Stabilized nucleic acid dark quencher-fluorophore probes

• US 8,466,266 B2
• Filed: 04/01/2009
• Issued: 06/18/2013
• Est. Priority Date: 04/01/2008
• Status: Active Grant

• Current Assignee: HSB Corporate Trust Company (UK) Limited
• Original Assignee: Biosearch Technologies Incorporated
• Inventors: Cook, Ronald M., Lyttle, Matt
• Primary Examiner(s): SAEED, KAMAL A
• Application Number:
  US12/416,901
• Publication Number:
  US 20090259030A1
• Time in Patent Office: 1,539 Days
• Field of Search: None
• US Class Current: 534/816
• CPC Class Codes: C07D 219/04 with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to carbon atoms of the ring system
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/073 with 2-deoxyribosyl as the saccharide radical
• CPC Class Codes: C09B 31/02 Disazo dyes
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes

Abstract

The present invention provides a new class of solids supports for synthesis of modified oligomers of nucleic acids, and nucleic acid probes that have a format expediently synthesized on the new supports. Exemplary solid supports include at least one quencher bound through a linker to the solid support. Various exemplary embodiments include a moiety that stabilizes a duplex, triplex or higher order aggregation (e.g., hybridization) of nucleic acids of which the oligomer of the invention is a component. Other components of the solid support include moieties that stabilize aggregations of nucleic acids, e.g., intercalators, minor groove binding moieties, bases modified with a stabilizing moiety (e.g., alkynyl moieties, and fluoroalkyl moieties), and conformational stabilizing moieties, such as those described in commonly owned U.S. Patent Application Publication No. 2007/0059752.

Claims

1. A compound of a structure according to Formula I:

2. The compound according to claim 1, wherein R^b is fluoroalkyl and R^c is a phosphorus-containing linker covalently bound to a nucleic acid.

3. The compound according to claim 1, wherein said quencher is of a structure according to Formula (II)

4. The compound according to claim 3, wherein said quencher is of a structure according to Formula (III):

5. The compound according to claim 3, wherein a member selected from R¹, R² and R³ includes a structure according to Formula IV:

6. The compound according to claim 1, wherein said quencher is of a structure according to Formula V:

7. The compound according to claim 1, wherein said quencher is of a structure according to Formula VI:

8. The compound according to claim 7, wherein said quencher is of a structure according to the formula:

9. The compound according to claim 1, wherein said quencher is of a structure which is a member selected from:

10. The compound according to claim 1, wherein said compound is of a structure according to Formula VII:

11. The compound according to claim 10, wherein said compound is of a structure according to Formula VIII:

12. The compound according to claim 1, wherein Z^a is a solid support and L²-Z^a comprises a structure according to Formula IX:

13. The compound according to claim 1, wherein said nucleic acid comprises a base of a formula selected from:

15. The compound according to claim 1, wherein X^a is a member selected from intercalating agents and minor groove binders.

16. The compound according to claim 15, wherein said intercalating agent is a member selected from acridines, anthracenes, anthracyclines, anthracyclinone, methylene blue, indole, anthraquinone, quinoline, isoquinoline, dihydroquinones, tetracyclines, psoralens, coumarins, ethidium halides, ethidium homodimers, homodimeric oxazole yellow (YOYO), thiazole orange (TOTO), dynemicins, 1,10-phenanthroline-copper, calcheamicin, porphyrins, distamycins, netropcins, and viologens.

17. The compound according to claim 16, wherein said intercalating agent is acridine.

18. The compound according to claim 1, wherein said nucleic acid is a probe.

19. The compound according to claim 18, wherein said probe is selected from molecular beacons, scorpion probes, sunrise probes, conformationally assisted probes, light up probes, invader detection probes, and taqman probes.

20. The compound according to claim 1, wherein Z^a is a solid support.

21. The compound according to claim 1, wherein said compound is of the structure:

14. A nucleic acid comprising at least one base of a formula selected from: