Method for preparing 3'-nitrogen containing polynucleotides

• US 5,625,052 A
• Filed: 12/21/1995
• Issued: 04/29/1997
• Est. Priority Date: 08/17/1994
• Status: Expired due to Term

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Perkinelmer Incorporated
• Inventors: Woo, Sam L., Fung, Steven
• Primary Examiner(s): Kunz, Gary L.
• Application Number:
  US08/576,206
• Time in Patent Office: 495 Days
• Field of Search: 536/25.33, 536/25.34, 536/25.32, 536/25.3
• US Class Current: 536/25.34
• 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 method for synthesizing a polynucleotide having a nitrogen atom at the 3'"'"'-end is disclosed. The methods include the following steps. A solid support reagent is provided having the structure shown below: ##STR1## where T is an acid-cleavable hydroxyl protecting group, e.g., 4,4'"'"'-dimethoxytritil; Q is a linker connecting the nitrogen and oxygen, e.g., n-hexyl; R₁ is a nitrogen substituent, e.g., hydrogen; R₂ through R₄ are separately hydrogen or lower alkyl; Y is an atom which is electronegative with respect to carbon, e.g., oxygen or sulfur; X₁ is an atom which is electronegative with respect to carbon, e.g., sulfone; Z is a bond or spacer arm, e.g., ethylsuccinate; and W is a derivatized solid synthesis support capable of linking to Z, e.g., an amino-dirivitized controlled pore glass. The solid support is treated with acid to remove the acid-cleavable hydroxyl protecting group. A protected nucleoside monomer and a weak acid is added forming a linkage, and the unreacted sites on the solid support are capped. An oxidizing reagent is added and the above steps are repeated until polynucleotide chain elongation is complete. The polynucleotide is cleaved from the solid support and then deprotected.

Claims

1. A method for synthesizing a polynucleotide having a nitrogen atom at the 3'"'"'-end comprising the steps of:

(a) providing a solid support reagent having the structure shown below;

##STR14## wherein;

T is an acid-cleavable hydroxyl protecting group;

Q is a linker for connecting nitrogen and oxygen;

R₁ is a nitrogen substituent;

R₂ through R₄ are separately hydrogen or lower alkyl;

Y is an atom which is electronegative with respect to carbon;

X₁ is an atom which is electronegative with respect to carbon;

Z is a bond or spacer arm; and

W is a derivatized solid synthesis support capable of linking to Z;

(b) treating the solid support with acid to remove the acid-cleavable hydroxyl protecting group;

(c) adding a protected nucleoside monomer and a weak acid, forming a linkage;

(d) capping unreacted sites on the solid support;

(e) adding an oxidizing reagent;

(f) repeating steps (b)-(e) until the polynucleotide chain elongation is complete;

(g) cleaving the polynucleotide from the solid support; and

(h) deprotecting the polynucleotide.

3. The method of claim 1 wherein T is 4,4'"'"'-dimethoxytrityl.

4. The method of claim 1 wherein Q is lower alkyl;

or when in combination with an adjacent oxygen Q is lower alkylene oxide.

5. The method of claim 1 wherein Y is oxygen.

6. The method of claim 1 wherein X₁ is sulphonyl, carbonyl, or sulfoxide.

7. The method of claim 1 wherein Z is, in combination with a terminal nitrogen of the solid synthesis support, carbamate, urea, amide, sulfonamide, or a group of the formula:

##STR16## wherein v is an integer between 0 and 20.

2. A method for synthesizing a polynucleotide having a nitrogen atom at the 3'"'"'-end comprising the steps of:

(a) providing a solid support reagent having a structure shown below;

##STR15## wherein;

T is an acid-cleavable hydroxyl protecting group;

Q is a linker connecting the nitrogen and oxygen;

R₁ is a nitrogen substituent;

R₂ and R₃ are separately hydrogen or lower alkyl;

Y is an atom which is electronegative with respect to carbon;

X₂ is an atom which is electronegative with respect to carbon;

Z is a bond or spacer arm; and

W is a derivatized solid synthesis support capable of linking to Z;

(b) treating the solid support with acid to remove the acid-cleavable hydroxyl protecting group,

(c) adding a protected nucleoside monomer and a weak acid, forming a linkage;

(d) capping unreacted sites on the solid support;

(e) adding an oxidizing reagent;

(f) repeating steps (b)-(e) until the polynucleotide chain elongation is complete;

(g) cleaving the polynucleotide from the solid support; and

(h) deprotecting the polynucleotide.

8. The method of claim 2 wherein T is 4,4'"'"'-dimethoxytrityl.

9. The method of claim 2 wherein Q is lower alkyl;

or when in combination with an adjacent oxygen Q is lower alkylene oxide.

10. The method of claim 2 wherein Y is oxygen.

11. The method of claim 2 wherein X₁ is sulphonyl, carbonyl, or sulfoxide.

12. The method of claim 2 wherein Z is, in combination with a terminal nitrogen of the solid synthesis support, carbamate, urea, amide, sulfonamide, or a group of the formula:

##STR17## wherein v is an integer between 0 and 20.