Abstract: Novel nucleotide compounds represented by the formula (I) wherein R1 represents a protective group or a PEG bearing organic group; R2, R2′, R2″, R3, R3′ and R3″ each represents a hydrogen atom or an alkyl, cycloalkyl, aryl or aralkyl group which may contain a hetero-atom; B1, B2, B3 and B4 each represents a base, if necessary, protected by a protective group common in nucleotide chemistry or by a PEG bearing organic group; X, X′ and X″ each represents an oxygen atom or a sulfur atom; Y represents an azolyl group, a mono- or di-alkylamino group or a saturated nitrogenous heterocyclic ring; A1, A2, A3 and A4 each represents a hydrogen atom, a hydroxyl group, an alkoxy group or a trialkylsilyloxy group; and m and n each represents 0 or an integer of 1 to 100.

Abstract: The present invention relates to a process for labeling a synthetic or natural ribonucleic acid (RNA). It also relates to RNA fragments, which have been labeled by fragmenting the RNA to free a terminal phosphate of each fragment for further reaction, and labeling each fragment at the freed terminal phosphate which is located at the 3′ end and/or the 5′ end of each fragment of the RNA, and to the use of such RNA fragments, for example, in the field of medical diagnosis.

Abstract: The invention provides a method for synthesizing oligonucleotides using carbonate protection of hydroxyl groups and nucleophilic deprotection reagents. The deprotection reagents irreversibly cleave the carbonate protecting groups while simultaneously oxidizing the internucleotide phosphite triester linkage, and can be used in aqueous solution at neutral to mildly basic pH. The method eliminates the need for separate deprotection and oxidation steps, and, since the use of acid to remove protecting groups is unnecessary, acid-induced depurination is avoided. Fluorescent or other readily detectable carbonate protecting groups can be used, enabling monitoring of individual reaction steps during oligonucleotide synthesis. The invention is particularly useful in the highly parallel, microscale synthesis of oligonucleotides. Reagents and kits for carrying out the aforementioned method are provided as well.

Abstract: Enzymatic nucleic acid molecule containing one or more non-nucleotide mimetics, and having activity to cleave an RNA or DNA molecule.

Abstract: A process for deprotecting RNA alkylsilyl groups comprising, contacting the groups with a solution of anhydrous triethylamine-hydrogen fluoride (aHF-TEA) in triethylamine and N-methylpyrrolidine at between 60° C.-70° C. for 0.25-24 h.

Abstract: Radiation-activated catalysts (RACs), autocatalytic reactions, and protective groups are employed to achieve a highly sensitive, high resolution, radiation directed combinatorial synthesis of pattern arrays of diverse polymers. When irradiated, RACs produce catalysts that can react with enhancers, such as those involved in autocatalytic reactions. The autocatalytic reactions produce at least one product that removes protecting groups from synthesis intermediates. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.

Abstract: A method for reducing evaporation of a liquid reagent solution during solid phase, micro-scale chemical synthesis of a molecule comprising sub-units on an open environment solid support surface. The method includes the steps of providing an open solid support surface including at least one binding site which is functionalized with a reactive chemical moiety; and depositing a substantially controlled and minute volume of liquid reagent solution onto the support surface, and in contact with the binding site. The reagent solution includes reactants contained in at least one relatively high boiling point solvent, in contrast to standard organic solvents for such reagents. Application of a high boiling point solvent substantially reduces evaporation of the reagent solution in the open environment during synthesis on the solid support while enabling the maintenance of a substantially high reaction yield.

Abstract: A method for the manufacture of a support matrix exhibiting amino groups I, possibly in acylated form, comprising the step of polymerizing one or more monovinyl monomers (monomer I) with one or more di- tri- or polyvinyl monomers (monomer II). The method is characterized in that that the polymerization is run in the presence of one or more amino-(C0-10)hydrocarbon vinyl aromatic monomers possibly in acylated form (monomer III). The preferred combination of monomers are ethyl vinyl benzene, divinyl benzene and amino styrene. The support matrix comprising a polyvinyl backbone [(—CH2CH2)n] and amino groups or groups derived from said amino groups while retaining the nitrogen of the amino group, each of which groups being attached to said backbone via a link structure containing an arylene group. The matrix is characterized in that each of said groups is directly attached via said nitrogen to said arylene group.

Abstract: The present invention provides novel methods for preparing oligonucleotide conjugates using a novel electrophilic haloacetyl linker. Novel compounds and intermediates are also disclosed.

Abstract: Immobilized nucleotide primers of this invention include a modified nucleotide tethered to a support substrate through a linking group. In particular, the modified nucleotide is constructed such that the C-5′ end of the nucleotide is tetherable to the linking group and the protected C-3′ end is available for further controlled modification, e.g., addition of other nucleotides in specific sequences to the immobilized nucleotide primer. Additionally, the linking group is of sufficient length to allow the immobilized nucleotide primer to be used to synthesize and screen arrays of oligonucleotides, e.g., enzymatic C-3′ primer extension.

Abstract: A method of preparing an immobilized oligonucleotide having a free 3′-end comprises the steps of: i) preparing an oligonucleotide attached in a first position to a solid support via its 3′-end and having a free 5′-end; ii) binding said oligonucleotide in a second position remote from the 3′-end to the solid support; and iii) selectively releasing the 3′-end of the oligonucleotide from the solid support to obtain the oligonucleotide attached to the support in said second position in a reversed orientation with a free 3′-end.

Abstract: A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.

Abstract: Method for one-pot deprotection of RNA molecules.

Abstract: A process for the isolation and purification of nucleic acids and/or oligonucleotides for use in gene therapy wherein said nucleic acids and/or oligonucleotides are isolated or purified from an essentially biological source, characterized in that said essentially biological sources are lysed, the fractions obtained are optionally freed or depleted from the remainder of said biological sources by per se known mechanical methods, such as centrifugation, filtration; the fractions thus treated are subsequently treated with affinity chromatographic material or with inorganic chromatographic material for the removal of endotoxins; followed by isolation of said nucleic acids and/or oligonucleotides on an anion exchanger which is designed such that DNA begins to desorb from the anion exchanger only at an ionic strength corresponding to a sodium chloride solution of a concentration higher by at least 100 mM than one corresponding to the ionic strength at which RNA begins to desorb from the anion exchanger material.

Abstract: Provided herein is a method for detecting the presence of a target nucleic acid sequence in a sample. The present method uses a combination of dual labeled probes and heterogeneous detection methods.

Abstract: The present invention relates to a support system for solid phase synthesis of oligomers, such as oligonucleotides, wherein the starting compound is bound to the support via a disiloxyl linkage. Furthermore, the invention relates to a method for synthesis of oligonucleotides on a solid support. The support system comprises a stable disiloxyl linkage providing high nucleoside loadings to the support and the method allows convenient non-laborious oligomer synthesis.

Abstract: Methods for the alkylation of alcohols, amines and thiols by the use of cyclic sulfates are disclosed. The alkylated sulfates formed are versatile intermediates which may be further elaborated by methods of the invention. In particular, methods for the alkylation of the 2′, 3′ or 5′-hydroxy position of nucleosides and nucleoside analogs with cyclic sulfates to form the 2′, 3′ or 5′-O-alkyl sulfate modified compounds are disclosed. Displacement of the 2′,3′ or 5′-O-sulfate with a nucleophile provides 2′, 3′ or 5′-O-modified nucleosides and nucleoside analogs useful for the synthesis of oligomeric compounds having improved hybridization affinity and nuclease resistance.

Abstract: In one embodiment, the invention provides a polymer comprising imidazole ring units having nitrogen at the 1 and 3 positions of the ring; a carbon at each of the 2, 4 and 5 positions of the ring; and radical substituents G1 and G2 carried at the 4 and 5 positions. G1 and G2 are each independently selected from cyano, substituents derived from cyano, and substituents which replace cyano. The polymers formed by at least two of the cyclic imidazole units. In another embodiment, the invention provides new imidazole compounds usable as monomers to form the polymers. In still another embodiment, the invention provides a method for using the polymers as a coupling/activator for synthon synthesis.

Abstract: Structural analogs of the six non-fluorescentN-nucleosides commonly found in RNA and DNA, which are inherently fluorescent under physiological conditions, are identified and methods for their preparation provided. Such analogs may be incorporated into DNA and/or RNA oligonucleotides via either enzymatic or chemical synthesis to produce fluorescent oligonucleotides having prescribed sequences. Such analogous sequences may be identical to, or the analogous complement of, template or target DNA or RNA sequences to which the fluorescent oligonucleotides can be hybridized. Methods of preparing either RNA or DNA oligonucleotide probes of the invention, intermediates used in such methods, and methods of using the probes of the invention in oligonucleotide amplification, detection, identification, and/or hybridization assays are also provided.

Abstract: Novel compounds that mimic and/or modulate the activity of wild-type nucleic acids. In general, the compounds are phosphorothioate oligonucleotides wherein the 5′-terminal internucleoside linkage or the 5′- and 3′-terminal linkages are modified.

Abstract: Processes for preparing 2′-O-alkylated guanosine, uridine, cytidine, and 2,6-diaminopurine 3′-O-phosphoramidites include the steps of alkylating nucleoside precursors, adding suitable blocking groups and phosphitylating. For the guanosine 2′-O-alkylated 3′-O-phosphoramidites, alkylation is effected on 2,6-diamino-9-(&bgr;-D-ribofuranosyl) purine followed by deamination. For uridine 2′-O-alkylated 3′-O-phosphoramidites, alkylation is effect on a dialkyl stannylene derivative of uridine. For cytidine 2′-O-alkylated 3′-O-phosphoramidites, alkylation is effected directly on cytidine. Alkylation is effected directly upon 2,6-diaminopurine.

Abstract: Sequence-specific oligonucleotides are provided having substantially pure chiral Sp phosphorothioate, chiral Rp phosphorothioate, chiral Sp alkylphosphonate, chiral Rp alkylphosphonate, chiral Sp phosphoamidate, chiral Rp phosphoamidate, chiral Sp phosphotriester, and chiral Rp phosphotriester linkages. The novel oligonucleotides are prepared via a stereospecific SN2 nucleophilic attack of a phosphodiester, phosphorothioate, phosphoramidate, phosphotriester or alkylphosphonate anion on the 3′ position of a xylonucleotide. The reaction proceeds via inversion at the 3′ position of the xylo reactant species, resulting in the incorporation of phosphodiester, phosphorothioate, phosphoramidate, phosphotriester or alkylphosphonate linked ribofuranosyl sugar moieties into the oligonucleotide.

Abstract: This invention is directed to novel purine-based compounds for inclusion into oligonucleotides. The compounds of the invention, when incorporated into oligonucleotides are especially useful as “antisense” agents—agents that are capable of specific hybridization with a nucleotide sequence of an RNA. The compounds of the invention may also be used for cross-linking oligonucleotides. Oligonucleotides are used for a variety of therapeutic and diagnostic purposes, such as treating diseases, regulating gene expression in experimental systems, assaying for RNA and for RNA products through the employment of antisense interactions with such RNA, diagnosing diseases, modulating the production of proteins, and cleaving RNA in site specific fashions. The compounds of the invention include novel heterocyclic bases, nucleosides, and nucleotides. when incorporated into oligonucleotides, the compounds of the invention can be useful for modulating the activity of RNA.

Abstract: Oligonucleotide analogs are disclosed having pyrimidine monomeric sub-units therein that are modified at the 2′ and 5 positions. Monomeric sub-units having these modifications may be further modified at the 2 position. Improved processes for the synthesis of 2′-O-substituted pyrimidine nucleosides are also provided. The processes feature alkylation of a 2,2′-anhydropyrimidine nucleoside or a 2S,2′-anhydropyrimidine nucleoside with a weak nucleophile in the presence of a Lewis acid.

Abstract: The invention provides a method for synthesizing oligonucleotides using carbonate protection of hydroxyl groups and nucleophilic deprotection reagents. The deprotection reagents irreversibly cleave the carbonate protecting groups while simultaneously oxidizing the intemucleotide phosphite triester linkage, and can be used in aqueous solution at neutral to mildly basic pH. The method eliminates the need for separate deprotection and oxidation steps, and, since the use of acid to remove protecting groups is unnecessary, acid-induced depurination is avoided. Fluorescent or other readily detectable carbonate protecting groups can be used, enabling monitoring of individual reaction steps during oligonucleotide synthesis. The invention is particularly useful in the highly parallel, microscale synthesis of oligonucleotides. Reagents and kits for carrying out the aforementioned method are provided as well.

Abstract: This invention provides reagents, libraries and sets of the reagents, and assay methods using the reagents, the reagents comprising an analyte moiety and a tag moiety, wherein the tag moiety contains information defining the identify and location of the analyte residues of the analyte moiety which is detectable by mass spectrometry.

Abstract: A method for the stepwise creation of phosphodiester bonds between desired nucleosides resulting in the synthesis of polynucleotides having a predetermined nucleotide sequence by preparing an initiation substrate containing a free and unmodified 3′-hydroxyl group; attaching a mononucleotide selected according to the order of the predetermined nucleotide sequence to the 3′-hydroxyl of the initiating substrate in a solution containing a catalytic amount of an enzyme capable of catalyzing the 5′ to 3′ phosphodiester linkage of the 5′-phosphate of the mononucleotide to the 3′-hydroxyl of the initiating substrate, wherein the mononucleotide contains a protected 3′-hydroxyl group, whereby the protected mononucleotide is covalently linked to the initiating substrate and further additions are hindered by the 3′-hydroxyl protecting group. Methods in which a mononucleotide immobilized on a solid support is added to a free polynucleotide chain are also disclosed.

Abstract: A DNA probe of the following structural formula (1) (wherein P* is an optically active phosphorus atom, each of R1 and R2 is a DNA oligomer having an arbitrary sequence, and R3 is a fluorescent intercalative dye attached via an appropriate linker) which has an optically active configuration about P*.

Abstract: Synthetic processes are provided wherein mixed backbone oligomeric compounds are prepared having at least one phosphodiester intemucleoside linkage in addition to one or more phosphorothioate, phosphoramidate and boranophosphate internucleoside linkages. Novel H-phosphonate intermediates are also disclosed that are useful in the synthetic processes. The synthetic processes use a novel oxidation step to oxidize H-phosphonate internuleoside linkages to phosphodiester internuleoside linkages without degradation of adjacent phosphorothioate, phosphoramidate and boranophosphate internucleoside linkages. Also provided are synthetic intermediates useful in such processes.

Abstract: Disclosed herein are methods for linking a protein or other biomolecule containing a carboxylic acid moiety to a PNA or DNA probe molecule. The methods disclosed herein involve activating the carboxylic acid moiety with an activating agent and reacting the activated carboxylic acid moiety with a PNA or DNA probe having an arylamine or aminooxyacetyl moiety. Conjugates produced by these methods are also disclosed.

Abstract: The invention relates to nucleoside derivatives bearing electrolabile protector groupings and their use in an oligonucleotide synthesis method comprising at least one step of electronic deprotection.

Abstract: A wash reagent employed for the bulk washing of the surface of a high-density array to remove unreacted reactants from cells of the array while, at the same time, reacting with the unreacted monomer in order to prevent reaction of the reacted monomer with functional groups on the surface of the HDA outside of the region of the surface to which the reactive monomer is applied. The wash reagent is chosen for a particular solid-state synthesis so that the unreacted reactants and catalyzing agents are soluble in the wash reagent, so that the wash reagent does not react with, or catalyze, reactions of the substrate or the biopolymers bound to the substrate, and so that the wash reagent reacts with unreacted reactive monomer in order to prevent subsequent reactions of the unreacted reactive monomer.

Abstract: The present invention pertains to a process for the chromatographic separation of nucleic acid mixtures into their double-stranded and single-stranded nucleic acid fractions by simultaneously absorbing said nucleic acids as a whole to a mineral support, followed by separation into double-stranded and single-stranded nucleic acids by fractional elution, or by selectively absorbing double-stranded or single-stranded nucleic acid of a liquid sample to a mineral support, as well as solutions and a kit for performing the process according to the invention.

Abstract: Peptide nucleic acid (PNA) oligomers are conjugated to a ligand which is capable of binding to a cell surface receptor. The ligand facilitates cellular uptake of the PNA oligomer. Where the ligand is a peptide, the conjugate may be produced as a unitary molecule by first synthesizing the peptide ligand by solid phase or solution peptide synthesis, followed by synthesis of the PNA oligomer as an extension of the peptide ligand. The PNA oligomer base sequence is selected to hybridize to a target polynucleotide sequence by either triplex (dsDNA) or duplex (ssDNA; RNA) formation.

Abstract: A method and system for polynucleotide synthesis are provided which employ solid phase synthesis on a nonswellable porous polystyrene support by phosphoramidite or hydrogen phosphonate chemistries. The polystyrene support gives rise to fewer tritylated failure sequences caused by chain growth from extraneous support sites, and allows lower amounts of monomer reactants to be used to achieve equal or better coupling efficiencies as those achieveable with CPG. The method and system also employ nucleoside intermediates whose exocyclic amines are protected by base-labile groups which permit simultaneous cleavage and deprotection of the completed polynucleotide chain in the presence of the solid phase support. This latter feature allows practical automation of both the synthesis and purification of polynucleotides.

Abstract: A process is provided which can easily produce a hydroxyl groups-containing cyclic ether compound in which at least one of the hydroxyl groups except a primary hydroxyl group thereof and its neighboring secondary hydroxyl group is protected. A hydroxyl groups-containing cyclic ether is reacted with a difunctional silicon compound represented by the following formula (2) R2R3SiX12  (2) wherein R2 and R3 each represent an aromatic group or a branched aliphatic group having at least 3 carbon atoms and X1 represents a residue of an acid, then with a monofunction al silicon compound represented by the following formula (3) R4R5R6SiX2  (3) wherein R4, R5 and R6 each represent an aromatic group or an aliphatic group and X2 represents an eliminative group, and then with hydrofluoric acid in the presence of a base.

Abstract: This invention presents novel processes for incorporating 2-aminoadenosine and 2-aminoadenosine analogs into oligonucleotides. A halogenated adeninosine is incorporated into an oligonucleotide using standard synthesis methods, such as phosphoramidited protocols. Subsequent reaction with an amine results in the desired product. The oligonucleotides produced provide stronger hybridization to their target sequences. These oligonucleotides can be useful compounds, inter alia for diagnostic and therapeutic applications.

Abstract: This invention presents novel methods for synthesizing phosphorothioate oligonucleotides, using support-bound phosphoramiditese. Novel intermediates useful in the methods are also provided.

Abstract: The present invention provides synthetic processes by which oligomeric compounds, having at least one phosphodiester or phosphorothioate linkage, are prepared. The synthetic processes use a novel mixture of concentrated ammonium hydroxide and a thiol compound during the deblocking step of all or selected internucleoside linkages. Alternatively, the deblocking is carried out in two steps using a mercapto compound in an aqueous amine followed by concentrated ammonium hydroxide. Also provided are synthetic intermediates useful in such processes. Novel oxidation procedures to give phosphodiester oligomers are also included.