Oligonucleotide polymeric support system with an oxidation cleavable link

• US 5,362,866 A
• Filed: 03/17/1992
• Issued: 11/08/1994
• Est. Priority Date: 09/02/1983
• Status: Expired due to Term

• Current Assignee: Molecular Biosystems, Inc (Alliance Pharmaceutical Corporation)
• Original Assignee: Molecular Biosystems, Inc (Alliance Pharmaceutical Corporation)
• Inventors: Arnold, Lyle J. Jr.
• Primary Examiner(s): Brown, Johnnie R.
• Assistant Examiner(s): Crane, L. Eric
• Application Number:
  US07/852,761
• Time in Patent Office: 966 Days
• Field of Search: 536/25.3, 536/25.32, 435/6
• US Class Current: 536/25.3
• 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: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

A versatile polymeric support system for the synthesis of oligonucleotides is provided featuring a universal primer which allows chain elongation, in either the 3'"'"' or 5'"'"' direction, with any currently available DNA or RNA synthesis method, by a process which utilizes oxidatively cleaved primers to facilitate chain elongation and release. The support system is capable of withstanding mildly basic and acidic reaction conditions, while still permitting a convenient and quantitative release, either before or after removal of protecting groups from reactive groups, of synthesized oligonucleotides from a single polymeric support. Removal of the protecting groups before cleavage of the oligomer from the support permits the use of the immobilized oligomer as an affinity hybridization support for both isolating and detecting complementary polynucleic acids.

Claims

1. A process comprising the steps of:

(a) providing a compound consisting essentially of a polymeric support and a primer, said compound having the structure;

##STR1## wherein S is a solid support, is a spacer of 1 to 50 atoms which is not cleaved under acidic or basic deprotecting conditions of oligonucleotide synthesis and is attached to said polymeric support, R₈ is a protecting group on an oxidizable substituent and R₇ is a protecting group for --OH;

(b) synthesizing an oligonucleotide having base-labile protective groups on the nucleotides onto the O of OR₇ ; and

(c) removing the protecting groups with a base.

5. The process of any one of claims 1-4 further comprising the steps of:

(d) oxidizing at least the oxidizable substituent OR₈ that is gamma to the oligonucleotide attachment site;

(e) cleaving the oligonucleotide from the primer with a second base; and

(f) recovering the oligonucleotide.

6. The process of any one of claims 1-4 further comprising the step of:

(d) hybridizing the oligonucleotide to a complementary oligonucleotide to form a duplex.

7. The process of claim 6 further comprising the step of:

(e) detecting the complementary oligonucleotide hybridized to the oligonucleotide.

8. The process of claim 6 further comprising the steps of:

(e) oxidizing at least the oxidizable substituent OR₈ that is gamma to the oligonucleotide attachment site;

(f) cleaving the oligonucleotide from the primer with a second base; and

(g) recovering the duplex.

2. A process comprising the steps of:

(a) providing a compound consisting essentially of a polymeric support and a primer, said compound having the structure;

##STR2## wherein S is a solid support, is a spacer of 1 to 50 atoms which is not cleaved under acidic or basic deprotecting conditions of oligonucleotide synthesis and is attached to said polymeric support, R₈ is a protecting group on an oxidizable substituent, R₇ is a protecting group for --OH, and R₉ are independently selected from the group consisting of H, alkyl, alkoxy and aryl; and

(b) synthesizing an oligonucleotide having base-labile protective groups on the nucleotides onto the O of OR₇ ; and

(c) removing the protecting groups with a base.

3. A process comprising the steps of:

(a) providing a compound consisting essentially of a polymeric support and a primer, said compound having the structure;

##STR3## wherein S is a solid support, is a spacer of 1 to 50 atoms which is not cleaved under acidic or basic deprotecting conditions of oligonucleotide synthesis and is attached to said polymeric support, R₈ is a protecting group on an oxidizable substituent, R₇ is a protecting group for --OH, and is a portion of the cyclic primer that does not directly participate in the cleavage reaction;

(b) synthesizing an oligonucleotide having base-labile protective groups on the nucleotides onto the O of OR₇ ; and

(c) removing the protecting groups with a base.

4. A process comprising the steps of:

(a) providing a compound consisting essentially of a polymeric support and a primer, said compound having the structure;

##STR4## wherein S is a solid support, is a spacer of 1 to 50 atoms which is not cleaved under acidic or basic deprotecting conditions of oligonucleotide synthesis and is attached to said polymeric support, R₈ is a protecting group on an oxidizable substituent, R₇ is a protecting group for --OH, R₉ are independently selected from the group consisting of H, alkyl, alkoxy and aryl and is the portion of the cyclic primer that does not directly participate in the cleavage reaction;

(b) synthesizing an oligonucleotide having base-labile protective groups on the nucleotides onto the O of OR₇ ; and

(c) removing the protecting groups with a base.