Cyclobutyl oligonucleotide surrogates

• US 5,359,044 A
• Filed: 12/13/1991
• Issued: 10/25/1994
• Est. Priority Date: 12/13/1991
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated, Novartis Ag
• Original Assignee: CIBA Vision Corporation (Bayer AG), ISIS Pharmaceuticals Incorporated
• Inventors: Cook, Phillip D., Baschang, Gerhard
• Primary Examiner(s): YARBROUGH, AMELIA
• Application Number:
  US07/808,201
• Time in Patent Office: 1,047 Days
• Field of Search: 544/234, 544/244, 544/242, 544/245, 536/27, 536/23.1, 536/24.31, 536/24.32, 435/6
• US Class Current: 536/23.1
• CPC Class Codes: C07C 2601/04 with a four-membered ring
• CPC Class Codes: C07C 43/196 containing hydroxy or O-metal groups
• CPC Class Codes: C07D 319/08 condensed with carbocyclic rings or ring systems
• CPC Class Codes: C07D 473/00 Heterocyclic compounds containing purine ring systems
• 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

Abstract

Oligonucleotide surrogates comprising a plurality of cyclobutyl moieties covalently joined by linking moieties are prepared and used as antisense diagnostics and research reagents. Methods of synthesis and use of both the oligonucleotide surrogates and intermediates thereof are disclosed.

Claims

1. An oligonucleotide surrogate comprising at least two cyclobutyl moieties wherein each of said cyclobutyl moieties include a purine or pyrimidine heterocyclic base attached at a C-1 cyclobutyl position and wherein said cyclobutyl moieties are joined through a C-2, C-3, or C-4 position on a first of said cyclobutyl moieties and a C-2, C-3, or C-4 position on a second of said cyclobutyl moieties by a linkage that contains 4 or 5 consecutive, covalently-bound atoms selected from the group consisting of C, N, O, S, Si and P.

2. An oligonucleotide surrogate of claim 1 wherein said purine or pyrimidine heterocyclic base is a naturally-occurring or synthetic purin-9-yl, pyrimidin-1-yl or pyrimidin-3-yl heterocyclic base.

3. An oligonucleotide surrogate of claim 2 wherein said purine or pyrimidine heterocyclic base is adenine, guanine, cytosine, thymine, uracil, 5-methylcytosine, hypoxanthine or 2-aminoadenine.

4. An oligonucleotide surrogate of claim 1 wherein each of said linkages connects two of the cyclobutyl moieties at a C-3 position of the cyclobutyl moieties.

5. An oligonucleotide surrogate of claim 1 wherein each of said linkages comprises a linkage that is 5 atoms long that joins two of the cyclobutyl moieties.

6. An oligonucleotide surrogate of claim 5 wherein each of said linkages is of the structure:

space="preserve" listing-type="equation">L.sub.1 -L.sub.2 -L.sub.3

wherein;

L₁ and L₃ are CH₂ ; and

L₂ is phosphodiester, phosphorothioate, phosphoramidate, phosphotriester, C₁ -C₆ alkyl phosphonate, phosphorodithioate, phosphonate, carbamate, sulfonate, C₁ -C₆ -dialkylsilyl or formacetal.

7. An oligonucleotide surrogate of claim 5 wherein each of said linkages is of the structure:

space="preserve" listing-type="equation">L.sub.1 -L.sub.2 -L.sub.3

where;

L₁ and L₃ are CH₂ ; and

L₂ is phosphodiester or phosphorothioate.

8. An oligonucleotide surrogate of claim 1 wherein each of said linkages comprises a linkage that is 4 atoms long that joins two of the cyclobutyl moieties.

9. An oligonucleotide surrogate of claim 8 wherein each of said linkages is of the structure:

space="preserve" listing-type="equation">L.sub.4 -L.sub.5 -L.sub.6 -L.sub.7

where;

(a) L₄ and L₇ are CH₂ ; and

L₅ and L₆, independently, are CR₁ R₂, C═

CR₁ R₂, C═

NR₃, C═

O, C═

S, O, S, SO, SO₂, NR₃ or SiR₄ R₅ ;

or

(b) L₄ and L₇ are CH₂ ; and

L₅ and L₆, together, are CR₁ ═

CR₂, C.tbd.C, part of a C₆ aromatic ring, part of a C₃ -C₆ carbocyclic ring or part of a 3, 4, 5 or 6 membered heterocyclic ring;

or

(c) L₄ -L₅ -L₆ -L₇, together, are CH═

N--NH--CH₂ or CH₂ --O--N═

CH;

where;

R₁ and R₂, independently, are H, OH, SH, NH₂, C₁ -C₁₀ alkyl, C₁ -C₁₀ substituted alkyl, C₁ -C₁₀ alkenyl, C₇ -C₁₀ aralkyl, C₁ -C₆ alkoxy, C₁ -C₆ thioalkoxy, C₁ -C₆ alkylamino, C₇ -C₁₀ aralkylamino, C₁ -C₁₀ substituted alkylamino, heterocycloalkyl, heterocycloalkylamino, aminoalkylamino, polyalkylamino, halo, formyl, keto, benzoxy, carboxamido, thiocarboxamido, ester, thioester, carboxamidino, carbamyl, ureido, guanidino, or an RNA cleaving group;

R₃ is H, OH, NH₂, C₁ -C₆ alkyl, substituted lower alkyl, alkoxy, lower alkenyl, aralkyl, alkylamino, aralkylamino, substituted alkylamino, heterocycloalkyl, heterocycloalkylamino, aminoalkylamino, polyalkylamino, or a RNA cleaving group; and

R₄ and R₅, independently, are C₁ -C₆ alkyl or alkoxy.

10. An oligonucleotide surrogate compound of claim 8 wherein each of said linkages is CH═

N--NH--CH₂, CH₂ NH--NH--CH₂, CH₂ -O--NH--CH₂ or CH₂ --O--N═

CH.

11. An oligonucleotide surrogate of claim 4 further including a substituent group attached to at least one of the cyclobutyl moieties at a C-2 position or a C-4 position of the cyclobutyl moieties.

12. An oligonucleotide surrogate of claim 11 wherein said substituent group is halogen, C₁ -C₁₀ alkoxy, allyloxy, C₁ -C₁₀ alkyl or C₁ -C₁₀ alkylamine.

13. An oligonucleotide surrogate of claim 12 wherein said substituent group is positioned trans to said heterocyclic base.