Abstract: Provided a polymerizable compound represented by the following Formula A-1 or Formula A-2: In Formula A-1 or Formula A-2, R1 represents an electron-donating group; n represents an integer from 1 to 5; R2 represents a hydrogen atom, a halogen atom, or —ORO, wherein RO represents a hydrogen atom, an alkyl group, or a protecting group of a hydroxy group; R3 represents a hydrogen atom or a protecting group of a hydroxy group; and X represents a structure represented by any one of Formula B-1 to Formula B-5.

Abstract: Compositions and methods for down modulating target gene expression are disclosed.

Abstract: The present invention provides compositions, apparatuses and methods for detecting one or more nucleic acid targets present in a sample. Methods of the invention include utilizing two or more oligonucleotide probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive ligation moieties. When such probes have bound to the target in the proper orientation, they are able to undergo a spontaneous chemical ligation reaction that yields a ligated oligonucleotide product. In accordance with the invention, the presence of the target(s) of interest can be determined by measuring the presence or amount of ligated oligonucleotide product.

Abstract: The technology described herein relates to siRNAs, e.g., methods and compositions relating to the production of siRNAs in bacterial cells.

Abstract: The present application, among other things, provides technologies, e.g., reagents, methods, etc. for preparing oligonucleotides comprising phosphorothiotriesters linkages, e.g., oligonucleotides having the structure of IIIa, IIIb or IIIc. In some embodiments, provided methods comprise reacting an H-phosphonate of structure Ia or Ib with a silylating reagent to provide a silyloxyphosphonate, and reacting the silyloxyphosphonate with a thiosulfonate reagent of structure IIa or IIb to provide an oligonucleotide of structure IIIa or IIIb.

Abstract: The present invention provides a method for preparing nucleotide oligomers, including (a) coupling a nucleotide dimer or nucleotide trimer to a nucleoside attached to solid supports or to universal solid supports as a starting material; (b) sequentially coupling nucleotide monomers to the resulting structures of Step (a) to prepare a nucleotide oligomer; and (c) removing the nucleotide oligomers from the solid supports. The method of the present invention provides nucleotide oligomers having 15-20% higher purity than the conventional art. The present invention enables the efficient and inexpensive synthesis of nucleotide oligomers with high purity within a shorter period of time.

Abstract: Disclosed herein are methods of preparing a phosphorothioate nucleotide analog, which are useful in treating diseases and/or conditions such as viral infections.

Abstract: A method for preparing a phosphorothioate RNA based on the oxazaphospholidine method, wherein cyanoethoxymethyl group is used instead of tert-butyldimethylsilyl group as a protective group of 2?-hydroxyl group of RNA.

Abstract: Disclosed herein are methods of preparing a phosphorothioate nucleotide analog, which are useful in treating diseases and/or conditions such as viral infections.

Abstract: Disclosed herein are nucleoside phosphoramidates and their use as agents for treating viral diseases. These compounds are inhibitors of RNA-dependent RNA viral replication and are useful as inhibitors of HCV NS5B polymerase, as inhibitors of HCV replication and for treatment of hepatitis C infection in mammals.

Abstract: A method and compositions for sulfurizing at least one phosphite or thiophosphite linkage in an oligonucleotide. The methods employ a phenylacetyl disulfide reagent (known as PADS), phenylthioacetic acid (PTAA) in the presence or absence or N-alkyl imidazole in industrially preferred solvents or solvents that are derived from renewable resources. The use of PTAA eliminates the need to “age” the PADS solution prior to its use in sulfurization reactions.

Abstract: Disclosed herein are nucleoside phosphoramidates and their use as agents for treating viral diseases. These compounds are inhibitors of RNA-dependent 5 RNA viral replication and are useful as inhibitors of HCV NS5B polymerase, as inhibitors of HCV replication and for treatment of hepatitis C infection in mammals.

Abstract: A method for preparing oligonucleotide comprising reacting the compound of Formula (1) with the compound of Formula (2) in a liquid reaction medium under the condition of condensation reaction to obtain the compound of formula (3) is provided. 1-(2-mesitylenesulfonyl)-3-nitro-1H-1,2,4-triazole (MSNT) is applied as condensing agent. Oligonucleotides synthesized in the liquid reaction medium could be obtained on a large scale.

Abstract: A method for modifying nucleic acid bases by a chemical means, which enables the discrimination of every base species in plural species of bases in a nucleic acid comprising plural nucleotide units, while retaining the base sequence information of the nucleic acid. A nucleic acid base-modified product provided by the method. The nucleic acid base-modified product is essentially a single strand. In accordance with the invention, a novel means for sequencing a nucleic acid by a microscopic means is provided.

Abstract: A method for synthesizing an oligonucleotide which comprises using a sulfurizing agent of general formula (I) for sulfurizing at least one phosphorus internucleotide linkage of a precursor of the oligonucleotide, wherein R is an aryl group or a heteroaryl group, which is bonded to the S-atom through an annular carbon atom; and R1 and R2 are independently organic residues, preferably a C1-C20 hydrocarbon residue. The method may further comprise purifying the oligonucleotide. Also included is a process for the synthesis of the sulfurizing agent.

Abstract: The present invention relates to a method for stereoselective synthesis of phosphorus compounds, whereby in the first reaction step a chiral auxiliary on the phosphorus atom of phosphoryl chloride, thiophosphoryl chloride or phosphorus trichloride is covalently bonded, the product from the first reaction step is reacted in the following step with an alcohol, thiol, or amine as the nucleophile in the presence of a base, and in the last step the chiral auxiliary is displaced from the product of the following step by a nucleophile.

Abstract: Methods for the preparation of the ? isomer of a 9-deazapurine derivatives using benzyl protecting groups as the protecting groups for the 2 and 3 hydroxyl groups in ribose are provided.

Abstract: Disclosed are a novel phosphorylating reagent and related methods. Specifically disclosed is a compound represented by general formula (A). In the formula, WG1 and WG2 independently represent a cyano group, a nitro group, a halogen atom, an alkylsulfonyl group or an arylsulfonyl group; X1, X2, X3 and X4 independently represent CR or N; and R represents H, a methyl group, a halogen atom, a trifluoromethyl group, a cyano group, a nitro group, an alkoxycarbonyl group, a carbamoyl group, a monoalkylcarbamoyl group, a dialkylcarbamoyl group, a sulfamoyl group, a monoalkylsulfamoyl group, a dialkylsulfamoyl group, or an alkylsulfonyl group.

Abstract: The present invention describes simple, efficient, and enzyme-free method of making oligonucleotides with 5?-triphosphate. This invention presents novel process for synthesizing triphosphate oligonucleotides using a diaryl phosphonate as reagent. The process of the present invention is amenable to large-scale, economic 5?-triphosphate oligonucleotide synthesis.

Abstract: The invention provides methods for the synthesis of cyclic dinucleotides and thiophosphate analogs thereof as well as a new family of analogs of cyclic diguanosine monophosphate that includes a series of seven phosphorothioate derivatives that includes diastereomers of mono-, di-, and trithiophosphates.

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

Abstract: The present invention describes simple, efficient, and enzyme-free method of making oligonucleotide phosphate derivatives. This invention presents novel process using automated synthesizer for synthesizing oligonucleotide phosphate derivatives using a diaryl phosphonate as reagent.

Abstract: A method for preparing oligonucleotide comprising reacting the compound of Formula (1) with the compound of Formula (2) in a liquid reaction medium under the condition of condensation reaction to obtain the compound of formula (3). In the method according to the present invention, the functional groups are protected by suitable protective groups to only expose the 5?-OH of the compound of Formula (1) (OH-component) and the 3?-phosphate of the compound of Formula (2) (P-component) which are to be connected, so that the condensation reaction is carried out in a liquid reaction medium to bond the OH-component and P-component to obtain DNA or RNA short chain. The method of the present invention does not need a solid phase column and can be carried out in a liquid reaction medium. Thus, oligonucleotides can be synthesized on a large scale.

Abstract: Hydrazino, oxyamino and carbonyl-based monomers and methods for incorporation into oligonucleotides during enzymatic synthesis are provided. Modified oligonucleotides are provided that incorporate the monomers provided herein. Immobilized oligonucleotides and oligonucleotide conjugates that contain covalent hydrazone or oxime linkages are provided. Methods for preparation of surface bound oligonucleotides are provided. Methods for the preparation of oligonucleotide conjugates are also provided.

Abstract: The invention comprises a viral cap-leader sequence which comprises at least three bases complementary to the 3?-ultimate residues of a (?)ssRNA virus template sequence. Preferably said consensus sequence is represented by the general formula 7mG(N)6-10-(A/U/G)?A/U?AGC, more preferably 7mG(N)7-8-(A/U/G)?A/U?AGC. Further comprised are modified cap-leader sequences that are able to block elongation by the viral polymerase or cleavage by the viral endonuclase. Such modified cap-leader sequences comprise a 3?-terminal phosphate group, one or more phosphorothioate or phosphorodiamidate bonds or one ore more morpholino rings. Also pharmaceutical products comprising such a modified cap-leader sequence are disclosed. Further, the invention comprises methods for inhibiting virus transcription, especially for influenza virus, using such a modified cap-leader sequence or pharmaceutical product.

Abstract: The present invention describes novel compounds and methods for capping reactive groups on support and during multistep synthesis. These new capping reagents are also useful for high quality synthesis on solid supports and surfaces used as microarrays, biosensors, or in general as biochips. The compounds are also useful for controlling surface density of reactive groups on a support. The compounds may also be used to modify the hydrophilic/hydrophobic characteristics of a surface or a molecule. The compounds have functional utility in various applications in the fields of genomics, proteomics, diagnostics and medicine.

Abstract: Method for synthesis, deprotection, and/or purification of nucleic acid molecules, such as oligonucleotides comprising one or more ribonucleotides. Such nucleic acid molecules include siRNA, dsRNA, ribozymes, antisense, and aptamers.

Abstract: Methods for synthesizing a collection of partially identical polynucleotides are disclosed.

Abstract: The present invention provides methods of extending nucleic acids and purifying target nucleic acids. The methods include the use of capping reagents to effect chain termination and provide a handle for purification via fluorous affinity methods.

Abstract: A process for providing regiospecific and highly stereoselective synthesis of 9-? anomeric purine nucleoside analogs is described. The introduction of the sugar moiety on to 6-(azolyl)-substituted purine bases is performed so that highly stereoselective formation of the ? anomers of only the 9 position regioisomers of the purine nucleoside analogs (either D or L enantiomers) is obtained. This regiospecific and stereoselective introduction of the sugar moiety allows the synthesis of nucleoside analogs, and in particular 2?-deoxy, 3?-deoxy, 2?-deoxy-2?-halo-arabino and 2?,3?-dideoxy-2?-halo-threo purine nucleoside analogs, in high yields without formation of the 7-positional regioisomers. Processes for providing novel 6-(azolyl)purines for the regiospecific and highly stereoselective synthesis of 9-? anomeric purine nucleoside analogs are described. The compounds are drugs or intermediates to drugs.

Abstract: The present invention provides a new labeling reagent for preparing modified oligonucleotides and processes for their production wherein these oligonucleotides contain at least once the structure P?N—SO2-benzole-L-M-X, characterized in that L is either —(CH2)n- or polyethylene glycol, M is selected from a group consisting of —NH—, —O—, —S—, and —COO—, and X is either a protecting group or a detectable unit. L is preferably either —(CH2)n- or polyethylene glycol.

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

Abstract: Labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays and others.

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

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

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

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

Abstract: Provided are processes for preparing a 3?-deoxypentopyranosyl oligomers with linkers for linking biomolecules. The processes can the steps of: bonding a 4?-protected-3?-deoxypentopyranosyl nucleoside to a solid support by coupling the 2?-OH group with a CPG support or other similar support with an amide linkage; deprotecting the 4?-protected-3?-deoxypentopyranosyl nucleoside at the 4? position; deprotecting the 4?-protected-3?-deoxypentopyranosyl nucleoside at the 4? position; and conjugating a linker to the free 4? position. The resulting product can be conjugated via the linker to a biomolecule. The method can include, prior to addition of the linker, reacting the 4?-OH group of the 4?-protected-3?-deoxypentopyranosyl nucleoside that is linked to the solid support with a 4?-protected-3?-deoxypentopyranosyl nucleoside phosphoramidite in the presence of a coupling reagent, and oxidizing the reaction product. This step can be repeated one or more times to produce an oligomer of desired length.

Abstract: The present invention provides solid support media for use in oligomer synthesis, methods of producing the media, and methods of using the media. In some embodiments, the processes of the invention comprise (a) providing an organic phase comprising an olefin monomer, a cross-linker, a functionalizing reagent and an initiator; and (b) contacting the organic phase with an aqueous phase under conditions of time and temperature effective to form the polymeric bead.

Abstract: Disclosed is a method of altering a nucleic acid. The method includes fragmenting a parent nucleic acid strand to generate nucleic acid fragments. At least a subset of the fragments are ligated to generate shuffled nucleic acid strands. A selected strand is identified from the shuffled nucleic acid strands for a criterion.

Abstract: Method for synthesis, deprotection, and/or purification of nucleic acid molecules, such as oligonucleotides comprising one or more ribonucleotides. Such nucleic acid molecules include siRNA, dsRNA, ribozymes, antisense, and aptamers.

Abstract: A process for the synthesis of an oligonucleotide is provided in which an oligonucleotide is assembled on a swellable solid support using the phosphoramidite approach in the presence of an activator, wherein the activator is not tetrazole or a substituted tetrazole. Preferred activators are pyridinium, imidazolinium and benzimidazolinium salts; benzotriazole and derivatives thereof; and saccharin or a saccharin derivative. Preferred swellable solid supports comprise functionalised polystyrene, partially hydrolysed polyvinylacetate or poly(acrylamide).

Abstract: A method for synthesizing a polynucleotide is disclosed. The method comprises providing a functionalized support comprising a triaryl methyl linker bound to the solid support through a substitution on one of the aryl groups, a nucleotide chain bound to the central methyl carbon of the triaryl methyl group and a nucleoside with a reactive site hydroxyl. The method further provides contacting that functionalized support with a precursor having a hydroxyl protecting group and a phosphorous derivative reactive group to produce internucleotide linkage. The resulting compound is then treated to both remove the hydroxyl protecting group on the precursor, and to oxidize the internucleotide bond.

Abstract: The present invention describes a flexible basestacking monomer that can be incorporated into an oligonucleotide or oligonucleotide analogue, as well as triplex forming oligonucleotides comprising the flexible basestacking monomer. Triplex forming oligonucleotides of the invention are capable of binding sequence specifically to doublestranded target nucleic acids and are therefore of interest for modulation of the activity of target nucleic acids and also detection of target nucleic acids.

Abstract: The present invention relates to improved methods for the preparation of nucleic acids. More particularly, conventional solid supports used for nucleic acid synthesis are derivatized with activators having pKas within the 4 to 7 range. Preferentially, CPG-based solid supports are reacted with trialkoxysilanes containing an activator moiety such as pyridine. During each deblocking step of the nucleic acid synthesis cycle, bound pyridiniums are generated, yielding a weak acidic medium spreads throughout the solid support. The bound activators efficiently activate the phosphoramidite reagents towards coupling with 5?-hydroxynucleosides bound to the solid supports, thus eliminating or supplementing external deliveries of activator during the coupling steps.

Abstract: Methods of forming polynucleotides are disclosed.

Abstract: The present invention relates to a method for producing an oligonucleic acid derivative characterized by using a phenoxyacetic acid derivative anhydride as an acylating agent and a pyridine derivative as the acylation reaction activator, in a capping step for protecting the 5?-hydroxyl group of a ribose of an oligonucleic acid derivative.

Abstract: Inkjet printhead solvents and methods of forming an addressable nucleotide array are disclosed.

Abstract: Compounds having structure (1) wherein R1 is —H a protecting group, a linker or a binding partner; and R2 and R34 are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.