Oligonucleotides containing 5-propynyl pyrimidines

• US 5,484,908 A
• Filed: 11/26/1991
• Issued: 01/16/1996
• Est. Priority Date: 11/26/1991
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: Gilead Sciences Inc.
• Inventors: Jones, Robert J., Froehler, Brian
• Primary Examiner(s): Robinson, Douglas W.
• Assistant Examiner(s): Kunz, Gary L.
• Application Number:
  US07/799,824
• Time in Patent Office: 1,512 Days
• Field of Search: 536/27, 536/23, 536/29, 536/28.52, 536/28.53, 536/24.3, 536/24.32, 536/24.5
• US Class Current: 536/24.31
• 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 19/20 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 1/6839 Triple helix formation or other higher order conformations in hybridisation assays
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine

Abstract

Oligonucleotides with enhanced hybridization binding possessing 5-propynyluracil and/or 5-propynylcytosine in place of uracil and cytosine, respectively. These oligonucleotides are useful in traditional hybridization assays for detection of a specific DNA sequence.

Claims

1. A nucleoside analog having the general structural formula:

##STR14## wherein in each of formula 4 and formula 5 one R¹ is a protecting group and the other is an activated group for oligonucleotide synthesis or is a solid support;

R² is selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl, o-pyridinyl, m-pyridinyl and p-pyridinyl; and

R³ is selected from the group consisting of H, OH, F, OCH₃, OC₂ H₅, OC₃ H₇, SCH₃, SC₂ H₅, SC₃ H₇, OC₃ H₅, and SC₃ H₅.

2. The nucleoside analog of claim 1, wherein the protecting group is DMT (dimethoxytrityl) or MMT (monomethoxytrityl).

3. The nucleoside analog of claim 1 wherein R³ is H or OH.

4. The nucleoside analog of claim 1 wherein R² is propynyl.

5. The nucleoside analog of claim 1 wherein the nucleoside is an α

anomer.

13. The nucleoside analog of claim 1 wherein the activated group is H-phosphonate, methyl phosphonate, methylphosphoramidite or β

-cyanoethylphosphoramidite.

14. The nucleoside analog of claim 1 wherein R¹ at the 5'"'"' position is DMT (dimethoxytrityl) or MMT (monomethoxytrityl);

R¹ at the 3'"'"' position is H-phosphonate, β

-cyanoethylphosphoramidite or methylphosphoramidite;

R² is propynyl or 3-methyl-1-butynyl; and

R³ is H.

6. An o-xyloso nucleoside dimer having the general structural formula:

##STR15## wherein each R¹ is H or a blocking group; and

each B is independently a purine or pyrimidine base, provided that at least one B is ##STR16## wherein R² is selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl, o-pyridinyl, m-pyridinyl and p-pyridinyl.

7. The nucleoside dimer of claim 6 wherein R² is propynyl.

8. The nucleoside dimer of claim 7 wherein the blocking group is selected from the group consisting of PO₃^-2, DMT MMT H-phosphonate, methyl phosphonate, methylphosphoramidite, or β

-cyanoethylphosphoramidite.

15. The dimer of claim 6 wherein one of R¹ is a protecting group and the other of R¹ is an activated group for oligonucleotide synthesis or is a solid support.

16. The dimer of claim 15 wherein the activated group is H-phosphonate, methyl phosphonate, methylphosphoramidite or β

-cyanoethylphosphoramidite.

9. A nucleoside analog dimer having the general structural formula 8:

##STR17## wherein X is selected from the group consisting of O and S;

B is independently a purine or pyrimidine base, provided that at least one B is ##STR18## wherein each R¹ is independently selected from the group consisting of H and a blocking group;

each R² is independently selected from the group consisting of propynyl, 3-buten-1-ynyl, 3-methyl-1-butynyl, 3,3-dimethyl-1-butynyl, propenyl, phenyl o-pyridinyl, m-pryridinyl and p-pyridinyl; and

each R³ is independently selected from the group consisting of H, OH, F, OCH₃, OC₂ H₅, OC₃ H₇, SCH₃, SC₂ H₅, SC₃ H₇, OC₃ H₅, or SC₃ H₅.

10. The dimer of claim 9 wherein R¹ is H, PO₃^-2, DMT, MMT, H-phosphonate, methylphosphoramidite or β

-cyanoethylphosphoramidite.

11. The dimer of claim 9 wherein at least one B is 5-propynyluracil, 3-methyl-1-butynyluracil or 5-propynylcytosine.

12. The dimer of claim 9 wherein at least one R² is propynyl, R³ is OC₃ H₅ and X is S.

17. The dimer of claim 9 wherein one of R¹ is a protecting group and the other of R¹ is an activated group for oligonucleotide synthesis or is a solid support.

18. The dimer of claim 17 wherein the activated group is H-phosphonate, methyl phosphonate, methylphosphoramidite or β

-cyanoethylphosphoramidite.