Modified nucleotides

• US 8,597,881 B2
• Filed: 10/25/2011
• Issued: 12/03/2013
• Est. Priority Date: 12/23/2002
• Status: Expired due to Term

• Current Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Inventors: Milton, John, Wu, Xiaolin, Smith, Mark, Brennan, Joseph, Barnes, Colin, Liu, Xiaohai, Ruediger, Silke
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US13/281,275
• Publication Number:
  US 20120095201A1
• Time in Patent Office: 770 Days
• Field of Search: 435/6, 536/26.6
• US Class Current: 435/6.1
• CPC Class Codes: C07H 1/00 Processes for the preparation of sugar derivatives
• CPC Class Codes: C07H 19/00 Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
• 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 19/14 Pyrrolo-pyrimidine radicals
• 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: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Provided herein is a method for replacing the allyl group in a compound of formula R—O-allyl, R₂N(allyl), RNH(allyl), RN(allyl)₂ or R—S-allyl with a hydrogen, using a transition metal and one or more phosphine ligands.

Claims

1. A method of converting a compound of formula R—

O-allyl, R₂N(allyl), RNH(allyl), RN(allyl)₂ or R—

S-allyl to a corresponding compound in which the allyl group is removed and replaced by hydrogen, said method comprising the steps of reacting a compound of formula R—

O-allyl, R₂N(allyl), RNH(allyl), RN(allyl)₂ or R—

S-allyl in aqueous solution with a transition metal comprising a transition metal and one or more ligands selected from the group comprising water-soluble phosphine and water-soluble nitrogen-containing phosphine ligands, wherein the or each R is a water-soluble biological molecule, which is part of a nucleoside, a nucleotide or a polynucleotide molecule, wherein said nucleoside, nucleotide or polynucleotide further comprises a detectable label linked to the base thereof by a cleavable or non-cleavable linker.

2. The method of claim 1 wherein said linker is cleavable.

3. The method of claim 1 wherein said detectable label is a fluorophore.

4. The method of claim 1 wherein said linker is acid labile, photolabile or contains a disulfide linkage.

5. The method of claim 1 wherein said allyl group and said label are removed in a single step.

6. The method of claim 1 wherein said transition metal is selected from the group comprising platinum, palladium, rhodium, ruthenium, osmium and iridium.

7. The method of claim 1 wherein said transition metal is palladium.

8. The method of claim 1 wherein said group of ligands comprise derivatised triaryl phosphine ligands or derivatised trialkyl phosphine ligands.

9. The method of claim 1 wherein said group of ligands are derivatised with one or more functionalities selected from the group comprising amino, hydroxyl, carboxyl and sulfonate groups.

10. The method of claim 1 wherein the group of ligands comprises 3,3′

,3″

-phosphinidynetris (benzenesulfonic acid) and tris(2-carboxyethyl)phosphines and their salts.

11. A method of converting a compound of formula R—

O-allyl to a corresponding compound in which the allyl group is removed and replaced by hydrogen, said method comprising the steps of reacting a compound of formula R—

O-allyl in aqueous solution with a transition metal comprising a transition metal and one or more ligands selected from the group comprising water-soluble phosphine and water-soluble nitrogen-containing phosphine ligands, wherein the R is a water-soluble biological molecule, which is part of a nucleoside, a nucleotide or a polynucleotide molecule, wherein said nucleoside, nucleotide or polynucleotide further comprises a detectable label linked to the base thereof by a cleavable or non-cleavable linker.

12. A method of converting a compound of formula R₂N(allyl) to a corresponding compound in which the allyl group is removed and replaced by hydrogen, said method comprising the steps of reacting a compound of formula R₂N(allyl) in aqueous solution with a transition metal comprising a transition metal and one or more ligands selected from the group comprising water-soluble phosphine and water-soluble nitrogen-containing phosphine ligands, wherein each R is independently a water-soluble biological molecule, which is part of a nucleoside, a nucleotide or a polynucleotide molecule, wherein said nucleoside, nucleotide or polynucleotide further comprises a detectable label linked to the base thereof by a cleavable or non-cleavable linker.

13. A method of converting a compound of formula RNH(allyl) to a corresponding compound in which the allyl group is removed and replaced by hydrogen, said method comprising the steps of reacting a compound of formula RNH(allyl) in aqueous solution with a transition metal comprising a transition metal and one or more ligands selected from the group comprising water-soluble phosphine and water-soluble nitrogen-containing phosphine ligands, wherein the R is a water-soluble biological molecule, which is part of a nucleoside, a nucleotide or a polynucleotide molecule, wherein said nucleoside, nucleotide or polynucleotide further comprises a detectable label linked to the base thereof by a cleavable or non-cleavable linker.

14. A method of converting a compound of formula RN(allyl)₂ to a corresponding compound in which the allyl group is removed and replaced by hydrogen, said method comprising the steps of reacting a compound of formula RN(allyl)₂ in aqueous solution with a transition metal comprising a transition metal and one or more ligands selected from the group comprising water-soluble phosphine and water-soluble nitrogen-containing phosphine ligands, wherein the R is a water-soluble biological molecule, which is part of a nucleoside, a nucleotide or a polynucleotide molecule, wherein said nucleoside, nucleotide or polynucleotide further comprises a detectable label linked to the base thereof by a cleavable or non-cleavable linker.

15. A method of converting a compound of formula R—

S-allyl to a corresponding compound in which the allyl group is removed and replaced by hydrogen, said method comprising the steps of reacting a compound of formula R—

S-allyl in aqueous solution with a transition metal comprising a transition metal and one or more ligands selected from the group comprising water-soluble phosphine and water-soluble nitrogen-containing phosphine ligands, wherein the R is a water-soluble biological molecule, which is part of a nucleoside, a nucleotide or a polynucleotide molecule, wherein said nucleoside, nucleotide or polynucleotide further comprises a detectable label linked to the base thereof by a cleavable or non-cleavable linker.