Substituted purines and oligonucleotide cross-linking

• US 5,811,534 A
• Filed: 10/09/1997
• Issued: 09/22/1998
• Est. Priority Date: 02/01/1994
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Manoharan, Muthiah, Cook, Phillip Dan, Ramasamy, Kanda S.
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/948,151
• Time in Patent Office: 348 Days
• Field of Search: 536/22.1, 536/23.1, 536/25.3, 536/25.34, 536/26.26, 536/26.7, 544/264
• US Class Current: 536/23.1
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• CPC Class Codes: A61P 31/04 Antibacterial agents
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07H 19/04 Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/16 Purine radicals
• 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: C07H 23/00 Compounds containing boron, silicon, or a metal, e.g. chelates, vitamin B12 esters with inorganic acids C07H11/00; metal salts, see parent compounds
• CPC Class Codes: C07J 43/003 not condensed
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 15/1137 against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 2310/3125 Methylphosphonates
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/32 of the sugar
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 : 2'-R Modification
• CPC Class Codes: C12N 2310/33 : of the base
• CPC Class Codes: C12N 2310/333 : Modified A
• CPC Class Codes: C12N 2310/336 : Modified G
• CPC Class Codes: C12N 2310/3511 : intercalating or cleaving agent
• CPC Class Codes: C12N 2310/3521 : Methyl
• CPC Class Codes: C12N 2310/3523 : Allyl
• CPC Class Codes: C12N 2310/3527 : Other alkyl chain
• CPC Class Codes: C12N 2310/3531 : Hydrogen
• CPC Class Codes: C12N 2310/3533 : Halogen
• CPC Class Codes: C12N 2740/16322 : New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 9/0069 : acting on single donors with incorporation of molecular oxygen, i.e. oxygenases (1.13)
• CPC Class Codes: C12Q 1/68 : involving nucleic acids
• CPC Class Codes: C12Q 1/6813 : Hybridisation assays
• CPC Class Codes: C12Y 113/11012 : Linoleate 13S-lipoxygenase (1.13.11.12)

Abstract

This invention is directed to novel purine-based compounds for inclusion into oligonucleotides. The compounds of the invention, when incorporated into oligonucleotides are especially useful as "antisense" agents--agents that are capable of specific hybridization with a nucleotide sequence of an RNA. The compounds of the invention may also be used for cross-linking oligonucleotides. Oligonucleotides are used for a variety of therapeutic and diagnostic purposes, such as treating diseases, regulating gene expression in experimental systems, assaying for RNA and for RNA products through the employment of antisense interactions with such RNA, diagnosing diseases, modulating the production of proteins, and cleaving RNA in site specific fashions. The compounds of the invention include novel heterocyclic bases, nucleosides, and nucleotides. When incorporated into oligonucleotides, the compounds of the invention can be useful for modulating the activity of RNA.

Claims

1. A compound having the formula:

##STR25## wherein;

G is CR₁ ;

R₁ is a hydrocarbyl group having from 1 to 6 carbon atoms;

X is halogen, NH₂, OH, NHR₂ Q₁ or OR₂ Q₁, wherein said R₂ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₁ comprises a reactive or non-reactive functionality;

Y is halogen, NH₂, H, R₃ Q₂, or NHR₃ Q₂, wherein said R₃ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₂ comprises a reactive or non-reactive functionality;

W is H, R₄ Q₃, or NHR₄ Q₃, wherein said R₄ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₃ comprises a reactive or non-reactive functionality;

Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"' position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

said reactive functionality is selected from the group consisting of halogens, heterocycles, heterocycloalkyls, heterocycloalkylamines, polyalkylamines, aminoalkylamines, ethers, esters, aldehydes, ketones, aryl groups, hydrazines, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, alcohols, and thiols; and

said unreactive functionality is selected from the group consisting of alkyl groups, polyamides, intercalators, and ethylene glycols.

2. The compound of claim 1 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety.

3. The compound of claim 2 wherein X is NHR₂ Q₁, said Q₁ is a nitrogen-containing heterocycle having a plurality of ring atoms, one to four of said ring atoms being nitrogen atoms and the remainder being carbon atoms.

4. The compound of claim 2 wherein X is NHR₂ Q₁, said Q₁ is a substituted or unsubstituted imidazole.

5. The compound of claim 2 wherein X is OR₂ Q₁, said Q₁ is a nitrogen-containing heterocycle having a plurality of ring atoms, one to four of said ring atoms being nitrogen atoms and the remainder being carbon atoms.

6. The compound of claim 2 wherein X is OR₂ Q₁, said Q₁ is a substituted or unsubstituted imidazole.

7. The compound of claim 2 wherein W is R₄ Q₃, said Q₃ is a nitrogen-containing heterocycle having a plurality of ring atoms, one to four of said ring atoms being nitrogen atoms and the remainder being carbon atoms.

8. The compound of claim 2 wherein W is R₄ Q₃, said Q₃ is a substituted or unsubstituted imidazole.

9. The compound of claim 2 wherein X is NHR₂ Q₁, said Q₁ is an amine.

10. The compound of claim 2 wherein X is OR₂ Q₁, said Q₁ is an amine.

11. The compound of claim 2 wherein W is R₄ Q₃, said Q₃ is an amine.

31. The compound of claim 1 further having a phosphate group at the 3'"'"' position of the sugar analog, wherein said phosphate group may be a native phosphate or a modified phosphate.

32. The compound of claim 31 wherein said modified phosphate is a methylphosphonate, phosphorothioate, phosphorodithioate, phosphoramidite, or phosphorotriester.

68. The compound of claim 2 wherein X is NHR₂ Q₁ and said Q₁ is an imidazole.

69. The compound of claim 2 wherein X is OR₂ Q₁ and said Q₁ is an imidazole.

12. A compound having the formula:

##STR26## wherein;

G is N;

X is NHR₂ Q₁ or OR₂ Q₁, wherein said R₂ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₁ comprises a reactive or non-reactive functionality;

Y is halogen, NH₂, H, R₃ Q₂, or NHR₃ Q₂, wherein said R₃ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₂ comprises a reactive or non-reactive functionality;

W is R₄ Q₃, or NHR₄ Q₃, wherein said R₄ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₃ comprises a reactive or non-reactive functionality;

Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"' position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

said reactive functionality is selected from the group consisting of halogens, heterocycles, heterocycloalkyls, heterocycloalkylamines, polyalkylamines, aminoalkylamines, ethers, esters, aldehydes, ketones, aryl groups, hydrazines, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, alcohols, and thiols; and

said unreactive functionality is selected from the group consisting of alkyl groups, polyamides, intercalators, and ethylene glycols.

13. The compound of claim 12 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety.

14. The compound of claim 12 further having a phosphate group at the 3'"'"' position of the sugar analog, wherein said phosphate group may be a native phosphate or a modified phosphate.

15. The compound of claim 14 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCHO and an RNA cleaving moiety; and

said modified phosphate is a methylphosphonate, phosphorothioate, phosphorodithioate, phosphoramidite, or phosphorotriester.

16. A compound having the formula:

##STR27## wherein;

G is N;

X is halogen, NH₂, OH, NHR₂ Q₁ or OR₂ Q₁, wherein said R₂ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₁ comprises a reactive or non-reactive functionality;

Y is R₃ Q₂, or NHR₃ Q₂, wherein said R₃ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₂ comprises a reactive or non-reactive functionality;

W is R₄ Q₃, or NHR₄ Q₃, wherein said R₄ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₃ comprises a reactive or non-reactive functionality;

Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"' position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

said reactive functionality is selected from the group consisting of halogens, heterocycles, heterocycloalkyls, heterocycloalkylamines, polyalkylamines, aminoalkylamines, ethers, esters, aldehydes, ketones, aryl groups, hydrazines, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, alcohols, and thiols; and

said unreactive functionality is selected from the group consisting of alkyl groups, polyamides, intercalators, and ethylene glycols.

17. The compound of claim 16 wherein W is R₄ Q₃, said Q₃ is a nitrogen-containing heterocycle having a plurality of ring atoms, one to four of said ring atoms being nitrogen atoms and the remainder being carbon atoms.

18. The compound of claim 16 wherein W is R₄ Q₃ and said Q₃ is an imidazole.

19. The compound of claim 16 wherein W is R₄ Q₃, said Q₃ is an amine.

20. The compound of claim 16 further having a phosphate group at the 3'"'"' position of the sugar analog, wherein said phosphate group may be a native phosphate or a modified phosphate.

21. The compound of claim 16 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety.

22. The compound of claim 16 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety; and

said modified phosphate is a methylphosphonate, phosphorothioate, phosphorodithioate, phosphoramidite, or phosphorotriester.

23. The compound of claim 22 wherein G is N;

and X is OR₂ Q₁, wherein said R₂ is a lower alkane and Q₁ is phenyl.

24. The compound of claim 23 wherein said R₂ is an alkane having from about 2 to about 4 carbon atoms.

25. The compound of claim 22 wherein G is N;

X is OR₂ Q₁, wherein R₂ is lower alkane and Q₁ is phenyl.

26. The compound of claim 25 wherein said R₂ is methyl.

27. The compound of claim 25 wherein said R₂ is propyl.

28. The compound of claim 22 wherein G is N;

X is OR₂ Q₁, wherein R₂ is propyl and Q₁ is nitrophenyl.

29. The compound of claim 22 wherein said R₂ is propyl;

Q₁ is nitrophenyl;

Y is NHR₃ Q₂ ;

R₃ is propyl; and

Q₃ is imidazole.

30. The compound of claim 22 wherein said R₂ is methyl;

said Q₁ is phenyl; and

Y is fluorine.

70. The compound of claim 21 wherein W is R₄ Q₃ and said Q₃ is an imidazole.

33. An oligonucleotide having at least one nucleotide of the formula:

##STR28## wherein;

G is CR₁ or N;

R₁ is H or a hydrocarbyl group having from 1 to 6 carbon atoms;

X is halogen, NH₂, OH, NHR₂ Q₁ or OR₂ Q₁, wherein said R₂ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₁ comprises a reactive or non-reactive functionality;

Y is halogen, NH₂, H, R₃ Q₂, or NHR₃ Q₂, wherein said R₃ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₂ comprises a reactive or non-reactive functionality;

W is H, R₄ Q₃, or NHR₄ Q₃, wherein said R₄ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₃ comprises a reactive or non-reactive functionality;

Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"' position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

said reactive functionality is selected from the group consisting of halogens, heterocycles, heterocycloalkyls, heterocycloalkylamines, polyalkylamines, aminoalkylamines, ethers, esters, aldehydes, ketones, aryl groups, hydrazines, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, alcohols, and thiols;

said unreactive functionality is selected from the group consisting of alkyl groups, polyamides, intercalators, and ethylene glycols; and

wherein at least one of X, Y and W is selected such that X is NHR₂ Q₁, or OR₂ Q₁, Y is R₃ Q₂ or NHR₃ Q₂, or W is NHR₄ Q₃.

34. The oligonucleotide of claim 33 wherein G is N.

35. The oligonucleotide of claim 33 having from 2 to 40 linked nucleotides.

36. The oligonucleotide of claim 33 having from 2 to 18 linked nucleotides.

37. The compound of claim 33 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety.

43. An oligonucleotide of claim 35 further comprising:

a third region of said oligonucleotide, said third region including at least one compound of said formula; and

wherein said second region is positioned in said oligonucleotide between said first and third regions.

38. An oligonucleotide for affecting RNase H cleavage of RNA comprising:

a first oligonucleotide region and a second oligonucleotide region;

together said first and said second region having a nucleotide sequence essentially complementary to at least a portion of said RNA;

said first region including at least one compound of the formula;

##STR29## wherein;

G is CR₁ or N;

R₁ is H or a hydrocarbyl group having from 1 to 6 carbon atoms;

X is halogen, NH₂, OH, NHR₂ Q₁ or OR₂ Q₁, wherein said R₂ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₁ comprises a reactive or non-reactive functionality;

Y is halogen, NH₂, H, R₃ Q₂, or NHR₃ Q₂, wherein said R₃ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₂ comprises a reactive or non-reactive functionality;

W is H, R₄ Q₃, or NHR₄ Q₃, wherein said R₄ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₃ comprises a reactive or non-reactive functionality;

Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"' position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

said reactive functionality is selected from the group consisting of halogens, heterocycles, heterocycloalkyls, heterocycloalkylamines, polyalkylamines, aminoalkylamines, ethers, esters, aldehydes, ketones, aryl groups, hydrazines, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, alcohols, and thiols;

said unreactive functionality is selected from the group consisting of alkyl groups, polyamides, intercalators, and ethylene glycols;

wherein at least one of X, Y and W is selected such that X is NHR₂ Q₁ or OR₂ Q₁, Y is R₃ Q₂ or NHR₃ Q₂, or W is NHR₄ Q₃ ; and

said second region including a plurality of consecutive phosphorothioate linked nucleotides having a 2'"'"'-deoxy-erythropentofuranosyl sugar moiety.

39. The oligonucleotide of claim 38 wherein G is N.

40. An oligonucleotide of claim 38 having from 2 to 40 linked nucleotides.

41. An oligonucleotide of claim 38 having from 2 to 18 linked nucleotides.

42. The oligonucleotide of claim 38 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety.

44. The cross-linked nucleic acid of claim 38 wherein each of said first and said second oligonucleotide regions comprise a nucleotide of said formula;

and

said covalent cross-linkage is between said nucleotides of said formula.

45. The cross-linked nucleic acid of claim 38 wherein said group J or K on said nucleotide of said formula in said first oligonucleotide region includes a first space-spanning group having a first active functional group;

said group J or K on said second nucleotide includes a second space-spanning group having a second active functional group; and

said covalent cross-linkage is between said first and second active functional groups.

46. The cross-linked nucleic acid of claim 44 wherein said group R₇ is from about 8 to about 13 atoms in length and said groups Q₄ and Q₅ are, independently, a thiol, an aldehyde, a protected aldehyde, an aldehyde precursor, an amine, hydrazine, hydroxylamine, semicarbazide, thiosemicarbazide, hydrazide, alcohol, or alkoxy.

47. The cross-linked nucleic acid of claim 38 wherein said X is NHJ, OJ, or SJ.

48. The cross-linked nucleic acid of claim 47 wherein said space-spanning group R₇ is from about 8 to about 13 atoms in length and said group Q₄ is, independently, a thiol, an aldehyde, a protected aldehyde, an aldehyde precursor, NH₂, polyalkylamine, aminoalkylamine, hydrazine (--NH--NH--), hydroxylamine (--NH--OH), semicarbazide (--NH--C(O)--NH--NH₂), thiosemicarbazide (--NH--C(S)--NH--NH₂), hydrazone (--N═

NH), hydrazide (--C(O)--NH--NH₂), alcohol, or alkoxy.

49. The cross-linked nucleic acid of claim 44 wherein Y is J.

50. The cross-linked nucleic acid of claim 49 wherein said group R₇ is from about 8 to about 13 atoms in length and said group Q₄ is a thiol, an aldehyde, a protected aldehyde, an aldehyde precursor, an amine, hydrazine, hydroxylamine, semicarbazide, thiosemicarbazide, hydrazide, alcohol, or alkoxy.

51. The cross-linked nucleic acid of claim 44 wherein W is K.

52. The cross-linked nucleic acid of claim 51 wherein said group R₇ is from about 8 to about 13 atoms in length and said group Q₅ is a thiol, an aldehyde, a protected aldehyde, an aldehyde precursor, an amine, hydrazine, hydroxylamine, semicarbazide, thiosemicarbazide, hydrazide, alcohol, or alkoxy.

53. The cross-linked nucleic acid of claim 38 wherein said first oligonucleotide region and said second oligonucleotide region are on a single oligonucleotide strand.

54. The cross-linked oligonucleotide of claim 48 wherein said first sequence region and said second sequence region are on a single oligonucleotide strand.

55. The cross-linked oligonucleotide of claim 50 wherein said first sequence region and said second sequence region are on a single oligonucleotide strand.

56. The cross-linked oligonucleotide of claim 52 wherein said first sequence region and said second sequence region are on a single oligonucleotide strand.

57. The cross-linked nucleic acid of claim 38 wherein said first oligonucleotide region and said second oligonucleotide region are on different oligonucleotide strands.

58. The cross-linked oligonucleotide of claim 48 wherein said first sequence region and said second sequence region are on different oligonucleotide strands.

59. The cross-linked oligonucleotide of claim 50 wherein said first sequence region and said second sequence region are on different oligonucleotide strands.

60. The cross-linked oligonucleotide of claim 52 wherein said first sequence region and said second sequence region are on different oligonucleotide strands.

61. The cross-linked nucleic acid of claim 38 wherein said first oligonucleotide region and said second oligonucleotide region are complementary to and specifically hybridizable with one another.

62. The cross-linked oligonucleotide of claim 48 wherein said first sequence region and said second sequence region are complementary to and specifically hybridizable with one another.

63. The cross-linked oligonucleotide of claim 50 wherein said first sequence region and said second sequence region are complementary to and specifically hybridizable with one another.

64. The cross-linked oligonucleotide of claim 52 wherein said first sequence region and said second sequence region are complementary to and specifically hybridizable with one another.

65. The cross-linked nucleic acid of claim 38 wherein said first nucleotide of said formula is located in a first nucleotide sequence and said second nucleotide is located in a second nucleotide sequence;

said second nucleotide sequence is complementary to and hybridizable with said first nucleotide sequence; and

said first and said second nucleotide sequences are located on a single strand of said cross-linked nucleic acid with said second nucleotide sequence located on said cross-linked nucleic acid at a distance separated from said first nucleotide sequence sufficient to allow said cross-linked nucleic acid to assume a conformation wherein said first and second nucleotide sequences are mutually aligned with and specifically hybridized with one another.

66. The cross-linked nucleic acid of claim 38 wherein said first nucleotide of said formula is located in a first nucleotide sequence and said second nucleotide is located in a second nucleotide sequence;

and said first and said second nucleotide sequences are located on a single strand of an oligonucleotide with said second nucleotide sequence located on said oligonucleotide at a non-hybridizable position with respect to said first nucleotide sequence and at a distance from said first nucleotide sequence sufficient to allow said oligonucleotide to assume a conformation wherein said first and second nucleotide sequences are located in spatial proximity with each other.

67. The cross-linked nucleic acid of claim 38 wherein said first nucleotide of said formula is located in a first nucleotide sequence and said second nucleotide is located in a second nucleotide sequence;

said second nucleotide sequence is complementary to and specifically hybridizable with said first nucleotide sequence; and

said first and said second nucleotide sequences are located on different oligonucleotide strands.

71. A compound having the formula:

##STR30## wherein;

G is N;

X is OR₂ Q₁, wherein said R₂ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₁ comprises a reactive or non-reactive functionality;

Y is halogen, H, R₃ Q₂, or NHR₃ Q₂, wherein said R₃ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₂ comprises a reactive or non-reactive functionality;

W is H;

Z is H, a nitrogen protecting group, or Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"' position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

provided that where Y is NHR₃ Q₂, said nucleoside sugar moiety is not a 2'"'"'-fluoro arabinofuranosyl sugar moiety;

said reactive functionality is selected from the group consisting of halogens, heterocycles, heterocycloalkyls, heterocycloalkylamines, polyalkylamines, aminoalkylamines, ethers, esters, aldehydes, ketones, aryl groups, hydrazines, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, alcohols, and thiols; and

said unreactive functionality is selected from the group consisting of alkyl groups, polyamides, intercalators, and ethylene glycols.

72. The compound of claim 71 further having a phosphate group at the 3'"'"' position of the sugar analog, wherein said phosphate group may be a native phosphate or a modified phosphate.

73. The compound of claim 71 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety.

74. The compound of claim 74 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety; and

said modified phosphate is a methylphosphonate, phosphorothioate, phosphorodithioate, phosphoramidite, or phosphorotriester.

75. A compound having the formula:

##STR31## wherein;

G is N;

X is NHR₂ Q₁ wherein said R₂ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₁ comprises a reactive or non-reactive functionality;

Y is R₃ Q₂, or NHR₃ Q₂, wherein said R₃ is a hydrocarbyl group having from 1 to about 20 carbon atoms, and Q₂ comprises a reactive or non-reactive functionality;

W is H;

Z is H, a nitrogen protecting group, or Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"'3 position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

provided that where X is NHR₂ Q₁ and Y is NHR₃ Q₂, said nucleoside sugar moiety is not a 2'"'"'-fluoro arabinofuranosyl sugar moiety;

said reactive functionality is selected from the group consisting of halogens, heterocycles, heterocycloalkyls, heterocycloalkylamines, polyalkylamines, aminoalkylamines, ethers, esters, aldehydes, ketones, hydrazines, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, alcohols, and thiols; and

said unreactive functionality is selected from the group consisting of alkyl groups, polyamides, intercalators, and ethylene glycols.

76. The compound of claim 75 further having a phosphate group at the 3'"'"' position of the sugar analog, wherein said phosphate group may be a native phosphate or a modified phosphate.

77. The compound of claim 75 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety.

78. The compound of claim 75 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety; and

said modified phosphate is a methylphosphonate, phosphorothioate, phosphorodithioate, phosphoramidite, or phosphorotriester.

79. A cross-linked nucleic acid comprising:

a first oligonucleotide region and a second oligonucleotide region, wherein said first region includes at least one nucleotide of the formula;

##STR32## wherein;

G is CR₅ or N;

R₅ is H or a hydrocarbyl group having from 1 to 6 carbon atoms;

X is halogen NH₂, OH, NHR₆ Q₁, OR₆ Q₁, NHJ, OJ or SJ wherein said R₆ is H or a hydrocarbyl group having from 2 to about 20 carbon atoms;

Q₁ comprises at least one reactive or non-reactive functionality;

J comprises a space spanning group R₇ and an active functional group Q₄ ;

Y is halogen, NH₂, H, SH, OH, NHJ, OJ or SJ where J comprises a space spanning group R₇ and an active functional group Q₄ ;

W is H, NHK, OK or SK where K comprises a space spanning group R₇ and an active non-psoralen functional group Q₅ ;

Z is a ribose sugar analog or a deoxyribose sugar analog which bears at least one substituent at the 3'"'"' or 5'"'"' position of said deoxyribose sugar analog, or at the 2'"'"', 3'"'"', or 5'"'"' position of said ribose sugar analog;

said substituent being selected from the group consisting of O, H, lower alkyl, substituted lower alkyl, aralkyl, heteroaralkyl, heterocycloalkyl, amino-alkylamino, heterocycloalkyl, polyalkylamino, substituted silyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, SOMe, SO₂ Me, ONO₂, NO₂, N₃, NH₂, NH-alkyl, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO, and an RNA cleaving moiety;

said space spanning group R₇ is a hydrocarbyl group having from 2 to about 20 carbon atoms;

at least one of said X or Y groups is NHJ, OJ or SJ, or at least one of said W groups is NHK, OK or SK; and

said second region includes a second nucleotide of said formula capable of covalently bonding with said J group or said W group of said nucleotide of said formula in said first oligonucleotide region thereby forming a covalent cross-linkage between said first and said second oligonucleotide regions.

80. The cross-linked nucleic acid of claim 79 wherein G is N.

81. The cross linked nucleic acid of claim 79 having from 2 to 40 linked nucleotides.

82. The cross linked nucleic acid of claim 79 having from 2 to 18 linked nucleotides.

83. The cross linked nucleic acid of claim 79 wherein said Z bears a substituent selected from the group consisting of F, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, NH-alkyl, SOMe, SO₂ Me, OCH₂ CH═

CH₂, OCH═

CH₂, OCH₂ CCH, OCCH, OCCHO and an RNA cleaving moiety.