Abstract: Nucelosides and nucleotides containing a tricyclic base portion thereof are useful for treating infectious diseases and proliferative disorders, such as viral infections or cancer respectively.

Abstract: Described are modified mononucleotides and processes for their production wherein these nucleotides contain at least once the structure P?N-Acc in which Acc is an electron acceptor or an electron acceptor substituted with a residue R, and R is any organic substituent.

Abstract: The present invention includes compositions and methods useful for modulating protein expression. In certain embodiments, the present invention includes oligomeric compounds comprising modified nucleosides and modified internucleoside linkages.

Abstract: The present invention provides for the selective covalent modification of nucleic acids with redox active moieties such as transition metal complexes. Electron donor and electron acceptor moieties are covalently bound to the ribose-phosphate backbone of a nucleic acid at predetermined positions. The resulting complexes represent a series of new derivatives that are bimolecular templates capable of transferring electrons over very large distances at extremely fast rates. These complexes possess unique structural features which enable the use of an entirely new class of bioconductors and photoactive probes.

Abstract: 4-Amino-1-((2R,3S,4S,5R)-5-azido-4-hydroxy-5-hydroxymethyl-3-methyl-tetrahydro-furan-2-yl)-1H-pyrimidin-2-one (22) and prodrugs thereof are hepatitis C (HCV) polymerase inhibitors. Also disclosed are compositions and methods for inhibiting HCV and treating HCV-mediated diseases, processes for making the compounds and synthetic intermediates employed in the process.

Abstract: The present invention relates to a method for nucleic acid replication and novel artificial base pairs. The method of the present invention for nucleic acid replication is characterized in that a deoxyribonucleoside 5?-triphosphate, in which the hydroxyl group of phosphoric acid at the ?-position is substituted with a group selected from the group consisting of an amino group, a methylamino group, a dimethylamino group, a mercapto group and a fluoro group, is used as a substrate during replication reaction. The novel artificial base pairs of the present invention are characterized in that 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) or an analog thereof forms a base pair with pyrrole-2-carbaldehyde (Pa) or an analog thereof.

Abstract: The invention provides a method for producing a cytosine nucleoside compound from pentose-1-phosphate and cytosine or a derivative thereof using a nucleoside phosphorylase reactive to cytosine or a bacterium having the enzyme activity. The invention also provides a method for specifically reducing an activity to degrade the substrates or the product, resulting in efficient production of the cytosine nucleoside compound. According to the invention, little by-product is produced in producing cytonucleocide compounds.

Abstract: The invention provides novel nucleoside compounds of formula I wherein R1, R2a, R2b, R3, R4, R5 R6, R8a, R9 and R10 are as defined herein which are useful for the treatment of Hepatitis C Virus (HCV) mediated diseases.

Abstract: Disclosed herein are linear donor molecules comprising homology arms of 50-750 base pairs (e.g., 50-100 base pairs) flanking one or more sequences of interest. The donor molecules and/or compositions comprising these molecules can be used in methods for targeted integration of an exogenous sequence into a specified region of interest in the genome of a cell.

Abstract: The present invention relates to novel chimeric oligomeric compounds having a plurality of alternating regions having either RNA like having northern or 3?-endo conformational geometry (3?-endo regions) or DNA like having southern or C2?-endo/O4?-endo conformational geometry. The oligomeric compounds of the present invention have shown reduction in mRNA levels in multiple in vitro and in vivo assay systems and are useful, for example, for investigative and therapeutic purposes.

Abstract: Engineered nucleotide compositions, having polymerase interacting components that improve the interactivity of the polymerase and the nucleotide, particularly for nucleic acid sequencing applications. Compositions include the interactive polymerases along with the nucleotide analogs. Kits, methods and systems are provided for analysis of nucleic acid synthesis reactions.

Abstract: Physical forms of beta-L-2?-deoxythymidine are disclosed that can be characterized by physical appearance, purity levels, Infra-Red and Raman spectroscopy, X-ray powder diffraction patterns, thermal properties, and methods of manufacture. These forms of beta-L-2?-deoxythymidine can be used in the manufacture of other forms of beta-L-2?-deoxythymidine, or in pharmaceutical compositions. Particularly preferred uses are in the treatment of hepatitis B.

Abstract: The present invention provides a family of dark quenchers, termed Black Hole Quenchers (“BHQs”), that are efficient quenchers of excited state energy but which are themselves substantially non-fluorescent. Also provided are methods of using the BHQs, probes incorporating the BHQs and methods of using the probes.

Abstract: The present invention relates to methods and reagents for detecting analytes, e.g. nucleic acids. The new methods and reagents allow a simple and sensitive detection even in complex biological samples.

Abstract: The present teachings provide methods, compositions, and kits for synthesizing and sequencing nucleic acids. In some embodiments, elaborated nucleotide phosphorothiolate compounds are employed along with efficient cleaving reactions. Improved sequencing efficiency is achieved by the rapid polymerase-mediated incorporation of elaborated nucleotide phosphorothiolate compounds. Increased sequencing efficiency is also achieved by the ability of the cleaving reactions to restore the incorporated nucleotides to their natural structure prior to subsequent elongation.

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: Novel compositions and methods are provided for identifying agents which affect chromosomal stability and aging.

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

Abstract: Novel phosphonate compounds are provided including a phosphonoglyoxylamide ester, an ?-keto phosphonophosphinate ester, a carbonylbisphosphonate analog of a nucleotide, and a diazomethylenebisphosphonate analog of a nucleotide, as well as methods of making synthetically and medically useful ?-keto phosphonate compounds.

Abstract: A method and composition for treating a host infected with flavivirus, pestivirus or hepacivirus comprising administering an effective flavivirus, pestivirus or hepacivirus treatment amount of a described base-modified nucleoside or a pharmaceutically acceptable salt or prodrug thereof, is provided.

Abstract: Nucleotide analogs characterized by the presence of an amidate linked amino acid or an ester linked group which is bonded to the phosphorus atom of phosphonate nucleotide analogs are disclosed. The analogs comprise a phosphoamidate or ester bond that is hydrolyzed in vivo to yield a corresponding phosphonate nucleotide analog. Methods and intermediates for their synthesis and use are described.

Abstract: Method for producing large lots of final sterile Poly-ICLC suitable for clinical use with reduced toxicity at effective dose levels, and method for using Poly-ICLC to regulate genes, and method for using Poly-ICLC to treat certain human and veterinary infectious, neoplastic and autoimmune disorders.

Abstract: A novel compound, 2?/3?-O-acetyl-ADP-ribose, is provided. The compound is a mixture of the 2? and 3? regioisomers of O-acetyl-ADP ribose, and is formed nonenzymatically from 2?-O-acetyl-ADP-ribose, which is the newly discovered product of the reaction of Sir2 enzymes with acetylated peptides and NAD+. Analogs of 2?/3?-O-acetyl-ADP-ribose are also provided. Additionally, methods of preparing 2?/3?-O-acetyl-ADP-ribose, methods of determining whether a test compound is an inhibitor of a Sir2 enzyme, methods of detecting Sir2 activity in a composition, methods of deacetylating an acetylated peptide, and methods of inhibiting the deacetylation of an acetylated peptide are provided. Prodrugs of 2?/3?-O-acetyl-ADP-ribose are also provided.

Abstract: Nucelosides and nucleotides containing a tricyclic base portion thereof are useful for treating infectious diseases and proliferative disorders, such as viral infections or cancer respectively.

Abstract: The present invention relates to compositions and methods for the preparation of modified nucleic acids. In particular, the present invention provides novel reagents and chemistries for the generation of linkers and modified phosphoramidates.

Abstract: Disclosed are compounds, compositions and methods for treating viral infections caused by a Flaviviridae family virus, such as hepatitis C virus.

Abstract: Embodiments of the invention include thioether substituted aryl carbonate protecting groups, and nucleoside monomers protected with thioether substituted aryl carbonate protecting groups. Aspects of the invention further included methods of synthesizing nucleic acids, e.g., oligonucleotides, using such protected nucleoside monomer monomers, as well as nucleic acids produced using methods of the invention and compositions thereof.

Abstract: Embodiments of labeled nucleotide compositions are described. Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled nucleotide composition to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.

Abstract: The invention provides novel inorganic boranophosphate salts that can be used as fertilizers, in detergent formulations, as additive in melts for the glass industry, in boron neutron-capture therapy of cancer, and as synthetic building blocks in the synthesis of boranonucleotides of various lengths.

Abstract: A compound of the formula (1): wherein R1 and R2 are the same or different and represent a hydrogen atom, a hydroxyl protecting group, a phosphate group, or —P(R3)R4, wherein R3 and R4 are the same or different and represent a hydroxyl group, an amino group, an alkoxy group having from 1 to 4 carbon atoms, a cyanoalkoxy group having from 1 to 5 carbon atoms or an amino group substituted by an alkyl group having from 1 to 4 carbon atoms; A represents an alkylene group having from 1 to 4 carbon atoms and B represents a purin-9-yl group, a 2-oxo-pyrimidin-1-yl group, a substituted purin-9-yl group or a substituted 2-oxo-pyrimidin-1-yl group having a substituent ? selected from the group consisting of a hydroxyl group which may be protected, an alkoxy group having from 1 to 4 carbon atoms, a mercapto group which may be protected, an alkylthio group having from 1 to 4 carbon atoms, an alkoxy group having from 1 to 4 carbon atoms, an amino group which may be protected, a mono- or di-alkylamino group which may b

Abstract: A method of prophylaxis or treatment of inflammatory conditions, including, but not limited to, intestinal epithelial inflammation due to intestine-specific conditions (e.g., Crohn's disease or ulcerative colitis) or systemic causes of inflammation (e.g., endotoxemia, sepsis, hemorrhagic shock/resuscitation or pancreatitis) is disclosed. In the method of the invention, an affected patient is administered a therapeutically effective amount of a composition including an NAD-related compound, in a form that is accessible to a receptor molecule, conveyed in a pharmaceutically acceptable carrier vehicle. NAD-related compounds include nicotinamide adenine dinucleotide (NAD+), cyclic adenosine diphosphate ribose (cADPR), or functionally equivalent analogues, derivatives, metabolites or agonists thereof or prodrugs therefor.

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

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

Abstract: 2-Substituted-5?-O-(1-boranotriphosphate)adenosine derivatives having at position 2 a radical R1 selected from the group consisting of H; halogen; O-hydrocarbyl; S-hydrocarbyl; NR3R4; and hydrocarbyl optionally substituted by halogen, CN, SCN, NO2, OR3, SR3 or NR3R4; wherein R3 and R4 are each independently H or hydrocarbyl or R3 and R4 together with the nitrogen atom to which they are attached form a saturated or unsaturated heterocyclic ring optionally containing 1-2 further heteroatoms selected from oxygen, nitrogen and sulfur, and pharmaceutically acceptable salts or diastereoisomers thereof or a mixture of diastereoisomers, are useful for treatment of type 2 diabetes.

Abstract: The invention relates to a labeling reactant of formula (I) useful for labeling an oligonucleotide wherein: R is a temporary protecting group. A is either a phosphorylating moiety or a solid support tethered to Z via a linker arm E?. Z is a bridge point and is formed from E is a linker arm between R and Z. E? is a linker arm between Z and Z?. E? is a linker arm between Z and A. E?? is a linker arm between Z? and G. Z? is a purine or pyrimidine base. G is a protected bivalent aromatic structure, tethered to two iminodiacetic acid ester groups N(CH2COOR?)2, or G is a structure selected from the group consisting of or G is a protected functional group, or G is a protected or unprotected organic dye, hapten or a spin label.

Abstract: Nucleosides and nucleotides containing a tricyclic base portion thereof are useful for treating infectious diseases and proliferative disorders, such as viral infections or cancer respectively.

Abstract: A process for the phosphitylation of an alcohol or thiol with a phosphitylation agent in the presence of an activator is provided. The activator has the formula: wherein p is 0 or an integer from 1 to 4 and R for each occurrence is a substituent. Preferably X7 is O and p is 0. The activator is commonly employed as a salt complex with an organic base. Preferred alcohols or thiols include nucleosides and oligonucleotides. The process is particularly suited for the synthesis of phosphoramidites.

Abstract: Pharmaceutical compositions comprise a nucleotide analog with a phosphonate group at a concentration effective to act as a substrate and/or inhibitor of a viral polymerase, and especially of the HCV RNA dependent RNA polymerase.

Abstract: The invention provides compositions and methods for performing primer extension reactions, including employment of amplification primers having 5? tags to incorporate into amplicons variant nucleotides of interest from target nucleic acids at known ratios, with or without sequences surrounding the variant nucleotides of interest. The invention provides identifying the variant nucleotides generated from the target nucleic acid and generated from the 5? tags, comparing the results, evaluating the efficiency of the primer extension reactions, and monitoring the efficacy of such reactions. The invention accounts for DNA sequence and experimental variables that may affect efficiency of incorporation of nucleotides, and provides a reference point for the interpretation of polymorphisms. The invention also provides methods of breeding scrapie-resistant sheep populations.

Abstract: The present invention provides a method of treating edematous retinal disorders. The method comprises administration of a pharmaceutical formulation comprising a hydrolysis-resistant P2Y receptor agonist to stimulate the removal of pathological extraneous fluid from the subretinal and retinal spaces and thereby reduce the accumulation of said fluid associated with retinal detachment and retinal edema. The P2Y receptor agonist can be administered with therapeutic and adjuvant agents commonly used to treat edematous retinal disorders. The pharmaceutical formulation useful in this invention comprises a P2Y receptor agonist with enhanced resistance to extracellular hydrolysis, such as dinucleoside polyphosphate compounds, or hydrolysis-resistant mononucleoside triphosphate salts. The present invention also provides P1-(2?-deoxycytidine 5?-)P4-(uridine 5?-)tetraphosphate, tetra-(alkali metal) salts such as tetrasodium, tetralithium, tetrapotassium, and mixed (tetra-alkali metal) salts.

Abstract: The present invention provides a nucleotide having the formula, wherein PM is a phosphate moiety, SM is a ribose or a deoxyribose sugar moiety, and BASE is a pyrimidine, purine or 7-deazapurine moiety. PM is attached to SM at a position independently selected from the 2?, 3?, and 5? positions of SM when the nucleotide is a ribonucleotide, and at a position independently selected from the 3? and 5? positions when the nucleotide is a deoxyribonucleotide. BASE is attached to the 1? position of SM from the N1 position when BASE is a pyrimidine, or the N9 position when BASE is a purine or 7-deazapurine. Sig is a detectable moiety covalently attached to SM directly or through a linkage group. Also provided are an oligo- or polynucleotide comprising at least one such sugar moiety labeled nucleotide, and other compositions including those wherein a polypeptide is terminal ligated or attached to the oligo- or polynucleotide.

Abstract: Various 2?-beta-methyl-6-substituted adenosine analogs (including 2,6-disubstituted adenosine, 8-aza-6-substituted adenosine, and 2-aza-6-substituted adenosine) are prepared by conventional and combinatorial library approaches. Contemplated compounds are particularly useful as therapeutic agents, and especially as antiviral agents.

Abstract: The invention comprises compositions and methods for performing primer extension reactions, including employment of amplification primers having 5? tags to incorporate into amplicons variant nucleotides of interest from target nucleic acids at known ratios, along with the sequences surrounding the variant nucleotides of interest. The invention comprises identifying the variant nucleotides generated from the target nucleic acid and generated from the 5? tags, comparing the results, evaluating the efficiency of the primer extension reactions, and monitoring the efficacy of such reactions. The invention accounts for DNA sequence and experimental variables which may affect efficiency of incorporation of nucleotides, and provides a reference point for the interpretation of polymorphisms.

Abstract: Purine nucleotide derivative disodium crystals having a minimized amount of remaining alcohol such as methanol, ethanol or a mixture thereof are produced by overdrying purine nucleotide derivative disodium crystals containing the alcohol; and bringing the overdried purine nucleotide derivative disodium crystals into contact with an aqueous solution containing a hydrophilic organic solvent to control the humidity of the purine nucleotide derivative disodium crystals under a high humidity condition.

Abstract: The invention features linker molecules that have at one terminus a amino-protecting group and at the other terminus a phosphorous activating group, typically phosphoramidite. The linker molecules can be used, for example, to produce amino-modified linkers that space an oligonucleotide from a solid support. The invention also features an amino-protected nucleotide that includes an activated phosphorous group such as a phosphoramidite for the production of a 5? amino-modified oligonucleotide. The invention further provides a phthalimido-modified support that can be used to synthesize a polynucleotide that includes an amino group at the 3? terminus.

Abstract: The present invention are directed to P1, P4-di(uridine 5?-)tetraphosphate, tetra-alkali metal salts such as tetrasodium, tetralithium, tetrapotassium, and mixed tetra-alkali metal cations thereof. The tetra alkali metal salts of P1, P4-di(uridine 5?-)tetraphosphate are water-soluble, nontoxic, and easy to handle during manufacture. These tetra-monovalent alkali metal salts are more resistant to hydrolysis than the mono-, di-, or tri-acid salts, therefore, they provide an improved stability and a longer shelf life for storage. The present invention also provides methods for the synthesis of P1, P4-di(uridine 5?-)tetraphosphate, and its pharmaceutically acceptably acceptable salts thereof, and demonstrates the applicability to the production of large quantities. The methods substantially reduce the time required to synthesize diuridine tetraphosphate, for example, to three days or less.

Abstract: Described herein are novel indicator molecules of general formula (1): wherein Q, F, N, Nuc, X1 and X2 are as defined herein, including their tautomeric forms and their additive salts. The present invention also concerns methods for the use of these molecules to monitor nucleic acid amplification in real time and their applications as diagnostics.

Abstract: The invention relates to the use of morpholino-nucleosides of formula: in which R1 represents a nucleic base and R2 represents a group corresponding to one of the following formulae: —(CH2)n—NH2 —(CH2)n—SH —(CH2)n—COOH —(CH2)n—OH —(CH2)n—NH—R3 —(CH2)n—SR3 —(CH2)n—CO—R3 —(CH2)n—OR3 in which n is an interger ranging from 1 to 12 and R3 is a group derived from a label, from a protein, from an enzyme, from a fatty acid or from a peptide, as chain terminators in a process of DNA or RNA sequencing by the Sanger method, or for the labelling of DNA or RNA fragments.

Abstract: The invention relates to novel oligomers containing PNA units that are substituted by phosphite ester, phosphonic acid, or carbaborane functions and PNA monomers that are substituted by phosphite ester, phosphonic acid, or carbaborane functions, from which the novel oligomers are produced.

Abstract: Compounds are provided containing purine nucleotides that bear moieties X at the 2? position thereof wherein X is R1—(R2)n; R1 is C3-C20 alkyl, C4-C20 alkenyl or C2-C20 alkynyl; R2 is halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether, a group that enhances the pharmacodynamic properties of oligonucleotides, or a group that enhances the pharmacokinetic properties of oligonucleotides; and n is an integer from 0 to about 6. Such compounds are useful for modulating the synthesis of proteins.