Abstract: The present invention provides dyes, reactive dyes and labeled reagents that may be used in the detection or quantification of desirable target molecules, such as proteins and nucleic acids. Dyes are provided that may be used free in solution where the binding of the dye to the target molecule provides signal generation. Dyes are also provided that comprise reactive groups that may be used to attach the dyes to probes that will bind to desirable target molecules. The novel dyes of the present invention have been modified by the addition of charged and polar groups to provide beneficial properties.

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: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a non-cleavable terminating group. The non-cleavable-fluorescent group is designed to terminate DNA synthesis so that DNA oligomers can be sequenced efficiently in a parallel format. These reagents and methods will lead to more accurate identification of polymorphisms and other valuable genetic information.

Abstract: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.

Abstract: The present invention provides a compound of Formula 1a, wherein R1 is H or phosphate and the double bond is between N? and C? or between N2 and C1; R2 is a mitochondrial targeting moiety; R3 an alkyl, alkylaryl, alkylheteroaryl spacer group, a cleavable linker, or absent; R4 is H or an alkyl, aryl, or heteroaryl group; and R5 is alkyl, aryl, or heteroaryl; or N? C?, and N3 together form a heterocyclic ring containing at least 5 atoms, wherein N1, N3, and R1-R5 are as defined above, or N3 and R5 together form a heterocyclic ring containing at least four atoms; or a pharmaceutically acceptable salt or prodrug thereof.

Abstract: The present invention relates to the fields of genetics, immunology and medicine. The present invention more specifically relates to in vitro or ex vivo methods for determining the susceptibility to a cancer treatment of a subject having a tumour. These methods comprise a step of determining the ability of the treatment, of the subject and/or of the tumour to induce an anticancer immune response, the inability of at least one of the treatment, the subject and the tumor to induce an anticancer immune response being indicative of a resistance of the subject to the therapeutic treatment of cancer. Inventors in particular identify genes specific of a human subject or of cancerous cells which can be used to predict or assess the sensitivity of a subject to a treatment of cancer. The invention also relates to particular compounds capable of activating or enhancing the immune system of a particular subject, when the subject is exposed to a therapeutic treatment of cancer or before such an exposition.

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: The present invention relates generally to labeled and unlabled cleavable terminating groups and methods for DNA sequencing and other types of DNA analysis. More particularly, the invention relates in part to nucleotides and nucleosides with chemically cleavable, photocleavable, enzymatically cleavable, or non-photocleavable groups and methods for their use in DNA sequencing and its application in biomedical research.

Abstract: The present disclosure relates to the use and methods of manufacture of bicyclic nucleosides and nucleotides for the treatment and prevention of infectious and proliferative diseases, including microbial infections and cancer.

Abstract: Immunostimulatory oligoribonucleotides (ORN) featuring 5?-triphosphates and various 5?-triphosphate analogs are provided. Also provided are physiologically acceptable salts of the immunostimulatory ORN and pharmaceutical compositions containing the immunostimulatory ORN of the invention. ORN of the invention are useful as adjuvants and can be combined with an antigen to promote an antigen-specific immune response. ORN of the invention are also particularly useful for promoting a Th1-type immune response. Also provided are methods of use of the compounds and pharmaceutical compositions of the invention to enhance an immune response in a subject, as well to treat a number of conditions including cancer, infection, allergy, and asthma, and to vaccinate a subject against an antigen.

Abstract: Disclosed, among other things, are compounds having the structure wherein X comprises a bond or a linker, LABEL comprises at least one detectable label, W1 taken alone is —H or —OH, W2 is —OH or a non-extendable moiety, W3 when taken alone is —H or when taken together with W1 is —CH2—O—, and W4 is OH, monophosphate, diphosphate, or triphosphate. Also disclosed are labeled polynucleotide compounds and methods of use thereof.

Abstract: Provided is a nucleic acid substrate which has nucleic acid substrate characteristics equivalent to those of dATP, has a low substrate specificity for luciferase, exerts no negative effect on enzymatic reactions such as a complementary-strand synthesis, and therefore is particularly suitable for the pyrosequencing method. As a nucleic acid substrate complementary to nucleotide T, a 7-substituted deoxyribonucleotide triphosphate whose 7-position of a purine group is modified by a substituent is used as a substitute for a nucleotide ?-thiotriphosphate analog.

Abstract: Provided are compounds of Formula I: nucleosides, nucleoside phosphates and prodrugs thereof, wherein R6 is CN, ethenyl, 2-haloethen-1-yl, or (C2-C8)-alkyn-1-yl. The compounds, compositions, and methods provided are useful for the treatment of Flaviviridae virus infections.

Abstract: An adenosine 5?-triphosphate analogs modified at the gamma-phosphate with a reactive reagent. A method of forming the analog by activating a 4-amino benzoic acid, incubating the activated acid to obtain an amine, and coupling the amine with ATP in the presence of water soluble EDCI. A method of detecting the efficacy of a therapeutic by adding a gamma-phosphate modified ATP analog to a protein substrate, reacting the target proteins with the ATP analog, and analyzing the resulting cross-linked product, wherein the amount of product present correlates to the efficacy of the therapeutic is also provided.

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

Abstract: The present invention relates to novel unnatural fluorescent nucleic acid bases, that is, a purine base, a 1-deazapurine base, and a 1,7-deazapurine base each having a functional group which consists of two or more heterocyclic moieties linked together, at the 6-position thereof (the 6-position of purine ring). The present invention also relates to a compound containing the unnatural base, a derivative thereof, and a nucleic acid containing a nucleotide having the unnatural base. The present invention also relates to a method of preparing the nucleic acid. The unnatural base of the present invention has excellent fluorescence characteristics and also has excellent properties as a universal base.

Abstract: The present invention describes Photolabile Compounds methods for use of the compounds. The Photolabile Compounds have a photoreleasable ligand, which can be biologically active, and which is photoreleased from the compound upon exposure to light. In some embodiments, the Photolabile Compounds comprise a light antenna, such as a labeling molecule or an active derivative thereof. In one embodiment, the light is visible light, which is not detrimental to the viability of biological samples, such as cells and tissues, in which the released organic molecule is bioactive and can have a therapeutic effect. In another embodiment, the photoreleasable ligand can be a labeling molecule, such as a fluorescent molecule.

Abstract: Fluorophores derived from photoactivatable azide-pi-acceptor fluorogens or from a thermal reaction of an azide-pi-acceptor fluorogen with an alkene or alkyne are disclosed. Fluorophores derived from a thermal reaction of an alkyne-pi-acceptor fluorogen with an azide are also disclosed. The fluorophores can readily be activated by light and can be used to label a biomolecule and imaged on a single-molecule level in living cells.

Abstract: The present invention discloses methods to identify targets, pathways and molecules regulating purinosomes and their uses for treating pathophysiological disorders associated with purinosomes. Disclosed are methods related to both label-free cellular assays and fluorescence imaging to confirm the regulatory roles of various targets and molecules in purinosome dynamics. Disclosed are methods to classify molecules and the uses of these molecules for different indications. Specifically, the purinosome-disrupting molecules can be used for improved prevention and treatment of cancer development.

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: This invention relates to the field of nucleic acid chemistry, more specifically to the field of compositions of matter that comprise triphosphates of modified 2?-deoxynucleosides and oligonucleotides that are formed when these are appended to the 3?-end of a primer, wherein said modifications comprise NH2 moiety attached to their 3?-hydroxyl group and a fluorescent species in a form of a tag affixed to the nucleobase via a linker that can be cleaved. Such compositions and their associated processes enable and improve the sequencing of oligonucleotides using a strategy of cyclic reversible termination, as outlined in U.S. Pat. No. 6,664,079. Most specifically, the invention concerns compositions of matter that are 5?-triphosphates of ribo- and 2?-deoxyribonucleosides carrying detectable tags and oligonucleotides that might be derived from them.

Abstract: The present invention provides nucleoside compounds and certain derivatives thereof which are inhibitors of RNA-dependent RNA viral polymerase. These compounds are inhibitors of RNA-dependent RNA viral replication and are useful for the treatment of RNA-dependent RNA viral infection. They are particularly useful as inhibitors of hepatitis C virus (HCV) NS5B polymerase, as inhibitors of HCV replication, and/or for the treatment of hepatitis C infection. The invention also describes pharmaceutical compositions containing such nucleoside compounds alone or in combination with other agents active against RNA-dependent RNA viral infection, in particular HCV infection. Also disclosed are methods of inhibiting RNA-dependent RNA polymerase, inhibiting RNA-dependent RNA viral replication, and/or treating RNA-dependent RNA viral infection with the nucleoside compounds of the present invention.

Abstract: Disclosed herein are biomolecule-polymer conjugates of Formula 1, as well as methods of preparing same and kits for preparing same.

Abstract: The present disclosure relates to the use and methods of manufacture of bicyclic nucleosides and nucleotides for the treatment and prevention of infectious and proliferative diseases, including microbial infections and cancer.

Abstract: The invention relates to a method for producing phosphate-bridged nucleoside conjugates. In the method, a cyclosaligenyl nucleotide is produced first, to which a linker is added, which is used to perform the immobilization on a solid phase. A subsequent reaction with corresponding nucleophiles results in the desired phosphate-bridged nucleoside conjugates, which can then again be cleaved from the solid phase-bound linker.

Abstract: The invention relates to analogous compounds of 6-thioguanosine triphosphate of general formula (I). A compound of the general formula (I); wherein the dashed bond in the sugar moiety can be either single or double and wherein R1, R2, R3, R4 or R5, equal or different between each other, have general formula -(Int)m-Ter, wherein m is between 0 and 12 and Int and Ter are Internal and Terminal building blocks, wherein Int is selected from the group consisting of formula (II); and Ter is selected from the group consisting of formula (III).

Abstract: This invention is directed to a method of enhancing or facilitating the clearance or the lung mucus secretions in a subject. This invention is also directed to a method of facilitating the hydration of the lung mucus secretions in a subject. This invention is further directed to a method of preventing or treating diseases or conditions associated with impaired lung or airway function in a human or other mammal. The method comprises administering to a subject a pharmaceutical composition comprising a therapeutic effective amount of P2Y6 receptor agonist compound, wherein said amount is effective to activate the P2Y6 receptors on the luminal surface of lung epithelia. The P2Y6 receptor agonist compounds useful for this invention include mononucleoside 5?-diphosphates, dinucleoside monophosphate, dinucleoside diphosphates, or dinucleoside triphosphates of general Formula I, or salts, solvates, hydrates thereof. This invention is also directed to novel P2Y6 receptor agonist compounds.

Abstract: Described are modified mononucleotides and processes for their production. The nucleotides have a structure in which B is a purine or pyrimidine, S is a sugar unit, Y is an OH, a monophosphate, or a diphosphate, and Acc is an electron acceptor selected from the group consisting of (a) —CN and (b) —SO2—R? in which R? contains one amino-substituted alkyl or one optionally substituted aryl.

Abstract: Disclosed herein are phosphorothioate nucleotide analogs, methods of synthesizing phosphorothioate nucleotide analogs and methods of treating diseases and/or conditions such as viral infections, cancer, and/or parasitic diseases with the phosphorothioate nucleotide analogs.

Abstract: Disclosed herein are nucleosides, nucleotides and analogs thereof, pharmaceutical compositions that include one or more of nucleosides, nucleotides and analogs thereof, and methods of synthesizing the same. Also disclosed herein are methods of ameliorating and/or treating a disease and/or a condition, including an infection from a paramyxovirus and/or an orthomyxovirus, with a nucleoside, a nucleotide and an analog thereof. Examples of viral infections include a respiratory syncytial viral (RSV) and influenza infection.

Abstract: The invention provides a novel class of cyanine dyes that are functionalized with a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

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

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: The invention provides prodrugs activated by RNA-dependent DNA-polymerases, and methods for treating hematological tumors, blood, and blood derivatives from patients affected by retroviral infections by administering the prodrugs. The invention also provides methods for the preparation of pharmaceutical compositions containing the prodrugs.

Abstract: Provided are methods for treating Paramyxoviridae virus infections by administering ribosides, riboside phosphates and prodrugs thereof, of Formula I: wherein the 1? position of the nucleoside sugar is substituted. The compounds, compositions, and methods provided are particularly useful for the treatment of Human parainfluenza and Human respiratory syncytial virus infections.

Abstract: Embodiments of the invention provide non-natural bifunctional nucleotides having both nuclease resistance and nucleic acid synthesis blocking properties and methods of sequencing nucleic acids that employ non-natural bifunctional nucleic acids. Additional embodiments provide non-natural oligonucleotides and methods for sequencing nucleic acids using the non-natural oligonucleotides. Methods according to embodiments of the invention employ electronic detection and fluorescent detection of nucleic acid sequencing reactions.

Abstract: Compounds of structural formula (I): and pharmaceutically acceptable salts thereof; wherein R1; R2; R3; Q1 and Q2 are as defined herein, processes for their preparation; pharmaceutical compositions containing them and their use in medicine, in particular the treatment or prevention of HCV infections, are disclosed.

Abstract: The invention relates to the use of 1-(?-D-Ribofuranosyl)-1,2-dihydropyrimidin-2-one derivative or mimetic or an analogue, derivatives, metabolites, variants or salts thereof for the manufacturing of a medicament to increase the amount of Indoleamine 2,3-dioxygenase (IDO) production in order to induce immunological tolerance as well as a method of treating a mammal in need thereof.

Abstract: This invention relates to the field of nucleic acid chemistry, more specifically to the field of compositions of matter that comprise triphosphates of modified 2?-deoxynucleosides and oligonucleotides that are formed when these are appended to the 3?-end of a primer, wherein said modifications comprise NH2 moiety attached to their 3?-hydroxyl group and a fluorescent species in a form of a tag affixed to the nucleobase via a linker that can be cleaved. Such compositions and their associated processes enable and improve the sequencing of oligonucleotides using a strategy of cyclic reversible termination, as outlined in U.S. Pat. No. 6,664,079. Most specifically, the invention concerns compositions of matter that are 5?-triphosphates of ribo- and 2?-deoxyribonucleosides carrying detectable tags and oligonucleotides that might be derived from them.

Abstract: The present disclosure relates to the field of nucleic acid chemistry, specifically to 5-position modified uridines as well as phosphoramidite and triphosphate derivatives thereof. The present disclosure also relates to methods of making and using the same.

Abstract: The present invention encompasses compositions and methods that activate P2Y receptors for the increased production of new synapses in the central nervous system. The formulations of the invention may be administered to a healthy subject or to a subject in need thereof to restore synapses.

Abstract: Processes are disclosed that use 3?-reversibly terminated nucleoside triphosphates to analyze DNA for purposes other than sequencing using cyclic reversible termination. These processes are based on the unexpected ability of terminal transferase to accept these triphosphates as substrates, the unexpected ability of polymerases to add reversibly and irreversibly terminated triphosphates in competition with each other, the development of cleavage conditions to remove the terminating group rapidly, in high yield, and without substantial damage to the terminated oligonucleotide product, and the ability of reversibly terminated primer extension products to capture groups. The presently preferred embodiments of the disclosed processes use a triphosphate having its 3?-OH group blocked as a 3?-ONH2 group, which can be removed in buffered NaNO2 and use variants of Taq DNA polymerase, including one that has a replacement (L616A).

Abstract: The invention provides adenosine analog compounds that act at P2Y receptors, e.g., the P2Y2 receptor, including pharmaceutical compositions; and uses thereof to treat or prevent diseases associated with that receptor, e.g., disorders relating to mucus secretion, such as cystic fibrosis, chronic obstructive pulmonary disorder (COPD), asthma, constipation, chronic idiopathic constipation, dry mouth (xerostomia), gum disease, and gastrointestinal problems caused by radiation and chemotherapy for cancer.

Abstract: A nucleotide triphosphate (NTP) participates in a phosphorylation reaction, wherein a phosphate group is transferred from the NTP to a substrate by a kinase. Provision in a kinase reaction of a NTP whose gamma phosphate is conjugated to an electroactive label results in the transfer of the gamma phosphate-electroactive label conjugate from the NTP to the substrate. The electroactive label is an organic moiety such as a quinone or a nitroheterocycle, or is a metallocene such as a ferrocene or a cobaltocene. Upon transfer of the gamma phosphate-electroactive label conjugate to an electrode-bound substrate by a kinase, the phosphorylation event is detected electrochemically by cyclic voltammetry. Phosphorylation can also be detected by mass spectrometry of a substrate carrying the electroactive label-conjugated gamma phosphate.

Abstract: Disclosed, among other things, are compounds having the structure wherein X comprises a bond or a linker, LABEL comprises at least one detectable label, W1 taken alone is —H or —OH, W2 is —OH or a non-extendable moiety, W3 when taken alone is —H or when taken together with W1 is —CH2—O—, and W4 is OH, monophosphate, diphosphate, or triphosphate. Also disclosed are labeled polynucleotide compounds and methods of use thereof.

Abstract: Methods, apparatus, systems, computer programs and computing devices related to biologically assembling and/or synthesizing peptides and/or proteins are disclosed.

Abstract: A novel nucleoside triphosphate derivative, a nucleic acid probe, and a multilabeled nucleic acid probe that can detect a target nucleic acid conveniently and with high sensitivity, as well as a method for producing the multilabeled nucleic acid probe, and a method for detecting a target nucleic acid using the multilabeled nucleic acid probe or the nucleic acid probe. A target nucleic acid can be detected conveniently and with high sensitivity by using a transglutaminase (TGase), and by using a multilabeled nucleic acid probe in which a plurality of labeling portions have been introduced in advance by covalent binding, or by introducing a plurality of labeling portions by covalent binding into a nucleic acid probe that has been hybridized with the target nucleic acid.

Abstract: Nucleotide triphosphate probes containing a molecular and/or atomic tag on a a ? and/or ? phosphate group and/or a base moiety having a detectable property are disclosed, and kits and method for using the tagged nucleotides in sequencing reactions and various assay. Also, phosphate and polyphosphate molecular fidelity altering agents are disclosed.

Abstract: The invention relates to a method for producing a biodegradable molded part, comprising: providing a binding agent which contains a lyzable biopolymer; forming a molded part from the binding agent, wherein the time stability of the molded part to biological lysis is set by at least one of the following measures: adding a pulverized inorganic solid matter in a proportion of 5% to 85% of the mass of the binding agent before forming the molded part; thawing at least one of the surfaces of the molded part using a chemical or biological method such that the surface has a structuring in the range between 1 nm and 10 ?m. The invention further relates to an accordingly produced molded part.

Abstract: Methods, apparatus, systems, computer programs and computing devices related to biologically assembling and/or synthesizing peptides and/or proteins are disclosed.