Pyrimidine derivatives for labeled binding partners

• US 6,414,127 B1
• Filed: 09/21/1999
• Issued: 07/02/2002
• Est. Priority Date: 11/07/1997
• Status: Expired due to Term

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Lin, Kuei-Ying, Matteucci, Mark D.
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US09/400,502
• Time in Patent Office: 1,015 Days
• Field of Search: 514/256, 514/267, 435/6, 435/87, 435/90, 544/242, 544/245, 544/249, 536/22.1, 536/23.1, 536/25.3, 536/25-1-, 536/25.4
• US Class Current: 536/22.1
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• 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: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Compounds having structure (1)

wherein R¹ is —H a protecting group, a linker or a binding partner; and R² and R³⁴ are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.

Claims

1. A compound having the structure (1):

and tautomers, solvates and salts thereof, wherein

R¹ is —

H or a binding partner having the structure 2, 2(A), 2(B), or 2(C);

wherein

D is —

OH, protected —

OH, an oligonucleotide coupling group or a solid support;

D¹ is an oligonucleotide coupling group, —

OH, protected —

OH or a solid support, wherein D¹ is bonded to one 2′

or 3′

position in the oligonucleotide of structure (2) and the adjacent 2′

or 3′

position in structure (2) is substituted with R²¹, provided that D and D¹ are not both an oligonucleotide coupling group or they are not both a solid support;

D² is —

CO₂R⁵, —

C(O)N(R⁵)₂, —

SO₃R⁵, —

SO₂N(R⁵)₂ or an activated derivative of —

CO₂H or —

SO₃H;

D³ is a protecting group, —

H or —

(CH₂)_2-6—

N(R⁵)₂,

R⁴ independently a phosphodiester linkage or a phosphodiester substitute linkage, wherein R⁴ is bonded to one 2′

or 3′

position in the structure (2) oligonucleotide and the adjacent 2′

or 3′

position in structure (2) substituted with R²¹;

R⁵ is independently —

H or a protecting group;

R²¹ is independently —

H, —

OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage;

R³⁷ is independently —

O—

, —

CH₂—

or —

CF₂—

;

n is an integer from 0 to 98; and

B independently is a purine or pyrimidine base or a protected derivative thereof, provided that at least one B is a base of structure (3)

R² is A(Z)_X1, wherein A is a spacer and Z independently is a label bonding group optionally bonded to a detectable label, but R² is not amine, protected amine, nitro or cyano;

R²⁷ is independently —

CH═

, —

N═

, —

C(C₁-C₈ alkyl)═

or —

C(halogen)═

, but no adjacent R²⁷ are both —

N═

, or two adjacent R²⁷ are taken together to form a ring having the structure,

 

where R^a is independently —

CH═

, —

N═

, —

C(C₁-C₈ alkyl)═

or —

C(halogen)═

, but no adjacent R^a are both —

N═

;

R³⁴ is —

O—

, —

S—

or —

N(CH₃)—

;

R⁴⁰ independently is hydrogen, C₁-C₁₂ alkyl, C₁-C₁₂ substituted alkyl, a protecting group or both R⁴⁰ together with the nitrogen atom to which they are attached form;

and X1 is 1, 2 or 3.

2. The compound of claim 1 wherein R² is —

R^2C—

R^2D, wherein R^2C is a short spacer chain and R^2D is a hydrogen bond donor moiety or a moiety having a net positive charge of at least about +0.5 at pH 6-8 in aqueous solutions.

3. The compound of claim 1 wherein R² is —

R⁶—

(CH₂)_tNR⁵C(NR⁵)(NR³)₂, —

R⁶—

CH₂—

CHR³¹—

N(R³)₂, —

R⁶—

(R⁷)_v—

N(R³)₂, —

R⁶—

(CH₂)_tN(R³)₂, —

(CH₂)_1-2—

O—

(CH₂)_t—

N(R³)₂,

R³ is independently —

H, —

CH₃, —

CH₂CH₃, CH₂)_w—

N(R³³)₂ or a protecting group, or both R³ together are a protecting group, or when R² is —

R⁶—

(CH₂)_t—

N(R³)₂, one R³ is —

H, —

CH₃, —

CH₂CH₃, a protecting group or —

(CH₂)_w—

N(R³³)₂ and the other R³ is —

H, —

CH₃, —

CH₂CH₃, —

(CH₂)_w—

N(R³³)₂, —

CH(N[R³³]₂)—

N(R³³)₂,

R⁵ is independently H or a protecting group;

R⁶ is independently —

S, —

NR⁵—

, —

O—

or —

CH₂—

;

R⁷ is independently linear alkyl having 1, 2, 3 or 4 carbon atoms optionally substituted with one —

CH═

CH—

, —

C≡

C—

or —

CH₂—

O—

CH₂—

moiety, or R⁷ is cyclic alkyl having 3, 4 or 5 carbon atoms, wherein one of the linear alkyl carbon atoms is optionally substituted with a single —

CH₃, —

CN, ═

O, —

OH or protected hydroxyl, provided that the carbon atoms in any —

CH═

CH—

or —

CH₂—

O—

CH₂—

moiety are not substituted with ═

O, —

OH or protected hydroxyl;

R⁸ is linear alkylene having 1 or 2 carbon atoms wherein one alkylene carbon atom is optionally substituted with a single —

CH₃, —

CN, ═

O, —

OH or protected hydroxyl, or R⁸ is absent;

R²⁸ is independently —

CH₂—

, —

CH(CH₃)—

, —

CH(OCH₃)—

, —

CH(OR⁵)—

or —

O—

, but both are not —

O—

;

R²⁹ is independently —

N—

, —

N(CH₃)—

, —

CH—

, —

C(CH₃)—

, but both are not —

N(CH₃)—

;

R³⁰ is —

H or —

N(R³)₂;

R³¹ is the side chain of an amino acid;

R³³ is independently —

H, —

CH₃, —

CH₂CH₃ or a protecting group;

R³⁵ is H, C₁-C₄ alkyl or a protecting group;

R³⁶ is —

H, —

CH₃, —

CH₂CH₃, a protecting group or an optionally protected monosaccharide;

t is 1, 2, 3 or 4, but when R⁶ is —

O—

, —

S—

or —

NR⁵—

, t is 2, 3 or 4;

v is independently 0, 1 or 2; and

w is independently 1 or 2.

4. The compound of claim 3 wherein R² is —

CH₂—

(CH₂)_tN(R³)₂, —

NR⁵—

(CH₂)_tN(R³)₂, —

S—

(CH₂)_tN(R³)₂, —

O—

(CH₂)_tN(R³)₂, —

O—

(CH₂)_tNR⁵C(NR⁵)(NR³)₂, —

(CH₂)_1-2—

O—

(CH₂)_tN(R³)₂, —

R⁶—

CH₂—

CHR³¹—

N(R³)₂, —

R⁶—

(R⁷)_v—

N(R³)₂, —

R⁶—

(CH₂)_t—

NR⁵C(NR⁵)(NR³)₂, or —

CH₂(CH₂)_tNR⁵C(NR⁵)(NR³)₂.

5. The compound of claim 4 wherein t is 2.

6. The compound of claim 5 wherein R³ independently is —

H, —

CH₃—

C₂H₅ or a protecting group.

7. The compound of claim 6 wherein R² is —

O—

(CH₂)₂—

NH₂, —

O—

(CH₂)₃—

NH₂, —

O—

(CH₂)₂—

N(CH₃)₂, —

O—

(CH₂)₃—

N(CH₃)₂, —

O—

(CH₂)₂—

NHCH₃, —

O—

(CH₂)₃—

NHCH₃, —

O—

CH₂—

CH(CH₃)—

NH₂, —

CH₂—

O—

(CH₂)₂—

NH₂, —

CH₂—

O—

(CH₂)₃—

NH₂ or —

(CH₂)₂—

O—

(CH₂)₂—

NH₂.

8. The compound of claim 3 wherein t is 2 or 3.

9. The compound of claim 1 wherein R⁴ is independently 3′

-O—

P(S)(S)—

O-5′

, 3′

-O—

P(S)(O)—

O-5′

, 3′

-O—

P(O)(O)—

O-5′

, 3′

-O—

P(Me)(O)—

O-5′

, 3′

-NH—

P(O)(O)—

O-5′

, 2′

-S—

CH₂—

O-5′

, 3′

-O—

CH₂—

O-5′

, 2′

-O—

CH₂—

O-5′

, 3′

-O—

P(Me)(S)—

O-5′

, 3′

-CH₂—

N(CH₃)—

O-5′

, or 3′

-R³⁸—

P(N(R⁴⁰)₂)(O)—

O-5′

, wherein

R³⁸ independently is —

O—

, —

CH₂—

, or —

NH—

.

10. The compound of claim 1, wherein R² is —

R⁶—

(CH₂)_tNR⁵CNR⁵N(R³)₂, —

R⁶CH₂—

CHR³¹—

N(R³)₂, —

R⁶—

(R⁷)_v—

N(R³)₂, —

R⁶—

(CH₂)_t—

N(R³)₂, —

O—

(CH₂)_1-2—

O—

(CH₂)_t—

N(R₃)₂,

R³ is independently —

H, —

CH₃, —

CH₂CH₃, —

O—

(CH₂)_w—

N(R³)₂ or a protecting group, or both R³ together are a protecting group, or when R² is —

R⁶—

(CH₂)_t—

N(R³³)₂, one R³ is —

H, —

CH₃, —

CH₂CH₃, a protecting group or —

(CH₂)_w—

N(R³³)₂ and the other R³ is —

H, —

CH₃, —

CH₂CH₃, —

(CH₂)_w—

N(R³³)₂, —

CH(N(R³³)₂)—

N(R³³)₂,

R⁵ is independently H or a protecting group;

R⁶ is independently —

S—

, —

NR⁵—

, —

O—

or —

CH₂—

;

R⁷ is independently linear alkyl having 1, 2, 3 or 4 carbon atoms optionally substituted with one —

CH═

CH—

, —

C═

C—

or —

CH₂—

O—

CH₂—

moiety, or R⁷ is cyclic alkyl having 3, 4 or 5 carbon atoms, wherein one of the linear alkyl carbon atoms is optionally substituted with a single —

CH₃, —

CN, ═

O, —

OH or protected hydroxyl, provided that the carbon atoms in any —

CH═

CH—

or —

CH₂—

O—

CH₂—

moiety are not substituted with ═

O, —

OH or protected hydroxyl;

R⁸ is linear alkylene having 1 or 2 carbon atoms wherein one alkylene carbon atom is optionally substituted with a single —

CH₃, —

CN, ═

O, —

OH or protected hydroxyl, or R⁸ is absent;

R²⁸ is independently —

CH₂—

, —

CH(CH₃)—

, —

CH(OCH₃)—

, —

CH(OR⁵)—

or —

O—

, but both are not —

O—

;

R²⁹ is independently —

N—

, —

N(CH₃)—

, —

CH—

, —

C(CH₃)—

, but both are not —

N(CH₃)—

;

R³⁰ is —

H or —

N(R³)₂;

R³¹ is the side chain of an amino acid;

R³³ is independently —

H, —

CH₃, —

CH₂CH₃ or a protecting group;

R³⁵ is H, C₁-C₄ alkyl or a protecting group;

R³⁶ is H, —

CH₃, —

CH₂CH₃, a protecting group or an optionally protected monosaccharide;

t is 1, 2, 3 or 4, but when R⁶ is —

O—

, —

S—

or —

NR⁵—

, t is 2, 3 or 4;

v is independently 0, 1 or 2; and

w is independently 1 or 2.

11. The compound of claim 10 wherein R² is —

CH₂—

(CH₂)_tN(R³)₂, —

NR⁵—

(CH₂)_tN(R³)₂, —

S—

(CH₂)_tN(R³)₂, —

O—

(CH₂)_tN(R³)₂, —

O—

(CH₂)_tNR⁵C(NR⁵)(NR³)₂, —

O—

(CH₂)_1-2—

O—

(CH₂)_tN(R³)₂, —

R⁶—

CH₂—

CHR³¹—

N(R³)₂, —

R⁶—

(R⁷)_v—

N(R³)₂, —

R⁶—

(CH₂)_tNR⁵C(NR⁵)(NR³)₂, or —

CH₂(CH₂)_tNR⁵C(NR⁵)(NR³)₂.

12. The compound of claim 11 therein t is 2 or 3.

13. The compound of claim 12 wherein R³ independently is —

H, —

CH₃, —

C₂H₅ or a protecting group.

14. The compound of claim 13 wherein R² is —

O—

(CH₂)₂—

NH₂, —

O—

(CH₂)₃—

NH₂, —

O—

(CH₂)₂—

N(CH₃)₂, —

O—

(CH₂)₃—

N(CH₃)₂, —

O—

(CH₂)₂—

NHCH₃, —

O—

(CH₂)₃—

NHCH₃, —

O—

CH₂—

CH(CH₃)—

NH₂, —

CH₂—

O—

(CH₂)₂—

NH₂, —

CH₂—

O—

(CH₂)₃—

NH₂ or —

(CH₂)₂—

O—

(CH₂)₂—

NH₂.

15. The compound of claim 1 wherein R²¹ is independently —

H, —

OH, halogen, protected hydroxyl, —

O-methyl, O-ethyl, O-n-propyl, O-allyl, —

O—

(CH₂)₂—

OH, —

O—

(CH₂)₃—

OH, —

O—

(CH₂)₂—

F, —

O—

(CH₂)_s—

F, —

O—

(CH₂)_s—

R⁶⁵, —

O—

(CH₂)₂—

(O—

(CH₂)₂)_r—

R⁶⁵, —

O—

(CH₂)_r—

O—

(CH₂)_r—

O—

(CH₂)_rR⁶⁵, —

NH-methyl, —

NH-ethyl, —

NH-n-propyl, —

NH—

(CH₂)₂OH, —

NH—

(CH₂)₃OH, —

NH—

(CH₂)_s—

R⁶⁵, —

S-methyl, —

S-ethyl, —

S-n-propyl, —

S-allyl, —

S—

(CH₂)₂—

OH, —

S—

(CH₂)₃—

OH, —

S—

(CH₂)₂—

F, —

S—

(CH₂)_s—

R⁶⁵, or —

S—

(CH₂)₂—

(O—

(CH₂)₂)_r—

R⁶⁵, wherein;

R⁶⁵ is —

H, —

F, —

OH, —

OCH₃, —

NH₂, —

SH, protected hydroxyl, protected amino or protected thiol;

r is 1, 2, 3, or 4; and

s is 2, 3, 4, 5, 6, 7 or 8.

16. A compound according to claim 1, having a structure selected from the group consisting of:

wherein R¹ is a binding partner, a protecting group, a linker or H.

17. The compound of claim 15 wherein R²¹ is independently —

H, —

OH, —

F, protected hydroxyl, —

OCH₃, —

O—

CH₂CH₃, —

O—

CH₂CH₂OH, —

O—

CH₂CH₂F, —

O—

CH₂CH₂CH₃, —

O—

CH₂CH₂CH₂OH, —

O—

CH₂CH₂CH₂F, —

O—

CH₂CF₂H, —

O—

CH₂CF₃ or —

O—

CH₂CH₂—

O—

CH₃.

18. The compound of claim 1 wherein B independently are selected from the group consisting of a base of structure (3), guanosine, adenine, thymine, uracil, cytosine, 5-methylcytosine, 5-(1-propynyl)uracil, 5-(1-propynly)cytosine, 5-(1-butynyl)uracil or 5-(1-butynyl)cytosine.

19. The compound of claim 1 wherein D¹ is H-phosphonate, a methylphosphonamidite, a β

-cyanoethylphosphoramidite or a phosphoramidite.

20. A compound having the structure (4):

and tautomers, solvates and salts thereof, wherein

R¹, R² and R²⁷ have the meanings given in claim 1;

R²⁴ is hydrogen;

R²⁵ is —

SH, —

OH, ═

S or ═

O.

21. The compound of claim 20 where R¹ is —

H or optionally protected monosaccharide.

22. The compound of claim 21 wherein the optionally protected monosaccharide is 2′

-deoxy-R²¹-substituted ribose.

23. The compound of claim 22 wherein R²¹ is —

H, —

OH, —

F, protected hydroxyl, —

OCH₃, —

O—

CH₂CH₃, —

O—

CH₂CH₂OH, —

O—

CH₂CH₂F, —

O—

CH₂CH₂CH₃, —

O—

CH₂CH₂CH₂OH, —

O—

CH₂CH₂CH₂F, —

O—

CH₂CF₂H, —

O—

CH₂CF₃or —

O—

CH₂CH₂—

O—

CH₃.

24. A compound having the structure (1):

or tautomers, solvates or salts thereof, wherein;

R¹ is an oligonucleotide, a protecting group, a linker or —

H;

R² is —

R⁶—

(CH₂)_tNR⁵C(NR⁵)N(R³)₂;

R³ is independently —

H, —

CH₃, —

CH₂CH₃, —

(CH₂)_w—

N(R³³)₂ or a protecting group, or both R³ together are a protecting group;

R⁵ independently H or a protecting group;

R⁶ is independently —

S—

, —

NR⁵—

, —

O—

, —

CH₂—

;

R³³ is independently —

H, —

CH₃, —

CH₂CH₃ or a protecting group;

each R²⁷ is, independently —

CH═

, —

N═

, —

C(C₁-C₈ alkyl)═

or —

C(halogen)═

, with the proviso that no two adjacent groups R²⁷ are both —

N═

;

alternatively, adjacent R²⁷ are taken together to form a ring having the structure;

wherein each R^a is, independently —

CH═

, —

N═

, —

C(C_1-8 alkyl)═

or —

C(halogen)═

, with the proviso that no two adjacent groups R^a are both —

N═

;

R³⁴ is —

O—

, —

S—

or —

N(CH₃)—

;

w is independently 1 or 2; and

t is 1, 2, 3, or 4.

25. The compound of claim 24 wherein t is 2 or 3.

26. The compound of claim 25 wherein R³ is independently is —

H, —

CH₃, —

C₂H₅ or a protecting group.

27. The compound of claim 25 wherein R¹ comprises —

H, an optionally protected monosaccaride, hydroxyl, phosphate or hydrogen phosphate.

28. The compound of claim 24 wherein R¹ is optionally protected 2′

-deoxy-R²¹-substituted ribose, 2′

-deoxyribose or ribose; and

R²¹ is selected from —

H, —

OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage.

29. The compound of claim 24 wherein R¹ is a binding partner having the structure 2:

wherein;

D is —

OH, protected —

OH, an oligonucleotide coupling group or a solid support;

D¹ is an oligonucleotide coupling group, —

OH, protected —

OH or a solid support, wherein D¹ is bonded to one 2′

or 3′

position in the oligonucleotide of structure (2) and the adjacent 2′

or 3′

position in structure (2) is substituted with R²¹, provided that D and D¹ are not both an oligonucleotide coupling group or they are not both a solid support;

R⁴ is independently a phosphodiester linkage or a phosphodiester substitute linkage, wherein R⁴ is bonded to one 2′

or 3′

position in the structure (2) oligonucleotide and the adjacent 2′

or 3′

position in structure (2) is substituted with R²¹;

R²¹ is independently —

H, —

OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage;

R³⁷ is independently —

O—

, —

CH₂—

, or —

CF₂—

;

n is an integer from 0 to 98; and

B is independently a purine or pyrimidine base or a protected derivative thereof, provided that at least one B is a base of structure (3);

30. The compound of claim 29 wherein R⁴ is independently 3′

-O—

P(S)(S)—

O-5′

, 3′

-O—

P(S)(O)—

O-5′

, 3′

-O—

P(O)(O)—

O-5′

, 3′

-O—

P(Me)(O)—

O-5′

, 3′

-NH—

P(O)(O)—

O-5′

, 2′

-S—

CH₂—

O-5′

, 3′

-O—

CH₂—

O-5′

, 2′

-O—

CH₂—

O-5′

, 3′

-O—

P(Me)(S)—

O-5′

, 3′

-CH₂—

N(CH₃)—

O-5′

, or 3′

R³⁸—

P(N(R⁴⁰)₂)(O)—

O-5′

, wherein

R³⁸ independently is —

O—

, —

CH₂—

, or —

NH—

;

R⁴⁰ independently is hydrogen, C₁-C₁₂ alkyl, C₁-C₁₂ substituted alkyl, a protecting group or both R⁴⁰ together with the nitrogen atom to which they are attached form;

 

or both R⁴⁰ together are a protecting group.

31. The compound of claim 29 wherein R³ is independently —

H, —

CH₃, —

CH₂CH₃, —

(CH₂)_w—

N(R³³)₂ or a protecting group, or both R³ together are a protecting group,

R⁵ is independently H or a protecting group;

R⁶ is independently —

S—

, —

NR⁵—

, —

O—

or —

CH₂—

;

R⁷ is independently linear alkyl having 1, 2, 3 or 4 carbon atoms optionally substituted with one —

CH═

CH—

, —

C═

C—

or —

CH₂—

O—

CH₂—

moiety, or R⁷ is cyclic alkyl having 3, 4 or 5 carbon atoms, wherein one of the linear alkyl carbon atoms is optionally substituted with a single —

CH₃, —

CN, ═

O, —

OH or protected hydroxyl, provided that the carbon atoms in any —

CH═

CH—

or —

CH₂—

O—

CH₂—

moiety are not substituted with ═

O, —

OH or protected hydroxyl;

R⁸ is linear alkylene having 1 or 2 carbon atoms wherein one alkylene carbon atom is optionally substituted with a single —

CH₃, —

CN, ═

O, —

OH or protected hydroxyl, or R⁸ is absent;

R²⁸ is independently —

CH₂—

, —

CH(CH₃)—

, —

CH(OCH₃)—

, —

CH(OR⁵)—

or —

O—

, but both are not —

O—

;

R²⁹ is independently —

N—

, —

N(CH₃)—

, —

CH—

, —

C(CH₃)—

, but both are not —

N(CH₃)—

;

R³⁰ is —

H or —

N(R³)₂;

R³¹ is the side chain of an amino acid;

R³³ is independently —

H, —

CH₃, —

CH₂CH₃ or a protecting group;

R³⁵ is H, C₁-C₄ alkyl or a protecting group;

R³⁶ is H, —

CH₃, —

CH₂CH₃, a protecting group or an optionally protected monosaccharide;

t is 1, 2, 3 or 4, but when R⁶ is —

O—

, —

S—

or —

NR⁵—

, t is 2, 3 or 4;

v is independently 0, 1 or 2; and

w is independently 1 or 2.

32. The compound of claim 31 wherein R³ independently is —

H, —

CH₃, —

C₂H₅ or a protecting group.

33. The compound of claim 29 wherein R² is independently —

H, —

OH, halogen, protected hydroxyl, —

O-methyl, O-ethyl, O-n-propyl, O-allyl, —

O—

(CH₂)₂—

OH, —

O—

(CH₂)₃—

OH, —

O—

(CH₂)₂—

F, —

O—

(CH₂)_s—

F, —

O—

(CH₂)_s—

R⁶⁵, —

O—

(CH₂)₂—

(O—

(CH₂)₂)_r—

R⁶⁵, —

O—

(CH₂)_r—

O—

(CH₂)_r—

O—

(CH₂)_rR⁶⁵, —

NH-methyl, —

NH-ethyl, —

NH-n-propyl, —

NH—

(CH₂)₂OH, —

NH—

(CH₂)₃OH, —

NH—

(CH₂)_s—

R⁶⁵, —

S-methyl, —

S-ethyl, —

S-n-propyl, —

S-allyl, —

S—

(CH₂)₂—

OH, —

S—

(CH₂)₃—

OH, —

S—

(CH₂)₂—

F, —

S—

(CH₂)_s—

R⁶⁵, or —

S—

(CH₂)₂—

(O—

(CH₂)₂)_r—

R⁶⁵, wherein;

R⁶⁵ is —

H, —

F, —

OH, —

OCH₃, —

NH₂, —

SH, protected hydroxyl, protected amino or protected thiol;

r is 1, 2, 3, or 4; and

s is 2, 3, 4, 5, 6, 7 or 8.

34. The compound of claim 33 wherein R²¹ is independently —

H, —

OH, —

F, protected hydroxyl, —

OCH₃, —

O—

CH₂CH₃, —

O—

CH₂CH₂OH, —

O—

CH₂CH₂F, —

O—

CH₂CH₂CH₃, —

O—

CH₂CH₂CH₂OH, —

O—

CH₂CH₂CH₂F, —

O—

CH₂CF₂H, —

O—

CH₂CF₃ or —

O—

CH₂CH₂—

O—

CH₃.

35. The compound of claim 29 wherein B independently are selected from the group consisting of a base of structure (3), guanosine, adenine, thymine, uracil, cytosine, 5-methylcytosine, 5-(1-propynyl)uracil, 5-(1-propynly)cytosine, 5-(1-butynyl)uracil or 5-(1-butynyl)cytosine.

36. The compound of claim 29 wherein D¹ is H-phosphonate, a methylphosphonamidite, a β

-cyanoethylphosphoramidite or a phosphoramidite.

41. A compound according to claim 24 having a structure selected from the group consisting of:

wherein R¹ is an oligonucleotide, a protecting group, a linker or H.

37. A compound having the structure (4)

or tautomers, solvates or salts thereof wherein,

R¹ is an oligonucleotide, a protecting group, a linker or —

H;

R² is —

R⁶—

(CH₂)_tNR⁵C(NR⁵)N(R³)₂;

R³ is independently —

H, —

CH₃, —

CH₂CH₃, —

(CH₂)_w—

N(R³³)₂ or a protecting group, or both R³ together are a protecting group;

R⁵ independently H or a protecting group;

R⁶ is independently —

S—

, —

NR⁵—

, —

O—

, —

CH₂—

;

R³³ is independently —

H, —

CH₃, —

CH₂CH₃ or a protecting group;

each R²⁷ is, independently —

CH═

, —

N═

, —

C(C₁-C₈ alkyl)═

or —

C(halogen)═

, with the proviso that no two adjacent groups R²⁷ are both —

N═

;

or alternatively adjacent R²⁷ are taken together to form a ring having the structure;

wherein each R^a is, independently —

CH═

, —

N═

, —

C(C_1-8 alkyl)═

or —

C(halogen)═

, with the proviso that no two adjacent groups R^a are both —

N═

;

t is 1, 2, 3, or 4;

w is independently 1 or 2;

R²⁴ is a halogen; and

R²⁵ is —

SH, —

OH, ═

S or ═

O.

38. The compound of claim 37 where R¹ is —

H or optionally protected monosaccharide.

39. The compound of claim 38 wherein the optionally substituted monosaccharide is 2′

-deoxy-R²¹-substituted ribose;

wherein R²′

is selected from —

H, —

OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage.

40. The compound of claim 39 wherein R²¹ is —

H, —

OH, —

F, protected hydroxyl, —

OCH₃, —

O—

CH₂CH₃, —

O—

CH₂CH₂OH, —

O—

CH₂CH₂F, —

O—

CH₂CH₂CH₃, —

O—

CH₂CH₂CH₃, —

O—

CH₂CH₂CH₂OH, —

O—

CH₂CH₂CH₂F, —

O—

CH₂CF₂H, —

O—

CH₂CF₃ or —

O—

CH₂CH₂—

O—

CH₃.