Compounds for protecting hydroxyls and methods for their use

• US 6,639,088 B2
• Filed: 09/12/2001
• Issued: 10/28/2003
• Est. Priority Date: 10/05/1999
• Status: Expired due to Term

• Current Assignee: Fluidigm Corporation
• Original Assignee: Quiatech AB (Quiapeg Pharmaceuticals Holding AB)
• Inventors: Kwiatkowski, Marek
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/952,719
• Publication Number:
  US 20020015961A1
• Time in Patent Office: 776 Days
• Field of Search: 435/6, 536/22.1, 536/23.1, 554/6, 554/85, 554/101, 554/102
• US Class Current: 554/6
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2563/107 fluorescence

Abstract

A hydrocarbyldithiomethyl-modified compound of the Formula:

R¹—O—CH₂—S—S—R²

or a salt thereof wherein R¹ is an organic molecule and R² is a hydrocarbyl is useful for protecting and/or blocking hydroxyl groups in organic molecules such as nucleotides. The hydrocarbyldithiomethyl-modified compounds can also be used for chemically synthesizing oligonucleotides and for sequencing nucleic acid compounds.

Claims

1. A hydrocarbyldithiomethyl-modified compound comprising the formula:

or a salt thereof, wherein

R¹ is an organic molecule;

R¹, R², and R⁴ are together or separately H, hydrocarbyl, or a residue of a solid support; and

said R² comprises a fluorescent labeling group.

2. The compound of claim 1 wherein said fluorescent labeling group is selected from the group consisting of bodipy, dansyl, fluorescein, rhodamin, Texas red, Cy 2, Cy 4, and Cy 6.

3. A hydrocarbyldithiomethyl-modified compound comprising the formula:

or a salt thereof, wherein

R¹ is an organic molecule further comprising at least one hydroxyl group that is not hydrocarbyldithiomethyl-modified; and

R², R³, and R⁴ are together or separately H, hydrocarbyl, or a residue of a solid support.

4. A hydrocarbyldithiomethyl-modified compound comprising the formula:

or a salt thereof,

wherein said R¹ is selected from the group consisting of modified or unmodified amino acids, peptides, proteins, carbohydrates, sterols, and steroids; and

R², R³, and R⁴ are together or separately H, hydrocarbyl, or a residue of a solid support.

5. The compound of claim 4 wherein said R² comprises a labeling group.

6. The compound of claim 4 wherein said R¹ further comprises at least one hydroxyl group that is not hydrocarbyldithiomethyl-modified.

7. The compound of claim 4, wherein R¹ is a modified amino acid.

8. The compound of claim 4, wherein R¹ is an unmodified amino acid.

9. The compound of claim 4, wherein R¹ is a peptide.

10. The compound of claim 4, wherein R¹ is a protein.

11. The compound of claim 4, wherein R¹ is a carbohydrate.

12. The compound of claim 4, wherein R¹ is a steroid.

13. The compound of claim 4, wherein R¹ is a steroid.

25. The compound of claim 11 wherein R¹ is a modified carbohydrate, said modified carbohydrate selected from the group consisting of oligonucleotides, ribonucleosides, ribonucleotides, base- and/or sugar-modified ribonucleosides, base- and/or sugar-modified ribonucleotides, deoxyribonucleosides, deoxyribonucleotides, base- and/or sugar-modified deoxyribonucleosides, and base- and/or sugar-modified deoxyribonucleotides.

14. A hydrocarbyldithiomethyl-modified compound comprising the Formula:

15. The compound of claim 14 wherein said R² comprises a fluorescent labeling group.

16. The compound of claim 15, wherein said fluorescent labeling group is selected from the group consisting of bodipy, dansyl, fluorescein, rhodamin, Texas red, Cy 2, Cy 4, and Cy 6.

17. The compound of claim 14, wherein said R² further comprises at least one hydroxyl group that is not hydrocarbyldithiomethyl-modified.

18. The compound of claim 14, wherein said organic molecule is a modified amino acid.

19. The compound of claim 14, wherein said organic molecule is an unmodified amino acid.

20. The compound of claim 14, wherein said organic molecule is a peptide.

21. The compound of claim 14, wherein said organic molecule is a protein.

22. The compound of claim 14, wherein said organic molecule is a carbohydrate.

23. The compound of claim 14, wherein said organic molecule is a sterol.

24. The compound of claim 14, wherein said organic molecule is a steroid.

26. The compound of claim 24 wherein R¹ is a modified carbohydrate, said modified carbohydrate selected from the group consisting of oligonucleotides, ribonucleosides, ribonucleotides, base- and/or sugar-modified ribonucleosides, base- and/or sugar-modified ribonucleotides, deoxyribonucleosides, deoxyribonucleotides, base- and/or sugar-modified deoxyribonucleosides, and base- and/or sugar-modified deoxyribonucleotides.