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

Abstract: 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: The present invention provides fluorescent nucleosides carrying polycyclic aromatic hydrocarbons such as anthracene, phenanthrene, pyrene stilbene, tetracene or pentacene. The subject nucleosides may be synthesized using a C-glycosidic bond formation method employing organocadmium or organozinc derivatives of the aromatic compounds and coupling with a 1-&agr;-chlororibose or deoxyribose synthon. The &agr;-anomers of the coupling reaction may be epimerized to the &bgr;-anomers by acid-catalyzed equilibration. The fluorescent nucleosides act as DNA or RNA base analogs and can be incorporated into nucleic acids. Resultant fluorescently tagged nucleic acids are useful as probes for target nucleic acids in tissues, solutions or immobilized on membranes.

Abstract: Synthetic processes are provided for the solution phase synthesis of oligonucleotides, especially phosphorothioate oligonucleotides, and intermediate compounds useful in the processes. Intermediates having structure are prepared in accord with preferred embodiments.

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: A nucleoside/tide compound having the structure NUC-L-S-LB/LG is described wherein NUC is a nucleoside/tide having a nucleobase portion B, L is a rigid linkage, S is a spacer; and LB/LG is a member of a linkage pair or a label. NUC is attached to L through B such that when B is a purine, L is attached to the 8-position of the purine, when B is 7-deazapurine, L is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, L is attached to the 5-position of the pyrimidine. In an important aspect of the invention, L has the structure wherein each of n, o and p are integers ranging from 0 to 3, and the sum of n, o and p is at least 2, and each of W, X, Y and Z is selected from the group consisting of carbon and nitrogen. The invention further includes polynucleotide compounds comprising the nucleoside/tide, and primer extension methods utilizing the nucleoside/tide, particularly when used in combination with certain mutant polymerase enzymes.

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: 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: The invention concerns pyrrolo-[3,2-d]pyrimidine, pyrazolo-[4,3-d]pyrimidine and pyrimidine-furanosides i.e. so-called C-nucleosides of the general formulae I-V or appropriate derivatives as well as processes for their production. The compounds are in particular suitable as substrates for RNA or DNA polymerases and can thus be incorporated into RNA or DNA oligonucleotides. Therefore the compounds are especially suitable for labelling and for detecting nucleic acids and for DNA sequencing.

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: 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: Oligonucleotides and other macromolecules are provided which have increased nuclease resistance, substituent groups (such as 2′-aminooxy groups) for increasing binding affinity to complementary strand, and subsequences of 2′-deoxy-erythro-pentofuranosyl nucleotides that activate RNase H. Such oligonucleotides and macromolecules are useful for diagnostics and other research purposes, for modulating the expression of a protein in organisms, and for the diagnosis, detection and treatment of other conditions susceptible to oligonucleotide therapeutics.

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.