Enhanced triple-helix and double-helix formation directed by oligonucleotides containing modified pyrimidines

• US 6,235,887 B1
• Filed: 11/14/1994
• Issued: 05/22/2001
• Est. Priority Date: 11/26/1991
• Status: Expired due to Term

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Jones, Robert J., Froehler, Brian
• Primary Examiner(s): McElwain, Elizabeth F.
• Application Number:
  US08/338,352
• Time in Patent Office: 2,381 Days
• Field of Search: 536/23.1, 536/24.3, 536/26.1, 536/18.7, 536/22.1, 536/24.33, 536/26.8, 514/43, 514/44
• US Class Current: 536/23.1
• 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

Novel oligomers are disclosed which have enhanced ability with respect to forming duplexes or triplexes compared with oligomers containing only conventional bases. The oligomers contain the base analog 5-propynyluracil, 5-propynylcytosine or related analogs. The oligomers of the invention are capable of (i) forming triplexes with various target sequences such as virus or oncogene sequences by coupling into the major groove of a target DNA duplex at physiological pH or (ii) forming duplexes by binding to single-stranded DNA or to RNA encoded by target genes. The oligomers of the invention may be constructed to have any desired sequence, provided the sequence normally includes one or more bases that is replaced with the analogs of the invention. Compositions of the invention can be used for diagnostic purposes in order to detect viruses or disease conditions.

Claims

1. A method making an oligonucleotide, comprising the steps:

(a) selecting a first oligonucleotide comprising a first covalent modification and a second covalent modification, said first covalent modification selected from the group consisting of a modified sugar, a modified base and a modified linkage and said second covalent modification selected from the group consisting of a modified sugar, a modified base and a modified linkage, wherein said first covalent modification increases the binding affinity of said first oligonucleotide for a complementary nucleic acid sequence relative to an otherwise identical unmodified second oligonucleotide that does not comprise said first covalent modification or said second covalent modification, and wherein said second covalent modification decreases the binding affinity of said first oligonucleotide for the complementary nucleic acid sequence relative to said otherwise identical unmodified second oligonucleotide that does not comprise the first covalent modification or the second covalent modification and wherein said second covalent modification results in a property selected from the group consisting of increased nuclease stability and enhanced cellular permeation in said first oligonucleotide for a complementary nucleic acid sequence relative to said otherwise identical unmodified second oligonucleotide;

(b) measuring the affinity of said first oligonucleotide for a complementary nucleic acid sequence;

(c) selecting an oligonucleotide of step (b) having a binding affinity for the complementary nucleic acid sequence that is greater than the sum of the increased binding affinity and the decreased binding affinity; and

(d) preparing the oligonucleotide of step (c).

2. The method of claim 1 wherein the first covalent modification is a modified purine or pyrimidine.

3. The method of claim 1 wherein the modified purine or pyrimidine is a 5-substituted pyrimidine.

4. The method of claim 1 wherein the second covalent modification is a modified internucleotide linkage.

5. The method of claim 1 wherein he modified internucleotide linkage is selected from the group consisting of thioate, dithioate, 1-12C alkylphosphonate, amidate and triester.

6. The method of claim 1 wherein the complementary nucleic acid is duplex DNA, single-stranded RNA or single-stranded DNA.

7. The method of claim 5 wherein the 1-12C alkylphosphonate linkage is a methylphosphonate linkage.