Nucleic acid binding compounds containing pyrazolo[3,4-d]pyrimidine analogues of purin-2,6-diamine and their uses

• US 7,238,795 B2
• Filed: 07/31/2001
• Issued: 07/03/2007
• Est. Priority Date: 08/03/2000
• Status: Expired due to Term

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: Roche Molecular Systems (Roche Holding AG)
• Inventors: Seidel, Christoph, Heindl, Dieter, Von Der Eltz, Herbert, Seela, Frank, Bergmann, Frank, Becher, Georg
• Primary Examiner(s): Wilson; James O.
• Assistant Examiner(s): Ward; Paul V.
• Application Number:
  US10/333,518
• Publication Number:
  US 20030198982A1
• Time in Patent Office: 2,163 Days
• Field of Search: 536/23.1, 536/24.3, 536/25.3, 536/26.6, 435/91.1, 435/6, 435/501
• US Class Current: 536/23.1
• CPC Class Codes: C07H 19/16 Purine 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: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention is in the field of nucleic acid binding compounds comprising 7-substituted 7-deaza-8aza-2,6-diamino-purine bases, compounds useful for the preparation of such compounds, various uses thereof and methods for the determination of nucleic acids using said compounds in the field of diagnostics.

Claims

1. A nucleic acid binding compound comprising a backbone, said backbone having attached one or more heterocyclic groups capable of base pairing to nucleobases, wherein at least one heterocyclic group is a group of formula I:

2. The nucleic acid binding compound according to claim 1, wherein said nucleic acid compound comprises one or more moieties of formula II:

3. The nucleic acid binding compound according to claim 1, wherein the backbone comprises a moiety of formula III, wherein t is 0 or 1,

4. The nucleic acid binding compound of claim 3, wherein t=0, R¹⁵ is —

H and R¹⁴ is —

H.

5. The nucleic acid binding compound according to claim 1, wherein said backbone comprises a moiety of the formula V

6. The compound of claim 5, wherein M′

is O, R¹⁶ is H and R¹⁴ is selected flow the group consisting of —

H and —

OH.

7. The nucleic acid binding compound according to claim 1, wherein the backbone comprises sugar and phosphate moieties.

8. The nucleic acid binding compound according to claim 7, wherein the sugar is in a locked conformation.

9. The nucleic acid binding compound according to claim 1, wherein the nucleic acid binding compound comprises a heterocyclic group which is a pyrrolo-[2,3-d]-pyrimidine, a pyrazolo[3,4-d]-pyrimidine or an analogue thereof.

10. The nucleic acid binding compound according to claim 1, wherein a protecting group substitutes one or two hydrogen atoms of a —

OH, —

SH, —

NH₂, —

NH-alkyl, —

NH-alkenylene, —

NH-alkynylene, or a NH-aryl group.

11. The nucleic acid binding compound according to claim 1, wherein said nucleic acid binding compound contains a reporter group.

12. The nucleic acid binding compound according to claim 11 wherein the heterocyclic group of formula I as defined in claim 1 is separated from the nucleotide to which the reporter group is attached by 1 to 5 nucleotides.

13. The nucleic acid binding compound according to claim 1, wherein a heterocyclic group is 7-bromo-7-deaza-8-aza-2,6,-diamino-purine or 7-iodo-7-deaza-8-aza-2,6-diamino-purine.

18. The binding product of a first nucleic acid binding compound according to claim 1, or a composition according to claim 15, with a second nucleic acid binding compound according to claim 1, wherein the first nucleic acid binding compound or the composition and the second nucleic acid binding compound are bound to each other by base pairing in parallel or antiparallel orientation.

19. A compound of formula VIII:

20. A compound of claim 19, wherein R¹⁴ is H and B is 7-bromo-7-deaza-8-aza-2,6-diaminopurine or 7-iodo-7-deaza-8-aza-2,6-diaminopurine.

21. A compound of formula VI:

22. A compound of formula VII:

23. A compound of formula IX:

24. A compound of formula X:

25. A precursor for the synthesis of a nucleic acid binding compound comprising a backbone, wherein the backbone comprises a moiety of the fonnula VI:

26. A precursor or intermediate of a nucleic acid binding compound, wherein the backbone comprises a moiety of formula III:

27. A precursor or intermediate compound comprising a backbone, said backbone having attached heterocyclic groups characterized in that a heterocyclic group is a group of the formula I:

28. A method for enzymatic synthesis of a nucleic acid binding compound, comprising reacting a triphosphate subunit with a primer using a nucleic acid as a template for the elongation of the primer, wherein the triphosphate subunit is a compound according to claim 19.

29. A method for the chemical synthesis of a compound using activated subunits, wherein said subunits contain a compound according to any one of claims 21 to 27.

30. A method according to claim 29 comprising the additional step of reacting the synthesized nucleic acid binding compound with a label.

14. A composition for analyzing interactions between nucleic acid binding compounds comprising an array of a plurality of nucleic acid binding compounds having different sequences, said plurality of nucleic acid binding compounds being coupled to a solid substrate at known locations and selected to bind to complementary nucleic acid binding compounds, wherein the nucleic acid binding compounds comprise a backbone, said backbone having attached heterocyclic groups capable of base pairing to nucleobases, and wherein at least one heterocyclic group is a 7-iodo- or 7-bromo-substituted pyrazolo[3,4-d]pyrimidine or an analogue thereof.

15. A composition according to claim 14 wherein the 7-iodo- or 7-bromo-substituted pyrazolo[3,4-d]pyrimidine analogue is a 7-iodo- or 7-bromo-pyrazolo[3,4-d]pyrimidine analogue of adenine or guanine, or a 7-iodo- or 7-bromo-substituted pyrazolo[3,4-d]pyrimidine analogue of adenine or guanine.

16. A composition according to claim 14, wherein said solid substrate is selected from the group consisting of silica, polymeric materials, glass, porous glass, beads, chips, and slides.

17. A composition according to claim 14, wherein said composition comprises an array of nucleic acid binding compounds 5 to 20 nucleotides in length.