Phosphate and thiophosphate protecting groups

• US 6,610,837 B1
• Filed: 03/16/2000
• Issued: 08/26/2003
• Est. Priority Date: 03/16/1999
• Status: Expired due to Fees

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Manoharan, Muthiah, Guzaev, Andrei P.
• Primary Examiner(s): Wilson, James O.
• Assistant Examiner(s): Crane, Lawrence E
• Application Number:
  US09/526,386
• Time in Patent Office: 1,258 Days
• Field of Search: 536/23.1, 536/24.5, 536/25.34, 435/91.1, 558/70
• US Class Current: 536/23.1
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Novel P(III) bisamidite reagents as phosphorus protecting groups, nucleoside phosphoramidite intermediates, and synthetic processes for making the same are disclosed. Furthermore, oligomeric compounds are prepared through the protection of one or more internucleosidic phosphorus functionalities, preferably followed by oxidation and cleavage of the protecting groups to provide oligonucleotides.

Claims

1. A method for the preparation of an oligonucleotide compound containing one or more moieties having Formula X:

wherein;

each W and X is, independently, O or S;

Y is O or NR²;

Z is a single bond, O or NR^2a;

each R¹ is, independently C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl, CN, NO₂, Cl, Br, F, I, CF₃, OR⁴, NR^5aR^5b or phenyl;

or two R¹ groups, when on adjacent carbons of the phenyl ring, together form a naphthyl ring that includes said phenyl ring;

each R² and R^2a is, independently, H, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

each R³ is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

or R² and one R³, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered, heterocarbocyclic ring containing one nitrogen atom in the ring;

each R^3a is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

or R² and R^3a, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered heterocarbocyclic ring containing one nitrogen atom in the ring;

R⁴ is C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl;

each R^5a and R^5b is, independently, C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl; and

each n and m is, independently, 0, 1, 2 or 3; and

comprising;

(a) providing a compound of Formula II;

wherein

R⁶ is H, a hydroxyl protecting group or a linker connected to a solid support;

R⁷ is H, hydroxyl, C_1-20 alkyl, C_3-20 alkenyl, C_2-20 alkynyl, halogen, SR^7a wherein R^7a is selected from hydrogen, a protecting group and substituted or unsubstituted C_1-20 alkyl, C_3-20 alkenyl, and C_2-20 alkynyl;

keto, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, O—

C_1-20 alkyl, NH—

C_1-20 alkyl, N-diC_1-20 alkyl, O-aryl, S-aryl, NH-aryl, O—

C_1-20 aralkyl, S—

C_1-20 aralkyl, NH—

C_1-20 aralkyl, amino, N-phthalimido, imidazolyl, azido, hydrazino, hydroxylamino, isocyanato, aryl, heterocyclyl, carbocyclyl, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether, or one of formula XII or XIII;

wherein;

E is C₁ to C₁₀ alkyl, N(R¹⁵)(R¹⁷) and N═

C(R¹⁵)R¹⁷);

each R¹⁵ and R¹⁷ is, independently, H, C₁ to C₁₀ alkyl, dialkylaminoalkyl, a nitrogen protecting group, a conjugate group, or a linker to a solid support;

or R¹⁵ and R¹⁷, together, are form a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O;

each q¹ and q² is, independently, an integer from 1 to 10;

R¹⁶ is OR¹⁸, SR¹⁸, or N(R¹⁸)₂;

R¹⁸ is H, C₁ to C₈ alkyl, C₁ to C₈ haloalkyl, C(═

NH)N(H)R¹⁹, C(═

O)N(H)R¹⁹ or OC(═

O)N(H)R¹⁹;

R¹⁹ is H or C₁ to C₈ alkyl;

L₁, L₂ and L₃ form a ring system having from about 4 to about 7 carbon atoms or having from about 3 to about 6 carbon atoms and 1 or 2 heteroatoms wherein each of said heteroatoms is, independently, oxygen, nitrogen or sulfur and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic;

L₄ is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(R¹⁵)(R¹⁷)OR¹⁵, halo, SR¹⁵ or CN;

q⁴ is 0, 1 or 2;

R⁸ is NR^8aR^8b, or a 5- or 6-membered heterocyclic system containing 1 to 4 heteroatoms

wherein each of said heteroatoms is, independently, N, O or S;

each R^8a and R^8b is, independently, C₁ to C₁₀ alkyl or C₃ to C₇ cycloalkyl;

X¹ is O or S;

each B is, independently, a protected or unprotected naturally occurring nucleobase, or a protected or unprotected non-naturally occurring nucleobase;

q is an integer from 1 to 10;

p is 0 or an integer from 1 to about 50;

each Q is, independently, OH, SH or

(b) reacting the compound of Formula II with a compound of Formula III;

wherein;

R¹⁰ is a hydroxyl protecting group or a linker connected to a solid support;

with the provisos that R⁶ and R¹⁰ are not both simultaneously a linker connected to a solid support;

p′

is 0 or an integer from 1 to about 50; and

either;

1) at least one n is other than zero and at least one R^3a is other than hydrogen wherein one of the central carbons of the group (R^3a—

C)_n—

C(R³)₂ is said chiral atom;

or

2) at least one moiety of Formula X contains a chiral atom;

to form said oligonucleotide compound.

2. The method of claim 1 further comprising treating said oligomeric compound with a reagent under conditions of time temperature and pressure effective to oxidize or sulfurize said oligomeric compound.

3. The method of claim 2 wherein R¹⁰ is a linker connected to a solid support further comprising treating said oligomeric compound with a reagent under conditions of time temperature and pressure effective to deprotect said oligomeric compound.

4. The method of claim 3 wherein the deprotection is effective to remove said oligomeric compound from the solid support.

5. The method of claim 3 further comprising treating said oligomeric compound with a reagent under conditions of time temperature and pressure effective to remove said oligomeric compound from the solid support.

6. The method of claim 1 wherein each R¹ is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂;

R² is H or C₁ to C₃ alkyl;

R³ is H;

Y is N—

R²;

Z is a single bond;

n is 1; and

m is 0 or 1.

7. The method of claim 6 wherein m is 1 and R¹ is OCH₃ in the para position of the phenyl ring.

8. The method of claim 7 wherein each R^8a and R^8b is isopropyl.

9. The method of claim 7 wherein X¹ is O.

10. The method of claim 7 wherein X₁ is S.

11. The method of claim 9 wherein W is S.

12. The method of claim 9 wherein W is O.

13. The method of claim 10 wherein W is S.

14. The method of claim 1 wherein the compound of Formula II is obtained by reaction of a compound of Formula V:

with a compound of Formula VI;

in the presence of an acid.

15. The method of claim 1 wherein the compound of Formula II is obtained by reaction of a compound of Formula V:

with a chiorophosphine compound of formula ClP(NR^8aR^8b)₂, followed by reaction with a compound of Formula I-i;

in the presence of an acid.

16. The method of claim 15 wherein W is O;

Z is a single bond or NR^2a;

each R¹ is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂;

each R³ is, independently, H or CH₃;

R⁴ is H;

n is 1 or 2; and

m is 0 or 1.

17. The method of claim 1 wherein said compound of formula II comprises at least one chirally pure phosphorus atom.

18. A method for the preparation of a compound of Formula II:

wherein;

each W and X is, independently, O or S;

Y is O or NR²;

Z is a single bond, O or NR^2a;

each R¹ is, independently C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl, CN, NO₂, Cl, Br, F, I, CF₃, OR⁴, NR^5aR^5b or phenyl;

or two R¹ groups, when on adjacent carbons of the phenyl ring, together form a naphthyl ring that includes said phenyl ring;

each R² and R^2a is, independently, H, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

each R³ is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

or R² and one R³, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered heterocarbocyclic ring containing one nitrogen atom in the ring;

each R^3a is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

or R² and R^3a, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered heterocarbocyclic ring containing one nitrogen atom in the ring;

R⁴ is C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl;

each R^5a and R^5b is, independently, C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl; and

each n and m is, independently, 0, 1, 2 or 3; and

R⁶ is H, a hydroxyl protecting group or a linker connected to a solid support;

R⁷ is H, hydroxyl, C_1-20 alkyl, C_3-20 alkenyl, C_2-20 alkynyl, halogen, SR^7a wherein R^7a is selected from hydrogen, a protecting group and substituted or unsubstituted C_1-20 alkyl, C_3-20 alkenyl, and C_2-20 alkynyl;

keto, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, O—

C_1-20 alkyl, NH—

C_1-20 alkyl, N-diC_1-20 alkyl, O-aryl, S-aryl, NH-aryl, O—

C_1-20 aralkyl, S—

C_1-20 aralkyl, NH—

C_1-20 aralkyl, amino, N-phthalimido, imidazolyl, azido, hydrazino, hydroxylamino, isocyanato, aryl, heterocyclyl, carbocyclyl, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether, or one of formula XII or XIII;

wherein;

E is C₁ to C₁₀ alkyl, N(R¹⁵)(R¹⁷) or N═

C(R¹⁵)(R¹⁷);

each R¹⁵ and R¹⁷ is, independently, H, C₁ to C₁₀ alkyl, dialkylaminoalkyl, a nitrogen protecting group, a conjugate group, or a linker to a solid support;

or R¹⁵ and R¹⁷, together, form a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O;

each q¹ and q² is, independently, an integer from 1 to 10;

q³ is 0 or 1;

R¹⁶ is OR¹⁸, SR¹⁸, or N(R¹⁸)₂;

R¹⁵ is H, C₁ to C₈ alkyl, C₁ to C₈ haloalkyl, C(═

NH)N(H)R¹⁹, C(═

O)N(H)R¹⁹ or OC(═

O)N(H)R¹⁹;

R¹⁹ is H or C₁ to C₈ alkyl;

L₁, L₂ and L₃ form a ring system having from about 4 to about 7 carbon atoms or having from about 3 to about 6 carbon atoms and 2 or 2 heteroatoms wherein each of said heteroatoms is, independently, oxygen, nitrogen or sulfur and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic;

L₄ is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(R¹⁵)(R¹⁷)OR¹⁵, halo, SR¹⁵ or CN;

q⁴ is 0, 1 or 2;

R⁸ is NR^8aR^8b, or a 5- or 6-membered heterocyclic system containing 1 to 4 heteroatoms wherein each of said heteroatoms is, independently, N, O or S;

each R^8a and R^8b is, independently, C₁ to C₁₀ alkyl or C₃ to C₇ cycloalkyl;

X¹ is O or S;

each B is, independently, a protected or unprotected naturally occurring nucleobase, or a protected or unprotected non-naturally occurring nucleobase;

q is an integer from 1 to 10;

p is 0 or an integer from 1 to about 50;

each Q is, independently, OH, SH or

 

comprising;

reacting a nucleoside of Formula V;

 

with a chlorophosphine compound of formula CIP-(R⁸)₂, in the presence of a base; and

protecting the product by reaction with a compound of Formula I-i;

in the presence of an acid to form the compound of Formula II;

with the proviso that structure I-i has a chiral atom wherein one of the central carbons of the group (R^3a—

C)_n—

C(R³)₂ is said chiral atom.

19. The method of claim 18, wherein each R¹ is, independently, in the meta or para position and is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂;

R² is CH₃, CH₂CH₃ or CH(CH₃)₂;

each R³ is, independently, H or CH₃;

n is 1 or 2; and

m is 0 or 1.

20. The method of claim 19 wherein W is O.

21. The method of claim 20 wherein R⁸ is NR^8aR^8b, and each R^8a and R^8b is isopropyl.

22. The method of claim 20 wherein p is 0.

23. A product of the method of claim 18.

24. The method of claim 18 wherein said compound of formula II comprises at least one chirally pure phosphorus atom.

25. A compound of Formula XI:

wherein;

each W and X is, independently, O or S;

Y is O or NR²;

Z is a single bond, O or NR^2a;

each R¹ is, independently C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl, CN, NO₂, Cl, Br, F, I, CF₃, OR⁴, NR^5aR^5b or phenyl;

or two R¹ groups, when on adjacent carbons of the phenyl ring, together form a naphthyl ring that includes said phenyl ring;

each R² and R^2a is, independently, H, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

each R³ is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C_{3 to C6} cycloalkyl or phenyl;

or R² and one R³, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered heterocarbocyclic ring containing one nitrogen atom in the ring;

each R^3a is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

or R² and R^3a, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered heterocarbocyclic ring containing one nitrogen atom in the ring;

R⁴ is C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl;

each R^5a and R^5b is, independently, C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl; and

R⁶ is H, a hydroxyl protecting group, or a linker connected to a solid support;

each R⁷ is, independently, H, hydroxyl, C₁ to C₂₀ alkyl, C₃ to C₂₀ alkenyl, C₂ to C₂₀ alkynyl, halogen, SR^7a, wherein R^7a is selected from hydrogen, a protecting group and substituted or unsubstituted C_1-20 alkyl, C_3-20 alkenyl, and C_2-20 alkynyl;

keto, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, O-alkyl, NH—

C_1-20 alkyl, N—

C_1-20 dialkyl, O-aryl, S-aryl, NH-aryl, O—

C_1-20 aralkyl, S—

C_1-20 aralkyl, NH—

C_1-20 aralkyl, amino, N-phthalimido, imidazolyl, azido, hydrazino, hydroxylamino, isocyanato, aryl, heterocyclyl, carbocyclyl, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether, or one of formula XII or XIII;

wherein;

E is C₁ to C₁₀ alkyl, N(R¹⁵)(R¹⁷) or N═

C(R¹⁵)(R¹⁷);

each R¹⁵ and R¹⁷ is, independently, H, C₁ to C₁₀ alkyl, dialkylaminoalkyl, a nitrogen protecting group, a conjugate group;

or a linker to a solid support;

or R¹⁵ and R¹⁷, together, form a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O;

each q¹ and q² is, independently, an integer from 1 to 10;

q³ is 0 or 1;

R¹⁶ is OR¹⁸, SR¹⁸, or N(R¹⁸)₂;

each R¹⁸ is, independently, H, C₁ to C₈ alkyl, C₁ to C₈ haloalkyl, C(═

NH)N(H)R¹⁹, C(═

O)N(H)R¹⁹ or OC(═

O)N(H)R¹⁹;

R¹⁹ is H or C₁ to C₈ alkyl;

L₁, L₂ and L₃ form a ring system having from about 4 to about 7 carbon atoms or having from about 3 to about 6 carbon atoms and 1 or 2 heteroatoms wherein said heteroatoms are selected from oxygen, nitrogen and sulfur and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic;

L₄ is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(R¹⁵)(R¹⁷)OR¹⁵, halo, SR¹⁵ or CN; and

q⁴ is 0, 1 or 2;

R⁸ is NR^8aR^8b, or a 5- or 6-membered heterocyclic system containing 1 to 4 heteroatoms wherein each of said heteroatoms is, independently, N, O or S;

each R^8a and R^8b is, independently, C₁ to C₁₀ alkyl or C₃ to C₇ cycloalkyl;

each n and m is, independently, 0, 1, 2 or 3;

each X¹ is, independently, O or S;

each B is, independently, a protected or unprotected naturally occurring nucleobase, or a protected or unprotected non-naturally occurring nucleobase;

each Q is, independently, SH, OH or

R¹⁰ is H, a hydroxyl protecting group, or a linker connected to a solid support; and

each p and p′

is, independently, 0 or an integer from 1 to about 50;

with the provisos that the sum of p and p′

does not exceed 50, R⁶ and R¹⁰ are not both simultaneously a linker connected to a solid support, and either;

1) at least one n is other than zero and at least one R^3a, is other than hydrogen;

or

2) the group;

26. The compound of claim 25 wherein R¹⁰ is a linker connected to a solid support.

27. The compound of claim 25 wherein R¹⁰ is H.

28. The compound of claim 25 wherein each R³ is, independently, H or CH₃;

n is 1 or 2;

m is 0 or 1;

each R¹ is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂, or N(CH(CH₃)₂)₂; and

W is O.

29. The compound of claim 25 wherein each R³ is, independently, H or CH₃;

n is 1 or 2;

m is 0 or 1;

R¹ is in the meta or para position and is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂; and

W is O.

30. The compound of claim 31 wherein R³ is H, Y is NR², R² is CH(CH₃)₂, X is O, Z is a single bond, m is 1, and R¹ is OCH₃ in the para position.

31. The compound of claim 25 wherein each O has the formula:

and p is an integer from 2 to 50.

32. The compound of claim 25 comprising at least one chirally pure phosphorus atom.

33. A compound of Formula VII:

wherein;

each W and X is, independently, O or S;

Y is O or NR²;

Z is a single bond, O or NR^2a;

each R¹ is, independently C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl, CN, NO₂, Cl, Br, F, I, CF₃, OR⁴, NR^5aR^5b or phenyl;

or two R¹ groups, when on adjacent carbons of the phenyl ring, together form a naphthyl ring that includes said phenyl ring;

each R² and R^2a is, independently, H, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

each R³ is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

or R² and one R³, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered cyclic structure containing 0, 1, or 2 heteroatoms;

each R^3a is, independently, hydrogen, C₁ to C₆ alkyl, C₂ to C₆ alkenyl, C₂ to C₆ alkynyl, C₃ to C₆ cycloalkyl or phenyl;

or R² and R^3a, together with the atoms to which they are attached, form a saturated or partially saturated 4 to 7 membered cyclic structure containing 0, 1, or 2 heteroatoms;

R⁴ is C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl;

each R^5a and R^5b is, independently, C₁ to C₆ alkyl, C₃ to C₆ cycloalkyl or phenyl;

each n and m is, independently, 0, 1, 2 or 3;

A is (R⁸)₂P, R⁸R¹¹P, R⁸R¹²PR¹¹R¹²P or X³X⁴P;

X³ is Br, Cl, or I;

X⁴ is NR^aR^b, or a 5- or 6-membered heterocyclic system containing 1 to 4 heteroatoms selected from N, O and S;

each R⁸ is, independently, NR^8aR^8b, or a 5- or 6-membered heterocyclic system containing 1 to 4 heteroatoms wherein each of said heteroatoms is, independently, N, O or S;

each R^8a and R^8b is, independently, C₁ to C₁₀ alkyl or C₃ to C₇ cycloalkyl;

R¹¹ is a substituent of Formula VIII;

wherein

each R⁷ is, independently, H, hydroxyl, C₁ to C₂₀ alkyl, C₃ to C₂₀ alkenyl, C₂ to C₂₀ alkynyl, halogen, SR^7a wherein R^7a is selected from hydrogen, a protecting group and substituted or unsubstituted C_1-20 alkyl, C_3-20 alkenyl, and C_2-20 alkynyl;

keto, carboxyl, nitro, nitroso, cyano, trifluoromethyl, trifluoromethoxy, O—

C_1-20 alkyl, NH—

C_1-20 alkyl, N-diC_1-20 alkyl, O-aryl, S-aryl, NH-aryl, O—

C_1-20 aralkyl, S—

C_1-20 aralkyl, NH—

C_1-20 aralkyl, amino, N-phthalimido, imidazolyl, azido, hydrazino, hydroxylamino, isocyanato, aryl, heterocyclyl, carbocyclyl, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether, or one of formula XII or XIII;

wherein;

E is C₁ to C₁₀ alkyl, N(R¹⁵)(R¹⁷) or N═

C(R¹⁵)(R¹⁷);

each R¹⁵ and R¹⁷ is, independently, H, C₁ to C₁₀ alkyl, dialkylaminoalkyl, a nitrogen protecting group, a conjugate group, or a linker to a solid support;

or R¹⁵ and R¹⁷, together, form a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O;

each q¹ and q² is, independently, an integer from 1 to 10;

q³ is 0 or 1;

R¹⁶ is OR¹⁸, SR¹⁸ or N(R¹⁸)₂;

each R¹⁸ is, independently, H, C₁ to C₈ alkyl, C₁ to C₈ haloalkyl, C(═

NH)N(H)R¹⁹, C(═

O)N(H)R¹⁹ or OC(═

O)N(H)R¹⁹;

R¹⁹ is H or C₁ to C₈ alkyl;

L₁, L₂ and L₃ form a ring system having from about 4 to about 7 carbon atoms or having from about 3 to about 6 carbon atoms and 1 or 2-heteroatoms wherein said heteroatoms are selected from oxygen, nitrogen and sulfur and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic;

L₄ is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(R¹⁵)(R¹⁷), OR¹⁵, halo, SR¹⁵ or CN;

q⁴ is, 0, 1 or 2;

each X¹ is, independently, O or S;

each B is, independently, a protected or unprotected naturally occurring nucleobase, or a protected or unprotected non-naturally occurring nucleobase;

R¹⁰ is H, a hydroxyl protecting group, or a linker connected to a solid support;

p′

is 0 or an integer from 1 to about 50;

each Q is, independently, SH, OH or

R¹² is a compound of Formula IX;

wherein;

R⁶ is H, a hydroxyl protecting group, or a linker connected to a solid support; and

p is 0 or an integer from 1 to about 50;

with the provisos that the sum of p and p′

does not exceed 50, when A is PR¹¹R¹², R⁶ and R¹⁰ are not both simultaneously a linker connected to a solid support, and either;

1) at least one n is other than zero and at least one R^3a is other than hydrogen;

or

2) the group;

contains a chiral atom wherein one of the central carbons of the group (R^3a—

C)_n—

C(R³)₂ is said chiral atom.

34. The compound of claim 33 wherein A is X³X⁴P.

35. The compound of claim 34 wherein X is Cl;

and each R^a and R^b is isopropyl.

36. The compound of claim 33 wherein A is PR¹¹R⁸.

37. The compound of claim 33 wherein R³ is hydrogen, Y is NR², and Z is a single bond.

38. The compound of claim 37 wherein m is 1, and each R¹ is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂.

39. The compound of claim 37 wherein W is O.

40. The compound of claim 33 wherein each R³ is hydrogen and Z is NR^2a.

41. The compound of claim 40 wherein m is 1 and each R¹ is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂.

42. The compound of claim 40 wherein W is O.

43. The compound of claim 40 wherein W is S.

44. The compound of claim 33 wherein A is P(R⁸)₂.

45. The compound of claim 44 wherein R⁸ is N(CH(CH₃)₂)₂.

46. The compound of claim 33 wherein A is PR¹²R⁸.

47. The compound of claim 46 wherein p is 0.

48. The compound of claim 47 wherein R⁶ is a hydroxyl protecting group.

49. The compound of claim 48 wherein Y is NR², R² is H, CH₃, CH₂CH₃ or CH(CH₃)₂;

n is 1 or 2;

m is 0 or 1, and each R¹ is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂.

50. The compound of claim 33 wherein the compound of Formula VIIb is:

51. The compound of claim 50 wherein Y is NR²;

R² is H, CH₃, CH₂CH₃ or CH(CH₃)₂;

n is 1 or 2; and

m is 0 or 1.

52. The compound of claim 50 wherein R¹⁰ is a linker connected to a solid support.

53. The compound of claim 50 wherein R¹⁰ is H.

54. The compound of claim 50 wherein each p and p′

is 0.

55. The compound of claim 50 wherein Y is NR²;

R² is H, CH₃, CH₂CH₃ or CH(CH₃)₂;

each R³ is, independently, H or CH₃;

n is 1 or 2;

m is 0 or 1;

each R¹ is, independently, CH₃, CH₂CH₃, CH(CH₃)₂, CN, NO₂, OCH₃, OCH₂CH₃, OCH(CH₃)₂, N(CH₃)₂, N(CH₂CH₃)₂ or N(CH(CH₃)₂)₂; and

W is O.

56. The compound of claim 33 comprising at least one chirally pure phosphorus atom.