Reagents based on a tertiary amine backbone to introduce chemical functionality in nucleic acids and sequence-controlled polymers

Patent metadata

Field	Value
Publication number	US-11358937-B2
Application number	US-201917263243-A
Country	US
Kind code	B2
Filing date	Aug 9, 2019
Priority date	Aug 10, 2018
Publication date	Jun 14, 2022
Grant date	Jun 14, 2022

Abstract

It is provided an achiral, non-nucleosidic backbone for phosphoramidites that can be inserted with high yields in nucleic acid strands and sequence-controlled oligo(phosphodiester)s through solid phase synthesis (SPS) using a DNA synthesizer. From this backbone, platforms with useful chemical handles were synthesized, further functionalized, transformed into phosphoramidites and attached to nucleic acid strands and sequence-controlled oligo(phosphodiester)s. The backbone is based on a tertiary amine with a 3-6 carbon spacer between the central nitrogen and the two external hydroxyls. The spacer has been optimized to increase coupling yields and stability.

First claim

What is claimed is:

1. A reagent having the following structure

wherein:
R1 is dimethoxytrityl (DMT), monomethoxytrityl (MMT), or other hydroxyl protecting group stable to oligonucleotide synthesis conditions;
R2 is a -phosphoramidityl residue

wherein Rx and Ry are independently selected from the group consisting of C1-10 branched alkyl, C1-12 alkyl, and cyclic hydrocarbyls; and Rz is a phosphite-protecting group; or
R2 is H,
R3 and R4 together form an alkyl, ethynyl or propargyl residue; or
R3 is:
a homo or heteroarylene residue

or R3 is an alkyl or oligo(ethylene glycol) chain with an amide or a heteroarylene residue on which is attached R4,
R4 is:
an optionally protected amino-acid or short peptide covalently attached to said R3;
a diaminoalkyl residue of general formula

wherein Rw is an amino protecting group; or
an optionally protected monosaccharide residue covalently attached to R3; or
a fluorophore, biotin, a strained alkyne, a disulfide, a protected thiol, a cross-linker or folic acid having suitable protecting groups,
n is an integer of 1 to 4,
m is an integer of 1 to 4, and
Q is an integer greater than 1.

2. The reagent of claim 1 , wherein Rx and Ry are CH(CH 3 ) 2 and Rz is O—(CH 2 ) 2 —CN.

3. The reagent of claim 1 , wherein R1 is dimethoxytrityl (DMT).

4. The reagent of claim 1 , wherein R3 is:

5. The reagent of claim 1 , wherein R4 is:

wherein PG is a protecting group.

6. The reagent of claim 1 , further comprising an amine functionalized with a carboxylic acid.

7. The reagent of claim 6 , wherein the amine is functionalized with an amino acid, a carbohydrate, a short peptide, a fluorophore, biotin, a strained alkyne, a disulfide, a protected thiol, a cross-linker or folic acid having suitable protecting groups.

8. The reagent of claim 5 , wherein the protecting group is an ester group or an acetate group.

9. The reagent of claim 5 , wherein the protecting group is, a silylated group, a trifluoroacetate group, a fluorenylmethyloxycarbonyl (FMOC) group, a monomethoxytrityl group, a 4-tertbutylbenzoyl group, a trityl group, an isobutyrate group, a trifluoroacetic acid (TFA) group or a methyl ester group.

10. The reagent of claim 1 , having the following structures:

11. A process to modify a synthetic oligonucleotide and/or to make a sequence-controlled oligomer, at any positions wherein the process comprises covalently attaching the reagent as defined in claim 1 , into said oligonucleotide and/or sequence-controlled oligomer by performing a phosphoramidite coupling during a synthesis of said oligonucleotide and/or sequence-controlled oligomer.

12. The process of claim 11 , further comprising the step of functionalizing the oligonucleotide and/or sequence-controlled oligomer using click chemistry.

13. The process of claim 12 , wherein the oligonucleotide and/or sequence-controlled oligomer is functionalized with a fluorophore, biotin, a strained alkyne, a disulfide, a protected thiol, a cross-linker or folic acid having suitable protecting groups.

14. The process of claim 13 , wherein the dye is a Cy5 sulfonated dye.

15. The process of claim 11 , wherein the synthetic oligonucleotide and/or sequence-controlled oligomer is modified or made in an automated synthesizer.

Assignees

• The Royal Institution For The Advancement Of Learning/Mcgill Univ

Inventors

• Sleiman Hanadi F
• De Rochambeau Donatien
• Sun Yuanye

Classifications

• C07H19/056

  Triazole or tetrazole radicals · CPC title

• C07F9/6518

  Five-membered rings · CPC title

• C07F9/5728

  condensed with carbocyclic rings or carbocyclic ring systems · CPC title

• C07D249/04

  1,2,3-Triazoles; Hydrogenated 1,2,3-triazoles · CPC title

• C07D309/14

  Nitrogen atoms not forming part of a nitro radical · CPC title