Targeted gene correction by single-stranded oligodeoxynucleotides

• US 20020119570A1
• Filed: 09/25/2001
• Published: 08/29/2002
• Est. Priority Date: 09/25/2000
• Status: Abandoned Application

• Current Assignee: Thomas Jefferson University (Main Line Health System)
• Original Assignee: Thomas Jefferson University (Main Line Health System)
• Inventors: Yoon, Kyonggeun, Igoucheva, Olga
• Application Number:
  US09/962,628
• Publication Number:
  US 20020119570A1
• Time in Patent Office: Days
• US Class Current: 435/455
• CPC Class Codes: C12N 15/102 Mutagenizing nucleic acids

Abstract

The present invention relates to using single-stranded oligonucleotides that are designed to specifically change a base in a target nucleic acid sequence. This alteration is maintained, expressed and regulated as the normal endogenous gene.

Claims

1. A method of targeting and modifying, by mismatch repair, a pre-selected target nucleic acid, wherein a single-stranded oligonucleotide contains a mismatch to a targeted base in said pre-selected target nucleic acid, comprising:

a) administering said single-stranded oligonucleotide to a cell;

b) base pairing of said single-stranded oligonucleotide to said pre-selected target nucleic acid; and

c) incorporating said mismatch into said target nucleic acid.

2. The method of claim 1, wherein said single-stranded DNA oligonucleotide is complementary to either strand of said target nucleic acid with the exception of a nucleotide mismatch.

3. The method of claim 1, wherein said single-stranded DNA oligonucleotide comprises deoxynucleotide residues having a base modification, a 3′

and/or 5′

end modification, a backbone modification or a sugar modification.

4. The method of claim 3, wherein said base modification comprises a modification of pyrimidines and/or purines, said modification selected from the group of consisting of:

5-fluoro-2′

-deoxyuridine, 5-bromo-2′

-deoxyuridine, 5-methyl-2′

-deoxycytidine, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo, 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine.

5. The method of claim 3, wherein said 3′

and/or 5′

end modification is at least one of the group of 2′

-O-methyl bases, 3′

amine groups, phosphothioates, or any modified base which is nuclease resistant.

6. The method of claim 3, wherein said backbone modification is one of the group of phophorothioates, phosphoramidites, methylphosphonates, and modifications with nonphosphate internucleotide bonds, said nonphosphate internucleotide bonds selected from the group consisting of carbonates, carbamates, siloxanes, sulfonamides and polyamides.

7. The method of claim 3, wherein said sugar modifications are chosen from the group of 2′

-O-methyl RNA, 2′

-fluoro RNA and 2′

-methoxyethoxy RNA.

8. A method of treating a genetic disorder, or other condition wherein an alteration of a target DNA sequence is desired, comprising:

a) administering to a mammal a therapeutically effective amount of an oligonucleotide;

b) base pairing of said oligonucleotide to said target DNA sequence, with the exception of a mismatch to a targeted base in said targeted DNA sequence; and

c) incorporating said mismatch into said targeted DNA sequence in a sequence-specific manner.

9. A method of targeting and modifying, by mismatch repair, a pre-selected target nucleic acid in a stem cell, wherein a single-stranded oligonucleotide contains a mismatch to a targeted base in said pre-selected target nucleic acid, comprising:

a) administering said single-stranded oligonucleotide to said stem cell;

b) base pairing of said single-stranded oligonucleotide to said pre-selected target nucleic acid; and

b) incorporating said mismatch into said target nucleic acid.

10.he. The method of claim 9, wherein said single-stranded DNA oligonucleotide is complementary to either strand of said target nucleic acid with the exception of a nucleotide mismatch.

11.he. The method of claim 9, wherein said single-stranded DNA oligonucleotide comprises deoxynucleotide residues having a base modification, a 3′

and/or 5′

end modification, a backbone modification or a sugar modification.

12.he. The method of claim 11, wherein said base modification comprises a modification at the 5-position of pyrimidines, said modification selected from the group of consisting of:

5-fluoro-2′

-deoxyuridine, 5-bromo-2′

-deoxyuridine and 5-methyl-2′

-deoxycytidine.

13.he. The method of claim 11, wherein said 3′

and/or 5′

end modification is at least one of the group of 2′

-O-methyl bases, 3′

amine groups, phosphothioates, or any modified base which is nuclease resistant.

14.he. The method of claim 11, wherein said backbone modification is one of the group of phophorothioates, phosphoramidites, methylphosphonates, and modifications with nonphosphate internucleotide bonds, said nonphosphate internucleotide bonds selected from the group consisting of carbonates, carbamates, siloxanes, sulfonamides and polyamides.

15. The method of claim 11, wherein said sugar modifications are chosen from the group of 2′

-O-methyl RNA, 2′

-fluoro RNA and 2′

-methoxyethoxy RNA.

16. A method of targeting and modifying, by mismatch repair, a pre-selected target nucleic acid in a skin cell, wherein a single-stranded oligonucleotide contains a mismatch to a targeted base in said pre-selected target nucleic acid, comprising:

a) administering said single-stranded oligonucleotide to said skin;

b) base pairing of said single-stranded oligonucleotide to said pre-selected target nucleic acid in a cell in said skin; and

b) incorporating said mismatch into said target nucleic acid.

17.he. The method of claim 16, wherein said single-stranded DNA oligonucleotide is complementary to either strand of said target nucleic acid with the exception of a nucleotide mismatch.

18.he. The method of claim 16, wherein said single-stranded DNA oligonucleotide comprises deoxynucleotide residues having a base modification, a 3′

and/or 5′

end modification, a backbone modification or a sugar modification.

19.he. The method of claim 18, wherein said base modification comprises a modification at the 5-position of pyrimidines, said modification selected from the group of consisting of:

5-fluoro-2′

-deoxyuridine, 5-bromo-2′

-deoxyuridine and 5-methyl-2′

-deoxycytidine.

20.he. The method of claim 18, wherein said 3′

and/or 5′

end modification is at least one of the group of 2′

-O-methyl bases, 3′

amine groups, phosphothioates, or any modified base which is nuclease resistant.

21.he. The method of claim 18, wherein said backbone modification is one of the group of phophorothioates, phosphoramidites, methylphosphonates, and modifications with nonphosphate internucleotide bonds, said nonphosphate internucleotide bonds selected from the group consisting of carbonates, carbamates, siloxanes, sulfonamides and polyamides.

22. The method of claim 18, wherein said sugar modifications are chosen from the group of 2′

-O-methyl RNA, 2′

-fluoro RNA and 2′

-methoxyethoxy RNA.