Nucleosidic and non-nucleosidic folate conjugates

• US 6,861,514 B2
• Filed: 10/09/2001
• Issued: 03/01/2005
• Est. Priority Date: 10/24/1991
• Status: Expired due to Fees

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Guzzaev, Andrei P., Bhat, Balkrishen, Manoharan, Muthiah, Cook, Phillip Dan
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/973,981
• Publication Number:
  US 20020049163A1
• Time in Patent Office: 1,239 Days
• Field of Search: 536/23.1, 536/24.3, 536/25.3, 536/25.31, 536/25.32, 536/27.1, 544/224, 514/49, 514/279
• US Class Current: 536/23.1
• CPC Class Codes: C07D 475/04 with a nitrogen atom directly attached in position 2
• CPC Class Codes: C07H 15/26 Acyclic or carbocyclic radicals, substituted by hetero rings

Abstract

Oligonucleotide-folate conjugates are described wherein folates are conjugated to one or more sites on an oligonucleotide including the 2′-, 3′-, 5′-, nucleobase and internucleotide linkage sites. The folate can be attached via the α- or γ-carboxylate, optionally through a linking group. Methods for the regiospecific synthesis of the conjugates are disclosed. Also disclosed are nucleosidic and non-nucleosidic linkers conjugated to folic acid and related folates.

Claims

1. A synthetic method comprising the steps of:

(a) providing compound of formula IA, IB, IC or ID;

 

wherein;

W_1a is W_1b—

H, OH, NH₂ or SH, where W_1b is a linking group;

R₁ is H or a hydroxyl protecting group;

B is a nucleobase;

each R₂₁ is H, OH, F, or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH, or N—

R₂₂—

(R₂₃)_v

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

v is from 0 to about 10;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

y2 is 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

q is from zero to about 50, provided that when said compound has formula ID, q is at least 1;

M is an optionally protected internucleoside linkage;

(b) reacting said compound of formula I with a compound of formula II;

 

wherein;

R₃₀ is an amino protecting group;

X₃ is a group of formula XII;

 

wherein m is 1 or 2;

R₄ is a hydroxyl group, or a protected hydroxyl group;

 

to form a compound of formula IVA, IVB, IVC, or IVD;

 

wherein;

W₄ has the formula;

where W₁ is a linking group, O, NH, or S; and

 

treating said compound of formula IVA, IVB, IVC or IVD with a deprotecting reagent to form a compound of formula VA, VB, VC or VD;

 

wherein W₅ has the formula;

(c) condensing said compound of Formula V with a compound of Formula VI;

 

wherein;

R₅ is H or an amino protecting group;

R₆ is H or an amino protecting group;

 

to form a compound of Formula VIIA, VIIB, VIIC, or VIID;

 

wherein W₇ has the formula;

17. The method of claim 1 wherein W₁ has the formula —

O—

(CH₂)_n—

NH—

, wherein n is from 1 to about 10.

18. The method of claim 17 wherein n is 6.

19. The method of claim 1 wherein R₁ is dimethoxytrityl, A has the formula —

O—

(CH₂)_n—

NH—

where n is 6, m is 2, R₄ is t-butoxy, R₅ is trifluoroacetoyl, R₆ is —

C(═

O)—

CH(CH₃)₂, and R₃₀ is FMOX.

2. A synthetic method comprising the steps of:

(a) providing a compound of formula IA, IB, IC or ID;

 

wherein;

W_1a is W_1b—

H, OH, NH₂ or SH, where W_1b is a linking group;

R₁ is H or a hydroxyl protecting group;

B is a nucleobase;

each R₂₁ is H, OH, F, or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH, or N—

R₂₂—

(R₂₃)_v

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

v is from 0 to about 10;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

y2 is 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

q is from zero to about 50, provided that when said compound has formula ID, q is at least 1;

M is an optionally protected internucleoside linkage;

(b) reacting said compound of formula I with a compound of formula II;

 

wherein;

R₃₀ is an amino protecting group;

X₃ is a group of formula XII;

 

wherein m is 1 or 2;

R₄ is a hydroxyl group, or a protected hydroxyl group;

 

to form a compound of formula IVA, IVB, IVC, or IVD;

 

wherein;

W₄ has the formula;

where W₁ is a linking group, O, NH, or S; and

 

treating said compound of formula IVA, IVB, IVC or IVD with a deprotecting reagent to form a compound of formula VA, VB, VC or VD;

 

wherein W₅ has the formula;

(c) condensing said compound of Formula V with a compound of Formula VI;

 

wherein;

R₅ is H or an amino protecting group;

R₆ is H or an amino protecting group;

 

to form a compound of Formula VIIA, VIIB, VIIC, or VIID;

 

wherein W₇ has the formula;

(d) contacting said compound of Formula VIIA or VIID with a phosphitylating regent to form a compound of Formula VIIIA or VIIID;

 

wherein W₇ has the Formula;

20. The method of claim 2 wherein R₁ is dimethoxytrityl, W₁ has the formula —

O—

(CH₂)_n—

NH—

where n is 6, m is 2, R₄ is t-butoxy, R₅ is trifluoroacetoyl, R₆ is —

C(═

O)—

CH(CH₃)₂, and R₃₀ is FMOX.

3. A synthetic method comprising the steps of:

(a) providing a compound of formula IA, IB, IC or ID;

 

wherein;

W_1a is W_1b—

H, OH, NH₂ or SH, where W_1b is a linking group;

R₁ is H or a hydroxyl protecting group;

B is a nucleobase;

each R₂₁ is H, OH, F, or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH, or N—

R₂₂—

(R₂₃)_v

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

v is from 0 to about 10;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

y2 is 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

q is from zero to about 50, provided that when said compound has formula ID, q is at least 1;

M is an optionally protected internucleoside linkage;

(b) reacting said compound of formula I with a compound of formula II;

 

wherein;

R₃₀ is an amino protecting group;

X₃ is a group of formula XI;

 

wherein;

p is 1 or 2;

R₄ is a hydroxyl group, or a protected hydroxyl group;

or X₃ is a group of formula XII;

 

wherein m is 1 or 2;

Z₁ is the sidechain of a naturally occurring amino acid, or a protected sidechain of a naturally occurring amino acid;

R₄ is a hydroxyl group, or a protected hydroxyl group;

p is 1 or 2;

to form a compound of formula IVA, IVB, IVC, or IVD;

 

wherein;

W₄ has the formula;

where W₁ is a linking group, O, NH, or S; and

 

treating said compound of formula IVA, IVB, IVC or IVD with a deprotecting reagent to form a compound of formula VA, VB, VC or VD;

 

wherein W₅ has the formula;

(c) condensing said compound of Formula V with a compound of Formula VI;

 

wherein;

R₅ is H or an amino protecting group;

R₆ is H or an amino protecting group;

 

to form a compound of Formula VIIA, VIIB, VIIC, or VIID;

 

wherein W₇ has the formula;

 

wherein said compound of formula VI is prepared by the steps of reacting a compound of formula IX;

 

with a compound of formula X;

 

and treating the product of said reaction with a protecting group reagent to form said compound of formula VI.

21. The method of claim 3 wherein said compound IX is prepared by reacting folic acid:

with a reagent effective to form pterin aldehyde;

and

protecting the amino group of said pterin aldehyde.

4. A compound having formula XVIA, XVIB, XVIC or XVID:

wherein;

W₁₄ has the formula

wherein;

X₄ is —

CH(X_4′

) or a group of formula;

X_4′

is the side chain of a naturally-occurring or non-naturally-occurring amino acid, or a protected side chain of a naturally-occurring or non-naturally-occurring amino acid;

t is 1 or 2;

X₅ is —

N(X_6′

)C(O)—

, —

C(O)NH—

, —

NHC(O)—

, —

OC(O)NH—

,—

C(S)NH—

, —

SC(S)NH—

, —

SC(O)NH—

, —

OC(S)NH—

, —

C(O)O—

, —

C(O)(CH₂)_n—

or a bond;

n is an integer from 1 to 50;

each X₆ and X_6′

is, independently, a bond, hydrogen or a hydrocarbyl group selected from C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl, C₆-C₁₄ aralkyl, C₃-C₁₄ cycloalkyl, C₅-C₁₄ fused cycloalkyl, C₄-C₁₄ heterocycle, C₄-C₁₄ heterocyclylalkyl, C₄-C₁₄ heteroaryl and C₄-C₁₄ heteroarylalkyl;

wherein said hydrocarbyl group is substituted with at least two hydroxyl groups, and is optionally substituted with oxo, acyl, alkoxy, alkoxycarbonyl, alkyl, alkenyl, alkynyl, amino, amido, azido, aryl, heteroaryl, carboxylic acid, cyano, guanidino, halo, haloalkyl, haloalkoxy, hydrazino, ODMT, alkylsulfonyl, nitro, sulfide, disulfide, sulfone, sulfonate, sulfonamide, thiol, and thioalkoxy;

provided that X₆ is not hydrogen and X_6′

is not a bond;

R₁ is hydrogen or a hydroxyl protecting group;

R₄ is a hydroxyl group or a protected hydroxyl group;

each R_5′

and R₄₀ is, independently, hydrogen, C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl or an amino-protecting group

R_5″

is hydrogen, C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl, C₆-C₁₄ aralkyl, C₃-C₁₄ cycloalkyl, formyl, aminoalkyl or hydroxymethyl;

R₆ is hydrogen or an amino protecting group;

R₂₀ is hydroxyl or a group of formula;

R₂ is —

N(R₇)₂, or a heterocycloalkyl or heterocycloalkenyl ring containing from 4 to 7 atoms, and having up to 3 heteroatoms selected from nitrogen, sulfur, and oxygen;

R₇ is straight or branched chain alkyl having from 1 to 10 carbons;

R₃ is a phosphorus protecting group;

R₂₁ is hydrogen, hydroxyl, fluoro or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH or N—

R₂₂—

(R₂₃)_v;

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₂ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

each y2 is, independently, 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

B is a nucleobase;

M is an optionally protected internucleoside linkage;

q is 0 to about 50; and

v is from zero to about 10;

provided that when said compound has formula XVID, q is at least 1.

6. The compound of claim 4 wherein said R₂₀ is a group of formula:

wherein R₂ is diisopropylamino and R₃ is β

-cyanoethyl.

13. The compound of claim 4 wherein said amino acid is amino caproic acid.

14. The compound of claim 4 wherein said X_4′

is the side chain of glutamic acid.

15. The compound of claim 4 wherein said X₆ has one of the formulas:

wherein;

SS is a solid support;

X₇ is O or CH₂;

Bx is a nucleobase, C₄-C₁₄ heterocyclyl or hydrogen;

z is an integer from 1 to 50; and

u is an integer from 2 to 5.

16. The compound of claim 4 wherein said R₁ is dimethoxytrityl.

33. The compound of claim 4 wherein said R₄ is a hydroxyl group protected with C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl or C₂-C₂₀ alkynyl.

5. A compound having the formula XIIIA, XIIIB, XIIIC or XIID:

wherein;

W₁₃ has the formula;

R₁ is H or a hydroxyl protecting group;

B is a nucleobase;

each R₂₁ is H, OH, F, or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH or N—

R₂₂—

(R₂₃)_v;

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

y2 is 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

v is from 0 to about 10;

q is 0 to about 50; and

v is from zero to about 10;

M is an optionally protected internucleoside linkage;

W₁ is a linking group, O, NH or S;

R₂₀ is hydroxyl or a group of Formula;

R₂ is —

N(R₇)₂, or a heterocycloalkyl or heterocycloalkenyl ring containing from 4 to 7 atoms, and having up to 3 heteroatoms selected from nitrogen, sulfur, and oxygen;

R₇ is straight or branched chain alkyl having from 1 to 10 carbons;

R₃ is a phosphorus protecting group;

R₅ is H or an amino protecting group;

R₆ is H or an amino protecting group;

X₃ is a group of formula XII;

wherein m is 1 or 2; and

R₄ is a hydroxyl group, or a protected hydroxyl group;

provided that when said compound has formula XIIIC, at least one R₂₁ is a group other than hydrogen, and when said compound has formula XIIIC or XIIID, q is at least 1.

7. The compound of claim 5 wherein m is 2.

10. The compound of claim 7 wherein W₁ is —

O—

(CH₂)₆—

NH—

.

22. The compound of claim 10 wherein R₄ is t-butoxy.

25. A composition comprising a compound of claim 7, said composition being substantially free of a compound of formula XVA, XVB, XVC or XVD:

wherein W₁₅ has the formula;

8. A compound having formula XVIA, XVIB, XVIC or XVID:

wherein;

W₁₄ has the formula;

wherein;

X₄ is —

CH(X_4′

) or a group of formula;

X_4′

is the side chain of a naturally-occurring or non-naturally-occurring amino acid, or a protected side chain of a naturally-occurring or non-naturally-occurring amino acid;

t is 1 or 2;

X₅ is —

N(X_6′

)C(O)—

, —

C(O)NH—

, —

NHC(O)—

, —

OC(O)NH—

, —

C(S)NH—

, —

SC(S)NH—

, —

SC(O)NH—

, —

OC(S)NH—

, —

C(O)O—

, —

C(O)(CH₂)_n—

or a bond;

n is an integer from 1 to 50;

each X₆, X_6′

and X₉ is, independently, a bond, hydrogen or a hydrocarbyl group selected from C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl, C₆-C₁₄ aralkyl, C₃-C₁₄ cycloalkyl, C₅-C₁₄ fused cycloalkyl, C₄-C₁₄ heterocycle, C₄-C₁₄ heterocyclylalkyl, C₄-C₁₄ heteroaryl and C₄-C₁₄ heteroarylalkyl;

wherein said hydrocarbyl group is substituted with at least two hydroxyl groups, and is optionally substituted with oxo, acyl, alkoxy, alkoxycarbonyl, alkyl, alkenyl, alkynyl, amino, amido, azido, aryl, heteroaryl, carboxylic acid, cyano, guanidino, halo, haloalkyl, haloalkoxy, hydrazino, ODMT, alkylsulfonyl, nitro, sulfide, disulfide, sulfone, sulfonate, sulfonamide, thiol, and thioalkoxy;

provided that each X₆ and X₉ is not hydrogen and X_6′

is not a bond;

R₁ is hydrogen or a hydroxyl protecting group;

R₄ is a hydroxyl group or a protected hydroxyl group;

each R_5′

and R₄₀ is, independently, hydrogen, C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl or an amino-protecting group

R_5″

is hydrogen, C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl, C₆-C₁₄ aralkyl, C₃-C₁₄ cycloalkyl, formyl, aminoalkyl or hydroxymethyl;

R₆ is hydrogen or an amino protecting group;

R₂₀ is hydroxyl or a group of formula;

R₂ is —

N(R₇)₂, or a heterocycloalkyl or heterocycloalkenyl ring containing from 4 to 7 atoms, and having up to 3 heteroatoms selected from nitrogen, sulfur, and oxygen;

R₇ is straight or branched chain alkyl having from 1 to 10 carbons;

R₃ is a phosphorus protecting group;

R₂₁ is hydrogen, hydroxyl, fluoro or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH or N—

R₂₂—

(R₂₃)_v;

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

each y2 is, independently, 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

B is a nucleobase;

M is a optionally protected internucleoside linkage;

q is 0 to about 50; and

v is from zero to about 10;

provided that when said compound has formula XVIC, at least one R₂₁ is a group other than hydrogen, and when said compound has formula XVIC or XVID, q is at least 1.

9. A compound having formula XVIA, XVIB, XVIC or XVID:

wherein;

W₁₄ has the formula;

wherein;

X₄ is —

CH(X_4′

) or a group of formula;

X_4′

is the side chain of a naturally-occurring or non-naturally-occurring amino acid, or a protected side chain of a naturally-occurring or non-naturally-occurring amino acid;

t is 1 or 2;

X₅ is —

N(X_6′

)C(O)—

, —

C(O)NH—

, —

NHC(O)—

, —

OC(O)NH—

, —

C(S)NH—

, —

SC(S)NH—

, —

SC(O)NH—

, —

OC(S)NH—

, —

C(O)O—

, —

C(O)(CH₂)_n—

or a bond;

n is an integer from 1 to 50;

each X₆ and X_6′

is, independently, a bond, hydrogen or a hydrocarbyl group selected from C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl, C₆-C₁₄ aralkyl, C₃-C₁₄ cycloalkyl, C₅-C₁₄ fused cycloalkyl, C₄-C₁₄ heterocycle, C₄-C₁₄ heterocyclylalkyl, C₄-C₁₄ heteroaryl and C₄-C₁₄ heteroarylalkyl;

wherein said hydrocarbyl group is substituted with at least two hydroxyl groups, and is optionally substituted with oxo, acyl, alkoxy, alkoxycarbonyl, alkyl, alkenyl, alkynyl, amino, amido, azido, aryl, heteroaryl, carboxylic acid, cyano, guanidino, halo, haloalkyl, haloalkoxy, hydrazino, ODMT, alkylsulfonyl, nitro, sulfide, disulfide, sulfone, sulfonate, sulfonamide, thiol, and thioalkoxy;

provided that X₆ is not hydrogen and X_6′

is not a bond;

R₁ is hydrogen or a hydroxyl protecting group;

R₄ is a hydroxyl group or a protected hydroxyl group;

each R_5′

and R₄₀ is, independently, hydrogen, C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl or an amino-protecting group

R_5″

is hydrogen, C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₂₀ alkynyl, C₆-C₁₄ aryl, C₆-C₁₄ aralkyl, C₃-C₁₄ cycloalkyl, formyl, aminoalkyl or hydroxymethyl;

R₆ is hydrogen or an amino protecting group;

R₂₀ is hydroxyl or a group of formula;

R₂ is —

N(R₇)₂, or a heterocycloalkyl or heterocycloalkenyl ring containing from 4 to 7 atoms, and having up to 3 heteroatoms selected from nitrogen, sulfur, and oxygen;

R₇ is straight or branched chain alkyl having from 1 to 10 carbons;

R₃ is a phosphorus protecting group;

R₂₁ is hydrogen, hydroxyl, fluoro or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH or N—

R₂₂—

(R₂₃)_v;

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

each y2 is, independently, 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

B is a nucleobase;

M is a optionally protected internucleoside linkage;

q is 0 to about 50; and

v is from zero to about 10;

provided that when said compound has formula XVID, q is at least 1.

11. A compound having the formula XVIA, XVIB, XVIC or XVID:

wherein;

W₁₆ has the formula;

R₁ is H or a hydroxyl protecting group;

B is a nucleobase;

each R₂₁ is H, OH, F, or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH or N—

R₂₂—

(R₂₃)_v;

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, C₂-C₂₀ alkynyl, C₁-C₂₀ akoxy, C₂-C₂₀ alkenyloxy, or C₂-C₂₀ alkynyloxy;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

y2 is 0 to 10;

y3 is 1 to 10;

E is N(₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄₁ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

v is from 0 to about 10;

q is 0 to about 50;

M is an optionally protected internucleoside linkage;

W₁ is a linking group;

R₂₀ is hydroxyl or a group of Formula;

R₂ is —

N(R₇)₂, or a heterocycloalkyl or heterocycloalkenyl ring containing from 4 to 7 atoms, and having up to 3 heteroatoms selected from nitrogen, sulfur, and oxygen;

R₇ is straight or branched chain alkyl having from 1 to 1 carbons;

R₃ is a phosphorus protecting group;

X₃ has the formula XII;

wherein m is 1 or 2;

R₄ is a hydroxyl group, or a protected hydroxyl group; and

provided that when said compound has formula XVID, q is at least 1.

27. The compound of claim 11 wherein m is 2.

28. The compound of claim 27 wherein W₁ is —

O—

(CH₂)_n—

NH—

wherein n is from 1 to about 10.

29. The compound of claim 28 wherein n is 6.

12. A compound having the formula XVIIA, XVIIB, XVIIC or XVIID:

wherein;

W₁₇ has the formula;

R₁ is H or a hydroxyl protecting group;

B is a nucleobase;

each R₂₁ is H, OH, F, or a group of formula Z—

R₂₂—

(R₂₃)_v;

Z is O, S, NH or N—

R₂₂—

(R₂₃)_v;

R₂₂ is C₁-C₂₀ alkyl, C₂-C₂₀ alkenyl, or C₂-C₂₀ alkynyl;

R₂₃ is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, polyether;

or R₂₁ has one of the formulas;

wherein;

y1 is 0 or 1;

y2 is 0 to 10;

y3 is 1 to 10;

E is N(R₄₁)(R₄₂) or N═

C(R₄₁)(R₄₂);

each R₄ and each R₄₂ is independently H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₄₁ and R₄₂ taken together form a nitrogen protecting group;

or R₄₁ and R₄₂ taken together with the N or C atom to which they are attached form a ring structure that can include at least one heteroatom selected from N and O;

v is from O to about 10;

q is 0 to about 50;

M is an optionally protected internucleoside linkage;

W₁ is a linking group, O, NH or S;

R₂₀ is hydroxyl or a group of Formula;

R₂ is —

N(R₇)₂, or a heterocycloalkyl or heterocycloalkenyl ring containing from 4 to 7 atoms, and having up to 3 heteroatoms selected from nitrogen, sulfur, and oxygen;

R₇ is straight or branched chain alkyl having from 1 to 10 carbons;

R₃ is a phosphorus protecting group;

X₃ has the formula XII;

wherein m is 1 or 2;

R₄ is a hydroxyl group, or a protected hydroxyl group; and

R₅ is H or an amino protecting group;

provided that when said compound has formula XVIID, q is at least 1.

30. The compound of claim 12 wherein m is 2.

31. The compound of claim 30 wherein W₁ is —

O—

(CH₂)_n—

NH—

wherein n is from 1 to about 10.

32. The compound of claim 31 wherein n is 6.

23. The compound of claim 23 wherein R₁ is dimethoxytrityl, R₅ is trifluoroacetoyl, and R₆ is —

C(═

O)—

CH(CH₃)₂.

24. The compound of claim 23 wherein q is 0.

26. The compound of claim 24 wherein R₂₀ is a group of formula:

where R₃ is β

-cyanoethyl, and R₂ is diisopropylamino.