Processes for the production of oligonucleotides

• US 10,640,812 B2
• Filed: 07/07/2017
• Issued: 05/05/2020
• Est. Priority Date: 07/11/2016
• Status: Active Grant

• Current Assignee: GlaxoSmithKline Intellectual Property Development Limited (Glaxosmithkline Holdings Ltd.)
• Original Assignee: GlaxoSmithKline Intellectual Property Development Limited (Glaxosmithkline Holdings Ltd.)
• Inventors: Crameri, Andreas, Hill, Malcolm Leithhead, Tew, David Graham
• Primary Examiner(s): Leith, Nancy J
• Application Number:
  US15/643,535
• Publication Number:
  US 20180023122A1
• Time in Patent Office: 1,033 Days
• Field of Search: None
• CPC Class Codes: C07H 1/00 Processes for the preparation of sugar derivatives
• 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: C07K 2319/20 containing a tag with affinity for a non-protein ligand
• CPC Class Codes: C12N 9/93 Ligases (6)
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Y 605/01001 DNA ligase (ATP) (6.5.1.1)
• CPC Class Codes: G01N 2030/027 Liquid chromatography

Abstract

Disclosed herein are novel processes for the production of oligonucleotides that are suitable for use in the production of chemically modified oligonucleotides, such as those for use in therapy.

Claims

1. A process for producing a single stranded oligonucleotide product having a least one modified nucleotide residue, wherein the modification is chosen from:

modification at the 2′

position of the sugar moiety of the nucleotide residue, modification of the nucleobase of the nucleotide residue, and modification of the backbone of the nucleotide residue, and wherein the product is produced at gram scale, or greater, comprising;

a) providing a template oligonucleotide (I) complimentary to the sequence of the product, said template is attached to a soluble support material having a property that allows it to be separated from the product;

b) providing a pool of oligonucleotides (II) containing oligonucleotides that are segments of the product sequence, wherein at least one segment contains at least one modified nucleotide residue, and wherein the modification is chosen from;

modification at the 2′

position of the sugar moiety of the nucleotide residue, modification of the nucleobase of the nucleotide residue, and modification of the backbone of the nucleotide residue;

c) contacting (I) and (II) in conditions to allow annealing of the template to the segments of the product sequence;

d) joining the oligonucleotides that are segments of the product sequence by enzymatic ligation with a ligase to form the product;

e) changing the conditions to separate any impurities, comprising denaturing the annealed template and impurity oligonucleotide strands and separating the impurities;

f) changing the conditions to separate the product, comprising denaturing the annealed template and product oligonucleotide strands and separating the product; and

g) recycling the template for use in future reactions.

2. The process as claimed in claim 1, whereby the denaturing results from a factor chosen from:

a temperature increase;

a change in pH; and

a change in salt concentration in a buffering solution.

3. The process as claimed in claim 2, including two steps of increasing the temperature:

i) to denature any annealed impurities; and

ii) to denature the annealed product.

4. The process as claimed in claim 1, wherein the segments are 3 to 15 nucleotides long.

5. The process as claimed in claim 1, wherein the product is a length chosen from:

10 to 200 nucleotides;

20 to 30 nucleotides; and

20 to 25 nucleotides.

6. The process as claimed in claim 5, wherein said product is 20 nucleotides long, said product comprising three segment oligonucleotides:

(i) a 5′

segment that is 7 nucleotides long, a central segment that is 6 nucleotides long and a 3′

segment that is 7 nucleotides long;

(ii) a 5′

segment that is 6 nucleotides long, a central segment that is 8 nucleotides long and a 3′

segment that is 6 nucleotides long;

or

(iii) a 5′

segment that is 5 nucleotides long, a central segment that is 10 nucleotides long and a 3′

segment that is 5 nucleotides long.

7. The process as claimed in claim 1, wherein multiple, repeated copies of the template are attached via a single attachment point to the support material.

8. The process as claimed in claim 1, wherein the property that allows the template to be separated from the product is the molecular weight of the template.

9. The process as claimed in claim 1, wherein the process is carried out using a flow process chosen from:

a continuous flow process; and

a semi-continuous flow process.

10. The process as claimed in claim 1, wherein the single stranded oligonucleotide product has a purity chosen from:

at least 90% pure;

at least 95% pure; and

at least 98% pure.

11. The process claimed in claim 1, wherein the process produces a therapeutic oligonucleotide.

12. The process as claimed in claim 1, wherein the soluble support material is chosen from:

polyethylene glycol, a soluble organic polymer, DNA, a protein, a dendrimer, a polysaccharide, an oligosaccharide, and a carbohydrate.

13. The process as claimed in claim 1, wherein the oligonucleotide comprises a phosphorodiamidate morpholino oligomer (PMO), a locked nucleic acid (LNA), a peptide nucleic acid (PNA), a bridged nucleic acid (BNA), or a SPIEGELMER.

14. The process as claimed in claim 1, wherein the modification in the nucleobase is chosen from:

5-methyl pyrimidine, a 7-deazaguanosine, and an abasic nucleotide.

15. The process as claimed in claim 1, wherein the modification in the backbone is chosen from:

phosphorothioate, phosphoramidate and phosphorodiamidate.

16. A process for producing a double stranded oligonucleotide product, wherein 2 complimentary single stranded oligonucleotides are produced by the method of claim 1, and then mixed under conditions to allow annealing.