Sulforhodamine phosphoramidite dyes

Patent metadata

Field	Value
Publication number	US-12071547-B2
Application number	US-201917053683-A
Country	US
Kind code	B2
Filing date	May 7, 2019
Priority date	May 7, 2018
Publication date	Aug 27, 2024
Grant date	Aug 27, 2024

Abstract

Automated oligonucleotide synthesis-compatible sulforhodamine dye phosphoramidite compounds and labeled polynucleotides incorporating these dyes are provided.

First claim

The invention claimed is:

1. A compound represented by Formula I:

or a stereoisomer, tautomer, or salt thereof, wherein:
R 1 is C 1 -C 6 alkyl or L 1 -X;
R 2 is halogen or SO 2 NH 2 ,
R 3 is H or halogen;
R 4 , R 7 , R 8 , and R 11 when taken alone are independently H, halogen, or optionally substituted C 1 -C 6 alkyl,
R 5 , R 6 , R 9 , and R 10 when taken alone are independently H or optionally substituted C 1 -C 6 alkyl;
R 4 and R 5 when taken together are an optionally substituted C 2 -C 3 alkylene chain connecting the atoms to which R 4 and R 5 are attached;
R 6 and R 7 when taken together are an optionally substituted C 2 -C 3 alkylene chain connecting the atoms to which R 6 and R 7 are attached;
R 8 and R 9 when taken together are an optionally substituted C 2 -C 3 alkylene chain connecting the atoms to which R 8 and R 9 are attached;
R 10 and R 11 when taken together are an optionally substituted C 2 -C 3 alkylene chain connecting the atoms to which R 10 and R 11 are attached;
R 5 and R 6 , when taken together with the nitrogen atom to which R 5 and R 6 are attached, form a 5-membered or a 6-membered unsaturated ring;
R 9 and R 10 , when taken together with the nitrogen atom to which R 9 and R 10 are attached, form a 5-membered or a 6-membered unsaturated ring;
L 1 is an optionally substituted C 2 -C 10 alkylene or optionally substituted C 2 -C 20 heteroalkylene;
X is —O—P(OCH 2 CH 2 CN)NR 12 R 13 or

 wherein
L 3 and L 4 are independently an optionally substituted C 2 -C 10 alkylene or optionally substituted C 2 -C 30 heteroalkylene;
Q is a hydroxyl protecting group;
Z is CH, N, NHC(O)N, or OC(O)N; and
R 12 and R 13 are independently optionally substituted C 1 -C 6 alkyl.

2. The compound of claim 1 , wherein R 2 is C 1 and R 3 is H.

3. The compound of claim 1 , wherein X is —OP(OCH 2 CH 2 CN)N(i-Pr) 2 .

4. The compound of claim 1 , wherein L 1 is a PEG 2-10 linker.

5. The compound of claim 1 , wherein L 1 is —CH 2 CH 2 OCH 2 CH 2 —.

6. The compound of claim 1 , wherein R 4 and R 5 taken together are an optionally substituted C 3 alkylene chain connecting the atoms to which R 4 and R 5 are attached; R 10 and R 11 taken together are an optionally substituted C 3 alkylene chain connecting the atoms to which R 10 and R 11 are attached; R 6 and R 7 taken together are an optionally substituted C 3 alkylene chain connecting the atoms to which R 6 and R 7 are attached; and R 8 and R 9 taken together are an optionally substituted C 3 alkylene chain connecting the atoms to which R 8 and R 9 are attached.

7. The compound of claim 1 , wherein R 4 and R 5 taken together are a propylene chain connecting the atoms to which R 4 and R 5 are attached; R 10 and R 11 taken together are a propylene chain connecting the atoms to which R 10 and R 11 are attached; R 6 and R 7 taken together are a propylene chain connecting the atoms to which R 6 and R 7 are attached; and R 8 and R 9 taken together are a propylene chain connecting the atoms to which R 8 and R 9 are attached.

8. The compound of claim 1 , wherein R 5 , R 6 , R 9 , and R 10 are each methyl.

9. The compound of claim 1 , wherein Q is an acid-labile hydroxyl protecting group.

10. The compound of claim 1 , wherein Q is a trityl or dimethoxytrityl group.

11. The compound of claim 1 , wherein L 3 and L 4 are independently C 2 -C 6 alkylene or —(OCH 2 CH 2 ) m — wherein m is an integer ranging from 2 to 6.

12. The compound of claim 1 , wherein L 3 and L 4 are independently CH 2 CH 2 .

13. The compound of claim 1 , wherein X is:

14. The compound of claim 1 , wherein the compound is represented by Formula IA:

or a stereoisomer, tautomer, or salt thereof, wherein R 1 is L 1 X and R 3 is H or halogen.

15. The compound of claim 1 , wherein the compound is:

Assignees

• Cepheid

Inventors

• Lund Kevin P
• Sergueev Dmitri
• Qabar Maher N
• Gall Alexander

Classifications

• C12Q1/6876

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title

• C09B57/00

  Other synthetic dyes of known constitution · CPC title

• C09B11/24 Primary

  Phthaleins containing amino groups {; Phthalanes; Fluoranes; Phthalides; Rhodamine dyes; Phthaleins having heterocyclic aryl rings; Lactone or lactame forms of triarylmethane dyes} · CPC title

• C07H21/00

  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 title

• C07H19/073

  with 2-deoxyribosyl as the saccharide radical · CPC title