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: 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: 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: 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: 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: 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: 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.