Thermolabile phosphorus protecting groups, associated intermediates and methods of use

A compound selected from the group consisting of compounds of the formulae:

• 46
• wherein:
• R is a thermolabile protecting group of the formula:
• 47
• R1 is H, R1a, OR1a, SR1a or NR1aR1a′, wherein R1a and R1a′ are the same or different and each is H, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, or an aralkyl;
• or, when R1 is NR1aR1a′, R1a and R1a′, together with the nitrogen atom to which they are bonded, comprise a heterocycle containing from 3 to about 7 atoms in the ring skeleton thereof,
• X1 is O, S or Se;
• X is O or S;
• W is a dialkylamino;
• Z is O, S, NR2a, CR2aR2a′ or CR2aR2a′CR2bR2b′, wherein R2a, R2a′, R2b and R2b′ are the same or different and each is H, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, or an aralkyl;
• or
• R1a or R1a′, in combination with R2a, R2a′, R2b or R2b′, together with C═X of the protecting group to which they are bonded, comprise a ring containing from 3 to about 7 atoms in the skeleton thereof;
• provided that R1 is not R1a when Z is S, Z is not CR2aR2a′ or CR2aR2a′CR2bR2b′ when R1 is SR1a, and Z is not O or S when R1 is H;
• R2, R2′, R3 and R3′ are the same or different and each is H, an alkyl an alkenyl, an alkynyl, a cycloalkyl, an aryl, or an aralkyl, or
• R2 or R2′, in combination with R3 or R3′, together with the carbon atoms to which they are bonded, comprise a cyclic substituent of the formula:
• 48
• wherein p is an integer from 0-6 and a-d are the same or different and each is selected from the group consisting of H, an alkyl, a nitro, a dialkylamino, an alkoxy, an alkylthio, a cyano and a halogen, provided that the aromatic ring, which bears the substituents a-d, is one carbon removed from the phosphate oxygen of formula (IIIa),
• wherein R1, R2a, R2a′, R2b, R2b′, R2, R2′, R3 or R3′ is unsubstituted or substituted with one or more substituents, which are the same or different, selected from the group consisting of OR8, CN, NO2, N3, and a halogen, wherein R8 is H or an alkyl;
• R4 and R15 are the same or different and each is H, a hydroxyl protecting group, or a solid support;
• Q1 is a nucleoside, an oligonucleotide or an oligomer comprising an oligonucleotide;
• n is an integer from 1 to about 300;
• and
• Q is a nucleoside, an oligonucleotide or an oligomer comprising an oligonucleotide and, when n is greater than 1, each Q is independently selected;
• provided that when R1 is not H, Z is not NR2a, wherein R2a is H, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, or an aralkyl.

A method of producing an oligonucleotide, which method comprises

• (a) reacting a nucleophile of the formula:
• R4—O—Q1—OH
• with an electrophile of the formula:
• 51
• wherein W is a dialkylamino group that is displaced by the nucleophile, under conditions to displace W and produce an adduct comprising a tricoordinated phosphorus atom;
• (b) reacting the product obtained in step (a) with a reagent selected from the group consisting of oxidizing agents, sulfurizing agents, and selenizing agents to produce a protected oligonucleotide of the formula:
• 52
• wherein n=1;
• (c) cleaving R15 from the protected oligonucleotide from step (b) to produce a nucleophile;
• (d) optionally repeating steps (a)-(c) until an oligomer of a specified length is obtained;
• and
• (e) heating the product from step (c) or (d) in a fluid medium, at a substantially neutral pH, at a temperature up to about 100° C. to produce a deprotected oligonucleotide of the formula:
• 53
• wherein R is a thermolabile protecting group of the formula:
• 54
• R1 is H, R1a, OR1a, SR1a or NR1aR1a′, wherein R1a and R1a′ are the same or different and each is H, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, or an aralkyl;
• or, when R1 is NR1aR1a′, R1a and R1a′, together with the nitrogen atom to which they are bonded, comprise a heterocycle containing from 3 to about 7 atoms in the ring skeleton thereof,
• X is O, S or Se;
• X is O or S;
• Z is O, S, NR2a, CR2aR2a′ or CR2aR2a′CR2bR2b′, wherein R2a, R2a′, R2b and R2b′ are the same or different and each is H, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, or an aralkyl;
• or
• R1a or R1a′, in combination with any of R2a, R2a′, R2b or R2b′, together with C═X of the protecting group to which they are bonded, comprise a ring containing from 3 to about 7 atoms in the skeleton thereof;
• provided that R1 is not R1a when Z is S, Z is not CR2aR2a′ or CR2aR2a′CR2bR2b′ when R1 is SR1a, and Z is not O or S when R1 is H;
• R2, R2′, R3 and R3′ are the same or different and each is H, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, or an aralkyl, or
• R2 or R2′, in combination R3 or R3′, together with the carbon atoms to which they are bonded, comprise a cyclic substituent of the formula:
• 55
• wherein p is an integer from 0-6 and a-d are the same or different and each is selected from the group consisting of H, an alkyl, a nitro, an amino, a hydroxyl, a thio, a cyano and a halogen, provided that the aromatic ring, which bears the substituents a-d, is one carbon removed from the phosphate oxygen of formula (IIIa),
• wherein R1, R2a, R2a′, R2b, R2b′, R2, R2′, R3 or R3′ is unsubstituted or substituted with one or more substituents, which are the same or different, selected from the group consisting of OR8, CN, NO2, N3, and a halogen, wherein R8 is H or an alkyl;
• R4 and R15 are the same or different and each is H, a hydroxyl protecting group, or a solid support;
• Q1 is a nucleoside, an oligonucleotide or an oligomer comprising an oligonucleotide;
• n is an integer from 1 to about 300;
• and
• Q is a nucleoside, an oligonucleotide or an oligomer comprising an oligonucleotide and, when n is greater than 1, each Q is independently selected.