Abstract: The invention provides improved processes for oligonucleotide synthesis utilizing arenes as solvents for detritylation of oligonucleotides.

Abstract: The invention relates to the chemical synthesis of oligonucleotides and to chemical entities useful in such synthesis. More particularly, the invention relates to sulfurization of the internucleotide linkages of oligonucleotides. The invention provides a process to synthesize new sulfur transfer reagents and a process for their use in sulfurizing oligonucleotides. The sulfur transfer reagents according to the invention are inexpensive to make, stable in storage and in solution, and highly efficient in sulfurization.

Abstract: The invention provides passivated organic polymer supports, processes for their preparation and processes for their use in oligonucleotide synthesis that allow for highly efficient solid phase synthesis of oligonucleotides.

Abstract: The invention relates to the chemical synthesis of oligonucleotides and to chemical entities useful in such synthesis. More particularly, the invention relates to sulfurization of the internucleoside linkages of oligonucleotides. The invention provides new sulfur transfer reagents and processes for their use in sulfurizing oligonucleotides. The sulfur transfer reagents according to the invention are inexpensive to make, stable in storage and highly efficient in sulfurization.

Abstract: In our research, 3-phenyl-1,2,4-dithiazoline-5-one is found to be a potential sulfur-transfer reagent. The efficiency and optimization of this new sulfur-transfer reagent was investigated by solid-phase syntheses of dinucleotide phosphorothioate and 25 mer oligonucleotide phosphorothioates at 1 &mgr;mol and 200 &mgr;mol scales. The results show that 3-phenyl-1,2,4-dithiazoline-5-one is a highly efficient sulfurizing reagent, and greater than 99.8% sulfur transfer efficiency can be achieved. In contrast to EDITH or Beaucage reagent, this novel sulfur-transfer reagent is highly stable in storage and in solution, highly soluble in CH3CN solvent, and can be synthesized at a low cost because of the single step reaction. Due to these advantages, 3-phenyl-1,2,4-dithiazoline-5-one can be considered as a better alternative to EDITH or Beaucage reagent, especially in large-scale preparation of oligonucleotide phosphorothioates.

Abstract: The invention provides novel bifunctional phosphitylating reagents and their application in in situ preparation of 5′-protected nucleoside phosphoramidites and synthesis of oligonucleotides. Bifunctional phosphitylating reagents according to the invention react quickly with nucleosides under neutral or weakly basic conditions, without an additional activation step. In addition, the bifunctional phosphitylating reagents according to the invention generate chemoselectively the corresponding nucleoside phosphoramidites in situ, without need to purify the nucleoside phosphoramidites before using them in oligonucleotide synthesis. Finally, the bifunctional phosphitylating reagents according to the invention are relatively stable and easy to handle.

Abstract: The present invention comprises an improved method of synthesizing oligonucleotides. The method comprises employing dinucleotides (or “dimer blocks”) as the basic synthetic unit building block. The method results in extremely high purity oligonucleotides in which the N−1 content is very low, generally less than 1-2% of the full length, N, oligonucleotide. We have found that synthesis using dinucleotide phosphorothioates results in oligonucleotides having very little phosphodiester content. Furthermore, we have found that the amount of dimer required in each coupling step can be less than about 6 and is preferably about 2 equivalents. Synthesis of oligonucleotides according to the dimer block approach described herein can also be conducted without the capping step that has heretofore been deemed necessary after each coupling.

Abstract: In our research, two commercially available compounds, 3-amino-1,2,4-dithiazole-5-thione (1) and xanthane hydride (2), and their derivatives 3-6 are found to be potential sulfur-transfer reagents. The efficiency and optimization of these new sulfur-transfer reagents were investigated by solid-phase syntheses of dinudeotide and oligonucleotide phosphorothioates. The results show that both compounds 1 and 2 are highly efficient sulfurizing reagents, and better than 99% sulfur transfer efficiency can be achieved at each step. In contrast to Beaucage reagent, these novel sulfur-transfer reagents are very stable in various solvents, and are available in bulk quantities at low cost. Due to these advantages, compounds 1 and 2 can be considered alternatives to Beaucage reagent, especially in large-scale preparation of oligonucleotide phosphorothioates. Furthermore, compounds 1 and 2 were modified to enhance their solubility in acetonitrile.

Abstract: The present invention comprises an improved method of synthesizing oligonucleotides. The method comprises employing dinucleotides (or "dimer blocks") as the basic synthetic unit building block. The method results in extremely high purity oligonucleotides in which the N-1 content is very low, generally less than 1-2% of the full length, N, oligonucleotide. We have found that synthesis using dinucleotide phosphorothioates results in oligonucleotides having very little phosphodiester content. Furthermore, we have found that the amount of dimer required in each coupling step can be less than about 6 and is preferably about 2 equivalents. Synthesis of oligonucleotides according to the dimer block approach described herein can also be conducted without the capping step that has heretofore been deemed necessary after each coupling.

Abstract: The present invention provides an improved method of synthesizing 2'-O--R substituted pyrimidine mononucleosides. The method comprises reacting an anhydropyrimidine with magnesium alkoxide in the corresponding alcohol at elevated temperatures to directly produce the 2'-O--R substituted pyrimidine nucleoside product. The method advantageously eliminates several steps from prior art methods, thereby reducing the time and cost of synthesis and increasing the yield of final product.

Abstract: The invention provides passivated organic polymer supports, processes for their preparation and processes for their use in oligonucleotide synthesis that allow for highly efficient solid phase synthesis of oligonucleotides.

Abstract: The invention relates to synthetic oligonucleotides and more particularly to the determination of nucleotide sequences of synthetic oligonucleotides having non-phosphodiester internucleotide linkages. The invention provides a method for sequencing such modified synthetic oligonucleotides.

Abstract: Disclosed are methods of producing a synthetic oligonucleotide of selected nucleotide sequence which is internally functionalized at at least one selected location with an aminoalkyl-phosphoramidate and labelled with a nonradioactive material. Also disclosed are oligonucleotides produced by this method.

Abstract: New methods of loading solid supports for oligonucleotide synthesis are presented. The new methods comprise coupling a succinylated nucleoside to a solid support using diisopropylcarbodiimide (DIC) as an activator and N-hydroxybenzotriazole (HOBT) as an acid catalyst. DIC is substantially cheaper than the currently used activating agent, 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide (DEC). Furthermore, in the preferred embodiment, when it is used in combination with HOBT, coupling is more efficient, requiring less nucleoside to achieve the same loading densities as in the prior art. The loading process is faster than prior art methods and the overall cost savings of about 43% are realized.

Abstract: Disclosed are methods of producing a synthetic oligonucleotide of selected nucleotide sequence which is internally functionalized at least one selected location with an aminoalkylphosphotriester, and labelled with a nonradioactive material. Also disclosed are oligonucleotides produced by this method.

Abstract: Disclosed are methods of producing a synthetic oligonucleotide of selected nucleotide sequence which is internally functionalized at at least one selected location with an aminoalkylphosphorothioamidate and labelled with a nonradioactive material. Also disclosed are oligonucleotides produced by this method.

Abstract: Oligonucleotides containing multiple free amino groups attached directly to the phosphorus atoms of the phosphodiester linkages having the structure shown below. ##STR1## wherein D=a ribonucleoside or deoxyribonucleotide;p=a 5' to 3'-phosphodiester or phosphoramidate linkage;n=1 to 20;a=1 to 20;b=1 to 20;c=1=20;z=0 to 20;t=1 to 100; andwhereinfor each repeating unit, "a" represents the same number or a different number than that number represented by "a" in every other repeating unit; and for each repeating unit "b" represents the same number or a different number than represented by "b" in every other repeating unit.Multiple reporter molecules can be incorporated into the oligonucleotide via the free amino groups allowing for increased probe sensitivity.

Abstract: The invention relates to synthetic oligonucleotides and more particularly to the determination of nucleotide sequences of synthetic oligonucleotides having non-phosphodiester internucleotide linkages. The invention provides a method for sequencing such modified synthetic oligonucleotides.