Novel photolabile protective groups for improved processes to prepare oligonucleotide arrays

A method for the preparation of a derivatized nucleoside or nucleoside analog thereof comprising the steps of:

• a) reacting an alcohol having the general formula 4:
• 35
• wherein
• R1 is COOY, wherein Y is selected from the group consisting of an optionally substituted alkyl group of up to 10 carbon atoms, under the proviso that R2 is selected from the group consisting of H, NO2, CN, OCH3, halogen or an optionally substituted alkyl or alkoxyl group, respectively, having up to 4 carbon atoms;
• or
• R1 is selected from the group consisting of H, NO2, CN OCH3 or halogen or an optionally substituted alkyl or alkoxyl group respectively, having up to 4 carbon atoms, under the proviso that R2 is selected from the group consisting of an optionally substituted aryl group, an optionally substituted heteroaryl group or an optionally substituted aroyl group;
• R3 is selected from the group consisting of H, NO2 or halogen;
• and
• R4 is selected from the group consisting of H, OCH3 or an optionally substituted alkyl group having up to 4 carbon atoms;
• with phosgene or a derivative or substitute thereof, or with the respective thiocarbonyl compound, to produce an activated carbonate ester or thiocarbonate ester and
• b) reacting the activated carbonate or thiocarbonate ester as formed in step a) with a nucleoside selected from the group consisting of compounds having the general formula (5):
• 36
• wherein
• R6 is selected from the group consisting of H, OH or an optionally substituted alkoxyl or alkenoxyl group respectively, having up to 4 carbon atoms, or WR8 wherein W is selected from oxygen or sulfur and R8 is selected from a protective group useful in oligonucleotide synthesis and
• B is a purine or pyrimidine base selected from the group consisting of adenine, cytosine, guanine, thymine, uracil or chemical modifications thereof and in the case of adenosine, cytosine and guanine the amino functions on the heterocycle may optionally bear a protective group useful in oligonucleotide synthesis;
• or with a nucleosidic derivative or analog comprising an unprotected primary hydroxyl function;
• or with a nucleoside selected from the group of compounds having general formula (6):
• 37
• wherein
• R6 is selected from the group consisting of H, OH or an optionally substituted alkoxyl or alkenoxyl group respectively, having up to 4 carbon atoms, or WR8 wherein W is selected from oxygen or sulfur and R8 is selected from a protective group useful in oligonucleotide synthesis and
• R7 is selected from an intermediate protective group or selected from the group of nucleosidic and nucleotidic derivatives as well as analogs thereof accordingly comprising an intermediately protected primary hydroxyl;
• c) optionally removing the intermediate protective group and purifying the product;
• and
• d) reacting the product from step b) or c) with a phosphitylation reagent to provide after purification a phosphoramidite.

A method for the preparation of a derivatized nucleoside or nucleoside analog thereof comprising the steps of:

• a) reacting a nucleoside selected from the group consisting of compounds having the general formula (5):
• 38
• wherein
• R6 is selected from the group consisting of H, OH or an optionally substituted alkoxyl or alkenoxyl group respectively, having up to 4 carbon atoms, or WR8 wherein W is selected from oxygen or sulfur and R8 is selected from a protective group useful in oligonucleotide synthesis and
• B is a purine or pyrimidine base selected from the group consisting of adenine, cytosine, guanine, thymine, uracil or chemical modifications thereof and in the case of adenosine, cytosine and guanine the amino functions on the heterocycle may optionally bear a protective group useful in oligonucleotide synthesis;
• or reacting a nucleosidic derivative or analog comprising an unprotected primary hydroxyl function;
• or reacting a nucleoside selected from the group of compounds having general formula (6):
• 39
• wherein
• R6 is selected from the group consisting of H, OH or an optionally substituted alkoxyl or alkenoxyl group respectively, having up to 4 carbon atoms, or WR8 wherein W is selected from oxygen or sulfur and R8 is selected from a protective group useful in oligonucleotide synthesis and
• R7 is selected from an intermediate protective group or selected from the group of nucleosidic and nucleotidic derivatives as well as analogs thereof accordingly comprising an intermediately protected primary hydroxyl function;
• or reacting a nucleosidic derivative or analog comprising an unprotected secondary hydroxyl function;
• with phosgene or a derivative or substitute thereof, or with the respective thiocarbonyl compound, to produce an activated carbonate ester or thiocarbonate ester;
• b) reacting the activated carbonate or thiocarbonate ester as formed in step a) with an alcohol having the general formula 4:
• 40
• wherein
• R1 is COOY, wherein Y is selected from the group consisting of an optionally substituted alkyl group of up to 10 carbon atoms, under the proviso that R2 is selected from the group consisting of H, NO2, CN, OCH3, halogen or an optionally substituted alkyl or alkoxyl group, respectively, having up to 4 carbon atoms;
• or
• R1 is selected from the group consisting of H, NO2, CN OCH3 or halogen or an optionally substituted alkyl or alkoxyl group respectively, having up to 4 carbon atoms, under the proviso that R2 is selected from the group consisting of an optionally substituted aryl group, an optionally substituted heteroaryl group or an optionally substituted aroyl group;
• R3 is selected from the group consisting of H, NO2 or halogen;
• and
• R4 is selected from the group consisting of H, OCH3 or an optionally substituted alkyl group having up to 4 carbon atoms;
• c) optionally removing the intermediate protective group and purifying the product;
• and
• d) reacting the product from step b) or c) with a phosphitylation reagent to provide after purification a phosphoramidite.

A compound having the following general formula:

• 41
• wherein
• R1 is COOY, wherein Y is selected from the group consisting of an optionally substituted alkyl group of up to 10 carbon atoms, under the proviso that R2 is selected from the group consisting of H, NO2, CN, OCH3, halogen or an optionally substituted alkyl or alkoxyl group, respectively, having up to 4 carbon atoms;
• or
• R1 is selected from the group consisting of H, NO2, CN OCH3 or halogen or an optionally substituted alkyl or alkoxyl group respectively, having up to 4 carbon atoms, under the proviso that R2 is selected from the group consisting of an optionally substituted aryl group, an optionally substituted heteroaryl group or an optionally substituted aroyl group;
• R3 is selected from the group consisting of H, NO2 or halogen;
• and
• R4 is selected from the group consisting of H, OCH3 or an optionally substituted alkyl group having up to 4 carbon atoms.

A method for derivatizing a compound having a primary amine, a secondary amine or a hydroxyl group said method comprising the step of reacting said compound with a compound having the general formula:

• 42
• wherein
• R1 is COOY, wherein Y is selected from the group consisting of an optionally substituted alkyl group of up to 10 carbon atoms, under the proviso that R2 is selected from the group consisting of H, NO2, CN, OCH3 or halogen or is an optionally substituted alkyl or alkoxyl group, respectively, having up to 4 carbon atoms;
• or
• R1 is selected from the group consisting of H, NO2, CN, OCH3 or halogen or an optionally substituted alkyl or alkoxyl group respectively, having up to 4 carbon atoms, under the proviso that R2 is selected from the group consisting of an optionally substituted aryl group, an optionally substituted heteroaryl group or an optionally substituted aroyl group;
• R3 is selected from the group consisting of H, NO2 or halogen;
• R4 is selected from the group consisting of H, OCH3 or an optionally substituted alkyl group having up to 4 carbon atoms;
• X is selected from oxygen or sulfur;
• and
• Z is selected from the group consisting of a leaving group.