Nucleotides for introducing selectably cleavable and/or abasic sites into oligonucleotides

• US 5,578,717 A
• Filed: 05/08/1995
• Issued: 11/26/1996
• Est. Priority Date: 10/16/1984
• Status: Expired due to Fees

• Current Assignee: Chiron Diagnostics Corp (Bayer AG)
• Original Assignee: Chiron Corporation (Novartis Ag)
• Inventors: Urdea, Michael S., Horn, Thomas
• Primary Examiner(s): Kunz, Gary L.
• Application Number:
  US08/436,663
• Time in Patent Office: 568 Days
• Field of Search: 536/24.3, 536/24.31, 536/24.32, 536/26.1
• US Class Current: 536/26.1
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07F 9/10 Phosphatides, e.g. lecithin
• CPC Class Codes: C07F 9/2429 of arylalkanols
• CPC Class Codes: C07F 9/65515 the oxygen atom being part of a five-membered ring
• CPC Class Codes: C07H 15/18 Acyclic radicals, substituted by carbocyclic rings
• 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 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: C07H 23/00 Compounds containing boron, silicon, or a metal, e.g. chelates, vitamin B12 esters with inorganic acids C07H11/00; metal salts, see parent compounds
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6823 Release of bound markers
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents
• CPC Class Codes: C12Q 2523/319 Photocleavage, photolysis, photoactivation
• CPC Class Codes: C12Q 2525/119 incorporating abasic sites
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2535/119 Double strand sequencing

Abstract

Novel reagents useful in a variety of biochemical and chemical contexts, including nucleic hybridization assays and chemical phosphorylation of hydroxyl-containing compounds. The reagents are particularly useful for introducing cleavable sites and/or abasic sites into oligonucleotide or polynucleotide chains.

Claims

1. A compound having the structure

wherein

R¹ is a base-stable, acid-sensitive blocking group;

R² is a phosphorous derivative selected to enable addition of the compound to the 5'"'"' position of an oligonucleotide chain; and

R is selected from the group consisting of 2-nitrobenzyl, 4-penten-1-yl, ##STR20## in which R'"'"' is hydrogen, aryl or aralkyl, the R_i may be the same or different and are selected from the group consisting of amino, nitro, halogeno, hydroxyl, lower alkyl and lower alkoxy, the R_j may be the same or different and are selected from the group consisting of amino, nitro, halogeno, hydroxyl, lower alkyl and lower alkoxy, i is zero, 1, 2 or 3, and j is zero, 1, 2, 3 or 4.

2. The compound of claim 1 wherein R¹ is selected from the group consisting of dimethoxytrityl, monomethoxytrityl, trityl and pixyl.

3. The compound of claim 1 wherein R² is selected from the group consisting of phosphoramidites, phosphotriesters, phosphodiesters, phosphites, H-phosphonates, and phosphorothioates.

4. The compound of claim 1 wherein R is 2-nitrobenzyl.

5. The compound of claim 1 wherein R is ##STR21##

6. The compound of claim 1 wherein R is --CH₂ CH₂ Si(CH₃)₃.

7. The compound of claim 1 wherein R is ##STR22##

8. The compound of claim 7 wherein R is the 2-methylene-9,10-anthraquinone acetal.

9. The compound of claim 7 wherein R is 4-penten-1-yl.

10. The compound of claim 7 wherein R is ##STR23##

11. The compound of claim 7 wherein R is ##STR24##