Abstract: A method and composition for treating a host infected with flavivirus or pestivirus comprising administering an effective flavivirus or pestivirus treatment amount of a described 1′, 2′ or 3′-modified nucleoside or a pharmaceutically acceptable salt or prodrug thereof, is provided.

Abstract: Excellent remedies for hepatitis C which contain as the active ingredients a 3′-deoxy-3′-fluorouridine derivatives and a 1-(3′-deoxy-fluoro-&bgr;-L-ribofuranosyl)uracil derivative and show little side effects.

Abstract: The present invention relates to nucleoside diphosphate mimics and nucleoside triphosphate mimics, which contain diphosphate or triphosphate moiety mimics and optionally sugar-modifications and/or base-modifications. The nucleotide mimics of the present invention, in a form of a pharmaceutically acceptable salt, a pharmaceutically acceptable prodrug, or a pharmaceutical formulation, are useful as antiviral, antimicrobial, and anticancer agents. The present invention provides a method for the treatment of viral infections, microbial infections, and proliferative disorders. The present invention also relates to pharmaceutical compositions comprising the compounds of the present invention optionally in combination with other pharmaceutically active agents.

Abstract: Described herein are novel indicator molecules of general formula (1): 1

Abstract: 2-(6-Cyano-1-hexyn-1-yl)adenosine, 2-(6-cyano-1-hexyn-1-yl)adenosine 5′-monophosphate, or salts thereof; and drugs containing the same as an active ingredient. The compounds have excellent effects of lowering ocular tension, promoting blood flow in retina, and protecting optic nerve failure and are highly soluble in water. Owing to these characteristics, the compounds are useful as drugs such as remedies for glaucoma and ocular hypertension.

Abstract: The invention relates to novel amidite derivatives and their use as linker units for synthesizing polymers, especially biopolymers such as nucleic acids, peptides and saccharides, on the surface of solid supports. Use of the linker derivatives of the invention makes it possible to regenerate the surfaces without damage.

Abstract: Oligonucleotide tagged nucleoside triphosphates, OTNTPs, which are substrates for polymerases and or terminal nucleotidyl transferases are provided as well as methods of making these OTNTPs. Further provided are OTNTPs with fluorescent dyes including energy transfer dyes, attached to the oligonucleotide chain, OTNTPs with unnatural bases incorporated in the oligonucleotide sequence and methods for incorporating these OTNTPs in DNA or RNA. Also provided are methods for using the oligonucleotides on OTNTPs for amplifying the oligo sequence on the OTNTP using an amplification method described above. Further provided are reactive bifunctional amidites, methods of making these compounds and methods for detecting single nucleotide polymorphisms using the above OTNTPs. Methods for detecting differential gene expression using the OTNTPs and methods of separating specifically modified DNA or RNA using the OTNTPs are also provided.

Abstract: This invention discloses a method for the preparation of 2′-modified nucleosides, using a palladium catalyst and an alkene functionalized with a heteroatom. Included in the invention are the novel pyrimidines and purines that can be prepared according to the method of the invention and oligonucleotides containing said modified pyrimidines and purines.

Abstract: Phosphinoamidite carboxylates and analogs are provided that have the structure of formula (I) wherein R1, R2, R3, R4, X, Y, Z and n are as defined herein. The compounds are useful as phosphitylating agents, e.g., in the phosphitylation of 3′ and 5′ hydroxyl groups of nucleosides and oligonucleotides. Also provided are phosphonocarboxylate and H-phosphonite carboxylate analogs of the compounds of formula (I). The compounds enable synthesis of phosphinocarboxylate and phosphonocarboxylate oligonucleotides having reduced internucleotide charge and enhanced nuclease resistance.

Abstract: The present invention relates to novel nucleoside 5′-monophosphate mimics, which contain novel nucleoside bases and phosphate moiety mimics optionally having sugar-modifications. The nucleotide mimics of the present invention, in a form of a pharmaceutically acceptable salt, a pharmaceutically acceptable prodrug, or a pharmaceutical formulation, are useful as antiviral, antimicrobial, anticancer, and immunomodulatory agents. The present invention provides a method for the treatment of viral infections, microbial infections, and proliferative disorders. The present invention also relates to pharmaceutical compositions comprising the compounds of the present invention optionally in combination with other pharmaceutically active agents.

Abstract: The invention concerns novel nucleotide analogues comprising a reactive hydrazide function used as initial synthons for preparing compounds (formula I) capable of inducing mutations or capable of inhibiting a DNA polymerase or a kinase. The invention also concerns nucleic acids comprising said nucleotide and nucleoside analogues. Among such compounds, can be cited in particular the compound of formula (I).

Abstract: A nucleoside phosphate may be separated from a solution containing it using the ability of the nucleoside phosphate to intercalate into a layered double hydroxide. In particular, a first nucleoside phosphate may be separated from a second nucleoside phosphate by treating a solution containing the first and second nucleoside phosphates with a layered double hydroxide to preferentially intercalate the first nucleoside phosphate into the layered double hydroxide. The layered double hydroxide containing the intercalated nucleoside phosphate may be subsequently treated to recover the nucleoside phosphate. The methods disclosed provide useful procedures whereby nucleoside phosphates of enhanced purity may be obtained.

Abstract: The present invention provides methods for the chemical synthesis of nucleosides and derivatives thereof, including 2′-amino, 2′-N-phthaloyl, 2′-O-methyl, 2′-O-silyl, 2′-OH nucleosides, C-nucleosides, nucleoside phosphoramidites, C-nucleoside phosphoramidites, and non-nucleoside derivatives.

Abstract: A compound, method and composition for treating a host infected with a hepatitis C viral comprising administering an effective hepatitis C treatment amount of a described 4′-disubstituted nucleoside or a pharmaceutically acceptable salt or prodrug thereof, is provided.

Abstract: The design, synthesis, and use of cyclic compounds, including cyclic polyamides, is described. Such compounds comprise at least two polymer portions, one of which comprises at least three molecular units, and the other comprises at least four molecular units. At least one molecular unit of such a compound is a hydrogen bond donor or acceptor. The polymer portions are covalently linked to form a cycle. These compounds are capable of targeting specific nucleotide sequences in double-stranded nucleic acids, particularly double-stranded DNA. Accordingly, such compounds can be used to modulate, e.g., increase or decrease, the expression of one or more genes in vitro or in vivo.

Abstract: The present invention relates to a method for the photolithographic synthesis of biochips in which photolabile protective groups of the 2-(2-nitrophenyl)ethyl type are used, whereby the irradiation step that is common in the photolithographic chip synthesis is carried out in the presence of a base, preferably a secondary or uerriary base.

Abstract: This invention relates to purine compounds of formula (I): 1

Abstract: The invention includes compositions and methods useful for treatment of a virus infection in a mammal by double-targeting the virus (i.e. targeting the virus at more than one stage of the virus life cycle) and thereby inhibiting virus replication. The compositions of the invention include compounds which comprise a phosphocholine moiety covalently conjugated with one or more antiviral agents (e.g. nucleoside analogue, protease inhibitor, etc.) to a lipid backbone. The invention also includes pharmaceutical compositions and kits for use in treatment of a virus infection in mammals. The methods of the invention comprise administering a compound of the invention, a pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the invention, in an amount effective to treat the infection, to a mammal infected with a virus. Additionally, the invention includes compositions and methods useful for combating a cancer in a mammal and for facilitating delivery of a therapeutic agent to a mammalian cell.

Abstract: Aryl phosphate derivatives of d4T with para-bromo substitution on the aryl group show markedly increased potency as anti-HIV agents without undesirable levels of cytotoxic activity. In particular, these derivatives are potent inhibitors of HIV reverse transcriptase. In a preferred aspect of the present invention, the phosphorus of the aryl phosphate group is further substituted with an amino acid residue that may be esterified or substituted, such as a methoxy alaninyl group.

Abstract: The invention relates to novel Acyl coenzyme-A mimics, compositions comprising ketone compounds, and methods useful for treating and preventing cardiovascular diseases, dyslipidemias, dysproteinemias, and glucose metabolism disorders comprising administering a composition comprising a ketone compound. The Acyl coenzyme-A mimics, compositions, and methods of the invention are also useful for treating and preventing Alzheimer's Disease, Syndrome X, peroxisome proliferator activated receptor-related disorders, septicemia, thrombotic disorders, obesity, pancreatitis, hypertension, renal disease, cancer, inflammation, bacterial infection and impotence. In certain embodiments, the Acyl coenzyme-A mimics, compositions, and methods of the invention are useful in combination therapy with other therapeutics, such as hypocholesterolemic and hypoglycemic agents.

Abstract: Provided are methods of producing phosphitylated compounds, including 3′-O-phosphoramidites, comprising the step of reacting a hydroxyl-containing compound with a phosphitylating agent in the presence of a phosphitylation activator selected from the group consisting of: (1) acid-base complexes derived from an amine base of Formula I 1

Abstract: A compound of the formula (1): 1

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 present invention is directed to nucleoside monomers wherein the 3′-O atom is replaced with a methylene group. The present invention also provides oligomers comprising a plurality of such monomers which are linked by methylene phosphonate linkages. Further, methods of preparing monomers and oligomers according to the present invention are provided.

Abstract: Nucleotides comprising a reporter moiety and a polymerase enzyme blocking moiety in which the reporter moiety does not also act as a polymerase enzyme blocking moiety are described. Also described are compounds of Formula (I): wherein W is a phosphate group, B is a base, Y is a linker comprising an enzyme-cleavable group, R2 is a reporter moiety, R3 is selected from H or OH, Z and Z′ are selected from H, OH, or a group X—R1, wherein X is a linker comprising an enzyme-cleavable group and R1 is a polymerase enzyme blocking group, provided that at least one of Z and Z′ is X—R1.

Abstract: The invention provides compounds having the following general formula (I): 1

Abstract: Novel, enantiopure, substituted 4-deoxypentenosides (4-DPs) and related dihydropyrans (DHPS) are prepared from common carbohydrates via a novel process. The 4-DPs and related DHPs are amenable to a broad range of stereoselective transformations and are used as synthetic intermediates to prepare a variety of enantiopure tetrahydropyrans (THPs), including rare or exotic sugars and other complex THPs of commercial or medicinal value. In one embodiment of the instant invention, 4-DPs are converted to L-sugars in a novel process that offers distinct advantages over known synthetic methods.

Abstract: The invention relates to the production of modified oligonucleotides and to their use for conjugation reactions. The invention further relates to reagents and to methods for producing aldehyde-modified oligonucleotides that contain aldehydes that are protected (masked) as acetals. Once said acetals are incorporated into the oligonucleotides the oligonucleotides are converted to aldehydes and are used for conjugation. The conjugation reaction can be carried out with the free oligonucleotide or with the oligonucleotide that is still immobilized on the substrate.

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: Propargylethoxyamino nucleosides are disclosed having the structure 1

Abstract: L-nucleosides are conformationally constrained by at least one additional ring formed by a bridge connecting at least two atoms within a sugar moiety of the nucleoside. While a single additional ring is formed by bridging C1-C4 atoms, two additional rings are formed by bridging both C1-C2, and C3-C4 atoms, or C1-C3 and C2-C4 atoms by bridges having the general structure A—B—Z. The conformationally constrained nucleosides may be incorporated into oligonucleotides and dinucleotides, and it is contemplated that compositions including the conformationally constrained nucleosides may have superior viral inhibitory or antineoplastic properties.

Abstract: Nucleoside derivatives as building blocks for templated libraries are described.

Abstract: Compounds are disclosed for treating AIDS, herpes, and other viral infections by means of lipid derivatives of antiviral agents. The compounds consist of nucleoside analogues having antiviral activity which are linked, commonly through a phosphate group at the 5′ position of the pentose residue, to one of a selected group of lipids. The lipophilic nature of these compounds provide advantages over the use of the nucleoside analogue alone. It also makes it possible to incorporate them into the lamellar structure of liposomes, either alone or combined with similar molecules. In the form of liposomes, these antiviral agents are preferentially taken up by macrophages and monocytes, cells which have been found to harbor the target HIV virus. Additional site specificity may be incorporated into the liposomes with the addition of ligands, such as monoclonal antibodies or other peptides or proteins which bind to viral proteins.

Abstract: A stable complex, we refer to as a PD-Loop, between double stranded nucleic acid and a nucleobase polymer is assembled with the aid of strand invading peptide nucleic acid (PNA). The PD-Loop can be used in the detection, analysis, quantitation and even in the affinity capture of the duplex nucleic acid. Alternatively, the PD-Loop can be used to initiate polymerase extension of a primer to thereby facilitate sequencing of the double stranded nucleic acid even in the presence of large excesses of unrelated double stranded nucleic acid. As an additional feature, the PD-Loop can also be used to generate a construct comprised of a double stranded nucleic acid through which is threaded a single stranded dosed circular nucleic acid wherein the closed circular nucleic acid can be used in a signal amplification methodology.

Abstract: The present invention provides a method of treating edematous retinal disorders. The method comprises administration of a 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 may be administered with therapeutic and adjuvant agents commonly used to treat edematous retinal disorders. The pharmaceutical composition useful in this invention comprises a P2Y receptor agonist with enhanced resistance to extracellular hydrolysis, such as dinucleoside polyphosphate compounds.

Abstract: The present invention is directed to &agr;-modified nucleoside triphosphates and methods for their preparation. The present invention also provides for methods of inhibiting RNA and viral replication in cells, as well as methods for treating viral infections.

Abstract: Novel orthoesters are provided which can be used as a 2′-hydroxyl protecting groups or 2′-modification in the synthesis of polymers containing ribonucleic acid (RNA) nucleotides. The RNA comprising the orthoester can be handled and analyzed while 2′-modified, thereby minimizing potential degradation. The orthoester is stable during oligonucleotide synthesis. The orthoester is subsequently modified and can then be removed under mild acidic conditions. The ease and dependability of this process and the quality of the RNA product synthesized with this invention are comparable to that previously associated only with DNA synthesis.

Abstract: Novel xylo nucleoside or xylo nucleotide analogs, polynucleotides comprising xylo nucleotide substitution, processes for their synthesis and incorporation into polynucleotides.

Abstract: Thiolester-activated amino acids; thiolester-activated nucleotides; polypeptide-oligonucleotide fusions comprising a polypeptide of interest and a thiolester-activated nucleotide; methods of producing the thiolester-activated nucleotides of the present invention; methods of producing polypeptide-oligonucleotide fusions of the present invention; and methods in which the polypeptide-oligonucleotide fusions are used, such as methods of delivering nucleic acid molecules into cells and cell lines.

Abstract: The invention relates to a labeling reactant of formula (I) useful for labeling an oligonucleotide 1

Abstract: An oligo- or polynucleotide analogue having one or more structures of the general formula 1

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: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.

Abstract: Labelled nucleotides and polynucleotides useful in the sequencing of nucleic acids are described. Methods of preparing photocleavable marker nucleotides and photocleavable marker-polynucleotide conjugates are described. Such photocleavable markere nucleotides can be incorporated into nucleic acid so as to create photocleavable marker-polynucleotide conjugates.

Abstract: The present invention provides oligomers which are specifically hybridizable with a selected sequence of RNA or DNA wherein at least one of the nucleoside moieties of the oligomer is modified to include a guanidinium group. These oligomers are useful for diagnostic, therapeutic and investigative purposes.

Abstract: The invention comprises short, thiophosphate nucleic acids (primarily mono-, di-, and tri-nucleotides), libraries comprising them, and methods of using them as therapeutic anti-viral (particularly anti-HBV) agents.

Abstract: Charged compounds are provided that comprise one or more regions of localized positive charge, compositions comprising such compounds, methods of synthesizing such compounds, methods of screening such compounds to identify those having anti-infective activity, and methods of using such compounds to prevent or inhibit infections. These compounds, and compositions containing them, have multiple applications, including use in human and animal medicine and in agriculture.

Abstract: The present invention describes methods of detecting a nucleic acid in a sample, based on the use of terminal-phosphate-labeled nucleotides as substrates for nucleic acid polymerases. The methods provided by this invention utilize a nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogue which has a colorimetric dye, chemiluminescent, or fluorescent moiety, a mass tag or an electrochemical tag attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer. Cleavage of the polyphosphate product of phosphoryl transfer via phosphatase leads to a detectable change in the label attached thereon. When the polymerase assay is performed in the presence of a phosphatase, there is provided a convenient method for real-time monitoring of DNA or RNA synthesis and detection of a target nucleic acid.

Abstract: The present invention provides a nucleoside comprising a pyrazolopyrimidine base and a process for producing the same. In particular, the processes of the present invention comprises using a halogenated pyrazolopyrimidine base and removing the halogen after the base is coupled to a sugar moiety. The presence of the halogen on the nucleoside base allows facile and economical production of a large quantity of nucleosides.

Abstract: This invention is directed to novel substituted nucleotide bases with a crosslinking arm which accomplish crosslinking between specific sites on adjoining strands of oligonucleotides a oligodeoxynucleotides. The invention is also directed to oligonucleotides comprising at least one of these crosslinking agents and to the use of the resulting novel oligonucleotides for diagnostic and therapeutic purposes.