eliminate the use of or reduce the dependence on formamide in hybridization applications. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

Abstract: Described are phosphoramidite nucleoside analog monomers, precursors thereof, and oligonucleotides including one or more of the monomers. The monomers can be used during automated synthesis of oligonucleotide derivatives, and allow for incorporation of one or several reporter groups, organic molecules, bio-molecules, small molecules or other chemical groups at the internucleoside phosphotriesters. Oligonucleotides including the monomers have a number of uses in therapeutic, diagnostic, and research applications.

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

Abstract: The invention provides highly sensitive, specific and efficient quantitative real-time PCR compositions, methods and assay kits to detect at least one IFN subtype and/or IFN subtype allotypic variants. Primer/probe sets complementary to the coding sequence of an IFN subtype of interest avoid spurious detection of degraded mRNA and enhances the correlation between the IFN subtype that is measured by the assays of the invention and the protein that is actually expressed. The invention also provides methods for designing primers and methods of using the compositions and assay kits. The compositions, kits, and methods of the invention may be used, for example, to monitor vaccine efficacy, autoimmune disease, chronic infections, or tumor therapy.

Abstract: The invention concerns novel regulatory elements as well as related vectors and cells. Furthermore, it relates to methods of improving expression of polypeptides from nucleic acids such as cloned genes and to the production of various polypeptides in host cells using said novel regulatory elements. Additionally, the invention relates to uses of said novel regulatory elements as insulators, in gene therapy or for improving host cell lines.

Abstract: The present invention relates to novel bicyclic and tricyclic nucleoside and nucleotide analogues as well as to oligonucleotides comprising such elements. The nucleotide analogues, LNAs (Locked Nucleoside Analogues), are able to provide valuable improvements to oligonucleotides with respect to affinity and specificity towards complementary RNA and DNA oligomers. The novel type of LNA modified oligonucleotides, as well as the LNAs as such, are useful in a wide range of diagnostic applications as well as therapeutic applications. Among these can be mentioned antisense applications, PCR applications, strand displacement oligomers, as substrates for nucleic acid polymerases, as nucleotide based drugs, etc. The present invention also relates to such applications.

Abstract: Double-stranded RNA (dsRNA) induces sequence-specific post-transcriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 19-23 nt short RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III-like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3? ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the produced siRNP complex.

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: The present invention is directed to sensitive and accurate multiplexed assays for target analyte detection and detection of methylation in nucleic acid samples.

Abstract: The invention provides for nucleotide analogs and methods of using the same, e.g., for sequencing nucleic acids.

Abstract: A method to make libraries of hybrid polynucleotide molecules of two parental polynucleotide molecules utilizing single-stranded DNA was invented. Example of the method comprises several steps: (i) preparation of two single-stranded polynucleotide molecules comprising sequences containing one or more parts of homology and one or more parts of heterology, (ii) random or non-random fragmentation of said polynucleotides, (iii) hybridization of the fragmented molecules followed by de novo polynucleotide synthesis (i.e. polynucleotide chain elongation) on the hybridized molecules, (iv) separation of the chain elongation products (i.e. double-stranded polynucleotide molecules) into single-stranded polynucleotide molecules (denaturation) (v) hybridization of the resultant single-stranded polynucleotide molecules followed by de novo polynucleotide synthesis on the hybridized molecules, and (vi) repeating at least two further cycles of steps (iv) and (v).

Abstract: Described herein are methods of syntheses of phosphorous atom-modified nucleic acids comprising chiral X-phosphonate moieties. The methods described herein provide backbone-modified nucleic acids in high diasteteomeric purity via an asymmetric reaction of an achiral molecule comprising a chemically stable H-phophonate moiety with a nucleoside/nucleotide.

Abstract: Methods for producing biomolecule-polymer conjugates, such as polypeptide-polymer conjugates, include attachment of an initiator agent to a biomolecule and in situ polymerization of a polymer from defined sites on the biomolecule. The conjugates may have desirable pharmacological properties and may be used therapeutically.

Abstract: The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5? end to prohibit degradation by a 5?-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface.

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