IP Library Granted Patent US 12,331,199
Granted Patent B2
US 12,331,199 · App. 18/130,212 · Granted Jun 17, 2025

Silicon containing detectable compounds

Inventors: Ronald Graham (Carlsbad, CA); Rodrigo Rodriguez (San Diego, CA)
Assignee: Singular Genomics Systems, Inc.
C09B11/24C07F7/0803C07F7/0825C07F7/083C07H21/02C07H21/04C09B69/008C07F7/0816C07H23/00
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Quick Facts
Patent No.
US 12,331,199
App. No.
18/130,212
Granted
Jun 17, 2025
Kind
B2
Abstract

Disclosed herein, inter alia, are silicon containing detectable compounds and methods of use thereof.

Claims (87)

1. A compound, or salt thereof, having the formula:

wherein,

L 3 is

L 1 -L 2 -comprises

R 1 is substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

R 2 and R 3 are independently substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl;

R 4 is hydrogen, R 34 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 34 -substituted or unsubstituted heteroalkyl, R 34 -substituted or unsubstituted cycloalkyl, or R 34 -substituted or unsubstituted heterocycloalkyl;

R 5 is hydrogen, R 35 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 35 -substituted or unsubstituted heteroalkyl, R 35 -substituted or unsubstituted cycloalkyl, or R 35 -substituted or unsubstituted heterocycloalkyl;

R 6 is hydrogen, R 36 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 36 -substituted or unsubstituted heteroalkyl, R 36 -substituted or unsubstituted cycloalkyl, or R 36 -substituted or unsubstituted heterocycloalkyl;

R 7 is hydrogen, R 37 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 37 -substituted or unsubstituted heteroalkyl, R 37 -substituted or unsubstituted cycloalkyl, or R 37 -substituted or unsubstituted heterocycloalkyl;

R 8 is a nucleotide;

R 9 is hydrogen, R 39 -substituted or unsubstituted alkyl, or R 39 -substituted or unsubstituted heteroalkyl;

R 10 is hydrogen, R 40 -substituted or unsubstituted alkyl, or R 40 -substituted or unsubstituted heteroalkyl;

R 11 is hydrogen, R 41 -substituted or unsubstituted alkyl, or R 41 -substituted or unsubstituted heteroalkyl;

R 12 is hydrogen, R 42 -substituted or unsubstituted alkyl, or R 42 -substituted or unsubstituted heteroalkyl;

R 4 and R 5 substituents bonded to the same nitrogen atom may optionally be joined to form a R 34 -substituted or unsubstituted heterocycloalkyl;

R 6 and R 7 substituents bonded to the same nitrogen atom may optionally be joined to form a R 36 -substituted or unsubstituted heterocycloalkyl;

R 4 and R 9 substituents may optionally be joined to form a R 34 -substituted or unsubstituted heterocycloalkyl, or R 39 -substituted or unsubstituted heteroaryl;

R 7 and R 10 substituents may optionally be joined to form a R 37 -substituted or unsubstituted heterocycloalkyl, or R 37 -substituted or unsubstituted heteroaryl;

R 5 and R 11 substituents may optionally be joined to form a R 35 -substituted or unsubstituted heterocycloalkyl, or R 35 -substituted or unsubstituted heteroaryl;

R 6 and R 12 substituents may optionally be joined to form a R 36 -substituted or unsubstituted heterocycloalkyl, or R 36 -substituted or unsubstituted heteroaryl;

R 34 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 35 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 36 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 37 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 39 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H;

R 40 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H;

R 41 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H; and

R 42 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H.

2. The compound of claim 1 , wherein R 1 is substituted or unsubstituted C 1 -C 6 alkyl.

3. The compound of claim 1 , wherein R 2 and R 3 are independently substituted or unsubstituted C 1 -C 6 alkyl, or substituted or unsubstituted 2 to 6 membered heteroalkyl.

4. The compound of claim 1 , wherein R 4 is hydrogen, R 34 -substituted or unsubstituted C 1 -C 6 alkyl, or R 34 -substituted or unsubstituted 2 to 6 membered heteroalkyl;

R 5 is hydrogen, R 35 -substituted or unsubstituted C 1 -C 6 alkyl, or R 35 -substituted or unsubstituted 2 to 6 membered heteroalkyl;

R 6 is hydrogen, R 36 -substituted or unsubstituted C 1 -C 6 alkyl, or R 36 -substituted or unsubstituted 2 to 6 membered heteroalkyl; and

R 7 is hydrogen, R 37 -substituted or unsubstituted C 1 -C 6 alkyl, or R 37 -substituted or unsubstituted 2 to 6 membered heteroalkyl.

5. The compound of claim 1 , wherein R 4 and R 5 substituents bonded to the same nitrogen atom are joined to form a R 34 -substituted or unsubstituted 5 membered heterocycloalkyl or R 34 -substituted or unsubstituted 6 membered heterocycloalkyl.

6. The compound of claim 1 , wherein R 6 and R 7 substituents bonded to the same nitrogen atom are joined to form a R 36 -substituted or unsubstituted 5 membered heterocycloalkyl or R 36 -substituted or unsubstituted 6 membered heterocycloalkyl.

7. The compound of claim 1 , wherein R 8 is

wherein

B is a divalent base;

R 15 is a 5′-nucleoside protecting group, monophosphate moiety, polyphosphate moiety, or nucleic acid moiety;

R 16 is hydrogen or —OH; and

R 17 is an —O-polymerase-compatible cleavable moiety, wherein said polymerase-compatible cleavable moiety has the formula:

8. The compound of claim 7 , wherein R 15 is a triphosphate moiety.

9. The compound of claim 7 , wherein

B is a divalent cytosine, divalent guanine, divalent adenine, divalent thymine, divalent uracil, divalent hypoxanthine, divalent xanthine, divalent 7-methylguanine, divalent 5,6-dihydrouracil, divalent 5-methylcytosine, or divalent 5-hydroxymethylcytosine.

10. A method of detecting the presence of an agent, said method comprising exposing a compound covalently bound to said agent to absorption light and detecting an emission wavelength, wherein said agent is an oligonucleotide, protein, or compound, and wherein said compound covalently bound to said agent has the formula:

wherein,

L 3 is

L 1 -L 2 -comprises

R 1 is substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

R 2 and R 3 are independently substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl;

R 4 is hydrogen, R 34 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 34 -substituted or unsubstituted heteroalkyl, R 34 -substituted or unsubstituted cycloalkyl, R 34 -substituted or unsubstituted heterocycloalkyl, R 34 -substituted or unsubstituted aryl, or R 34 -substituted or unsubstituted heteroaryl;

R 5 is hydrogen, R 35 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 35 -substituted or unsubstituted heteroalkyl, R 35 -substituted or unsubstituted cycloalkyl, R 35 -substituted or unsubstituted heterocycloalkyl, R 35 -substituted or unsubstituted aryl, or R 35 -substituted or unsubstituted heteroaryl;

R 6 is hydrogen, R 36 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 36 -substituted or unsubstituted heteroalkyl, R 36 -substituted or unsubstituted cycloalkyl, R 36 -substituted or unsubstituted heterocycloalkyl, R 36 -substituted or unsubstituted aryl, or R 36 -substituted or unsubstituted heteroaryl;

R 7 is hydrogen, R 37 -substituted or unsubstituted alkyl, halogen, —CF 3 , —CBr 3 , —CCl 3 , —CI 3 , —CHF 2 , —CHBr 2 , —CHCl 2 , —CHI 2 , —CH 2 F, —CH 2 Br, —CH 2 Cl, —CH 2 I, —OH, —NH 2 , —COOH, —CONH 2 , —SH, R 37 -substituted or unsubstituted heteroalkyl, R 37 -substituted or unsubstituted cycloalkyl, R 37 -substituted or unsubstituted heterocycloalkyl, R 37 -substituted or unsubstituted aryl, or R 37 -substituted or unsubstituted heteroaryl;

R 9 is hydrogen, R 39 -substituted or unsubstituted alkyl, or R 39 -substituted or unsubstituted heteroalkyl;

R 10 is hydrogen, R 40 -substituted or unsubstituted alkyl, or R 40 -substituted or unsubstituted heteroalkyl;

R 11 is hydrogen, R 41 -substituted or unsubstituted alkyl, or R 41 -substituted or unsubstituted heteroalkyl;

R 12 is hydrogen, R 42 -substituted or unsubstituted alkyl, or R 42 -substituted or unsubstituted heteroalkyl;

R 4 and R 5 substituents bonded to the same nitrogen atom may optionally be joined to form a R 34 -substituted or unsubstituted heterocycloalkyl;

R 6 and R 7 substituents bonded to the same nitrogen atom may optionally be joined to form a R 36 -substituted or unsubstituted heterocycloalkyl;

R 4 and R 9 substituents may optionally be joined to form a R 34 -substituted or unsubstituted heterocycloalkyl, or R 39 -substituted or unsubstituted heteroaryl;

R 7 and R 10 substituents may optionally be joined to form a R 37 -substituted or unsubstituted heterocycloalkyl, or R 37 -substituted or unsubstituted heteroaryl;

R 5 and R 11 substituents may optionally be joined to form a R 35 -substituted or unsubstituted heterocycloalkyl, or R 35 -substituted or unsubstituted heteroaryl;

R 6 and R 12 substituents may optionally be joined to form a R 36 -substituted or unsubstituted heterocycloalkyl, or R 36 -substituted or unsubstituted heteroaryl;

R 34 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 35 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 36 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 37 is independently oxo, halogen, —CF 3 , —CCl 3 , —CI 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —CH 2 F, —CH 2 Cl, —CH 2 I, —CH 2 Br, —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —OCHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCCl 3 , —OCI 3 , —OCBr 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC═(O)NHNH 2 , —NHC═(O)NH 2 , —NHSO 2 H, —NHC═(O)H, —NHC(O)OH, —NHOH, —PO 4 H, —PO 3 H, —N 3 , unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, or unsubstituted heterocycloalkyl;

R 39 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H;

R 40 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H;

R 41 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H; and

R 42 is independently —PO 3 H, —PO 4 H, —SO 2 NH 2 , —SO 3 H, or —SO 4 H.

11. The compound of claim 1 having formula:

wherein, the symbol B is a divalent base; and

the symbol in formula (XI) or (XII) refers to an attachment point to hydrogen, a phosphate moiety, or a reversible terminator moiety.

12. The compound of claim 1 , wherein R 4 and R 9 substituents are joined to form a R 34 -substituted or unsubstituted 7 membered heterocycloalkyl, or R 39 -substituted or unsubstituted 7 membered heteroaryl.

13. The compound of claim 1 , wherein R 7 and R 10 substituents are joined to form a R 37 -substituted or unsubstituted 7 membered heterocycloalkyl, or R 37 -substituted or unsubstituted 7 membered heteroaryl.

14. The compound of claim 1 , wherein R 5 and R 11 substituents are joined to form a R 35 -substituted or unsubstituted 6 membered heterocycloalkyl, or R 35 -substituted or unsubstituted 6 membered heteroaryl.

15. The compound of claim 1 , wherein R 6 and R 12 substituents are joined to form a R 36 -substituted or unsubstituted 6 membered heterocycloalkyl, or R 36 -substituted or unsubstituted 6 membered heteroaryl.

16. The compound of claim 1 , wherein

R 4 and R 9 substituents are joined to form a R 34 -substituted or unsubstituted 6 membered heterocycloalkyl, or R 39 -substituted or unsubstituted 6 membered heteroaryl;

R 7 and R 10 substituents are joined to form a R 37 -substituted or unsubstituted 6 membered heterocycloalkyl, or R 37 -substituted or unsubstituted 6 membered heteroaryl;

R 5 and R 11 substituents are joined to form a R 35 -substituted or unsubstituted 6 membered heterocycloalkyl, or R 35 -substituted or unsubstituted 6 membered heteroaryl; and

R 6 and R 12 substituents are joined to form a R 36 -substituted or unsubstituted 6 membered heterocycloalkyl, or R 36 -substituted or unsubstituted 6 membered heteroaryl.

17. The compound of claim 1 , having formula

Assignments (3)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 17, 2025
From: GRAHAM, RONALD; RODRIGUEZ, RODRIGO
To: SINGULAR GENOMICS SYSTEMS, INC.
Reel/Frame 070876/0076 →
SECURITY INTEREST Recorded Mar 7, 2025
From: SINGULAR GENOMICS SYSTEMS, INC.
To: FIRST-CITIZENS BANK & TRUST COMPANY
Reel/Frame 070440/0465 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded May 2, 2023
From: GRAHAM, RONALD; RODRIGUEZ, RODRIGO
To: SINGULAR GENOMICS SYSTEMS, INC
Reel/Frame 063505/0042 →
Continuity (3)
Continuation 16415700 · May 17, 2019
Provisional Application 62673579 · May 18, 2018
Related Publication 20230295437A1 · Sep 21, 2023
References Cited (78)
US 5268486A · Waggoner et al. · 1993 [cited by applicant]
US 6130101A · Mao et al. · 2000 [cited by applicant]
US 6664079B2 · Ju et al. · 2003 [cited by applicant]
US 9139868B2 · Zhou et al. · 2015 [cited by applicant]
US 9649389B2 · Groves et al. · 2017 [cited by applicant]
US 9714260B2 · Nagano et al. · 2017 [cited by applicant]
US 9933417B2 · Lavis et al. · 2018 [cited by applicant]
US 10087199B2 · Erdmann et al. · 2018 [cited by applicant]
US 10564164B2 · Majima et al. · 2020 [cited by applicant]
US 10738072B1 · Graham · 2020 [cited by examiner]
US 11180657B2 · Kemnitzer et al. · 2021 [cited by applicant]
US 11535754B2 · Cila et al. · 2022 [cited by applicant]
US 11697736B2 · Graham · 2023 [cited by examiner]
US 20040096825A1 · Chenna · 2004 [cited by examiner]
US 20100009353A1 · Barnes · 2010 [cited by examiner]
US 20140272990A1 · Zhou et al. · 2014 [cited by applicant]
US 20140342384A1 · Nagano · 2014 [cited by examiner]
US 20150353585A1 · Nagano et al. · 2015 [cited by applicant]
US 20160115180A1 · Erdmann et al. · 2016 [cited by applicant]
US 20170363636A1 · Majima et al. · 2017 [cited by applicant]
US 20180274024A1 · Ju · 2018 [cited by examiner]
US 20190100653A1 · Kemnitzer et al. · 2019 [cited by applicant]
US 20190352508A1 · Graham et al. · 2019 [cited by applicant]
US 20220332752A2 · Graham et al. · 2022 [cited by applicant]
EP 3461815A1 · 2019 [cited by applicant]
WO WO2019164977A1 · 2019 [cited by examiner]
WO WO2019222653A1 · 2019 [cited by applicant]
WO WO2020005172A2 · 2020 [cited by applicant]
WO WO2021092035A1 · 2021 [cited by applicant]
U.S. Appl. No. 18/598,995, filed Mar. 7, 2024, Graham; Ronald. [cited by examiner]
Brauch et al., “Fast and Efficient MCR-based synthesis of clickable rhodamine tags for protein profiling” Organic and Biomolecular Chemistry vol. 10 pp. 958-965, DOI:10/1039/c1ob06581e (Year: 2012). [cited by examiner]
Koide et al., “Development of NIR Fluorescent Dyes Based on Si-rhodamine for in vivo Imaging” J Am Chem Soc vol. 134 pp. 5029-5031 DOI: 10.1021/ja210375e (Year: 2012). [cited by examiner]
Xu et al., “Cellular thermal shift and clickable chemical probe assays for the determination of drug-target engagement in live cells” Org Biomol Chem vol. 14 pp. 6179-6183 DOI:10.1039/c6ob01078d (Year: 2016). [cited by examiner]
Mathews et al., “Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis” Organic and Biomolecular Chemistry vol. 14 pp. 8278-8288 DOI:10.1039/c6ob01371f (Year: 2016). [cited by examiner]
Shen et al., “Near-infrared probes based on fluorinated Si-rhodamine for live cell imaging” RSC Adv vol. 7 pp. 10922-10927 DOI:10.1039/c6ra28455h (Year: 2017). [cited by examiner]
Ju et al., “Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators” PNAS vol. 103 No. 52 pp. 19635-19640 DOI:10.1073/pnas.0609513103 (Year: 2006). [cited by examiner]
Berlier, J.E. et al. (Dec. 2003). “Quantitative comparison of long-wavelength Alexa Fluor dyes to Cy dyes: fluorescence of the dyes and their bioconjugates,” [cited by applicant]
Extended European Search Report mailed on Jan. 31, 2022, for EP Patent Application No. 19803002.5, 10 pages. [cited by applicant]
Goldstein, S.W. et al. (2017). “Nucleophilic aromatic substitution-addition and identification of an amine,” [cited by applicant]
Hutter, D. et al. (Nov. 2010). “Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups,” [cited by applicant]
International Search report mailed on Oct. 24, 2019, for PCT application PCT/US2019/032907, filed May 17, 2019, 4 pages. [cited by applicant]
Needleman, S.B .et al. ( Mar. 1970). “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” [cited by applicant]
Pearson, W.R. et al. (Apr. 1988). “Improved tools for biological sequence comparison,” [cited by applicant]
Randolph, J.B. et al. (Jul. 15, 1997). “Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes,” [cited by applicant]
Rosenblum, B.B. et al. (Nov. 15, 1997). “New dye-labeled terminators for improved DNA sequencing patterns,” [cited by applicant]
Smith T.F. et al. (Dec. 1981). “Comparison of biosequences,” [cited by applicant]
Written Opinion mailed on Oct. 24, 2019, for PCT application PCT/US2019/032907, filed May 17, 2019, 5 pages. [cited by applicant]
Bentley, D. R. et al. (Nov. 6, 2008). “Accurate whole human genome sequencing using reversible terminator chemistry,” [cited by applicant]
Berlier, J. E. et al. (Dec. 2003). “Quantitative comparison of long-wavelength Alexa Fluor dyes to Cy dyes: fluorescence of the dyes and their bioconjugates,” [cited by applicant]
Birtalan, E. et al. (Mar. 1, 2011). “Investigating rhodamine B-labeled peptoids: Scopes and limitations of its applications,” [cited by applicant]
Brauch, S. et al. (Oct. 25, 2011). “Fast and efficient MCR-based synthesis of clickable rhodamine tags for protein profiling,” [cited by applicant]
Buckley, M. et al. (Jan. 2016, e-published Dec. 10, 2015). “Enhancer scanning to locate regulatory regions in genomic loci,” [cited by applicant]
Choi, A. et al. (Aug. 3, 2018, e-published Jul. 17, 2018). “Silicon substitution in oxazine dyes yields near-infrared azasiline fluorophores that absorb and emit beyond 700 nm,” [cited by applicant]
Extended European Search Report mailed on Jan. 31, 2022, for EP Patent Application No. EP 19803002.5, 9 pages. [cited by applicant]
Extended European Search Report mailed on Dec. 4, 2023, for EP Patent Application No. EP 20883841.7, 14 pages. [cited by applicant]
Goldstein, S. W. et al. (Sep. 12, 2017, e-published Jul. 28, 2017). “Nucleophilic aromatic substitution-addition and identification of an amine,” [cited by applicant]
Grimm, J. B. et al. (Sep. 27, 2017, e-published Aug. 9, 2017). “General Synthetic Method for Si-Fluoresceins and Si-Rhodamines,” [cited by applicant]
Guo, J. et al. (Jul. 8, 2008, e-published Jun. 30, 2008). “Four-color DNA sequencing with 3′- O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides,” [cited by applicant]
Hutter, D. et al. (Nov. 2010, e-published Dec. 1, 2010). “Labeled nucleoside triphosphates with reversibly terminating aminoalkoxyl groups,” [cited by applicant]
International Search Report and Written Opinion mailed on Feb. 8, 2021, for PCT application PCT/US2020/058916, filed Nov. 4, 2020, 7 pages. [cited by applicant]
International Search Report and Written Opinion mailed on Oct. 24, 2019, for PCT Application No. PCT/US2019/032907, filed May 17, 2019, 9 pages. [cited by applicant]
Ju, J. et al. (Dec. 26, 2006, e-published Dec. 14, 2006). “Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators,” [cited by applicant]
Koide, Y. et al. (Mar. 21, 2012, e-published Mar. 7, 2012). “Development of NIR fluorescent dyes based on Si-rhodamine for in vivo imaging,” [cited by applicant]
Kolmakov, K. et al. (Sep. 14, 2015, e-published Aug. 13, 2015) “Far-Red Emitting Fluorescent Dyes for Optical Nanoscopy: Fluorinated Silicon-Rhodamines (SiRF Dyes) and Phosphorylated Oxazines” [cited by applicant]
Lee, M. H. et al. (Jul. 10, 2013, e-published Apr. 12, 2013). “Disulfide-cleavage-triggered chemosensors and their biological applications,” [cited by applicant]
Leicher, T. et al. (Dec. 25, 1998). “Coexpression of the KCNA3B gene product with Kv1.5 leads to a novel A-type potassium channel,” [cited by applicant]
Marcaccini, S. et al. (Mar. 2007, e-published Mar. 22, 2007). “The use of the Ugi four-component condensation,” [cited by applicant]
Mathews, A. S. et al. (Aug. 9, 2016). “Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis,” [cited by applicant]
Needleman, S. B. et al. (Mar. 28, 1970, e-published Oct. 28, 2004). “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” [cited by applicant]
Pearson, W. R. et al. (Apr. 1, 1988). “Improved tools for biological sequence comparison,” [cited by applicant]
Randolph, J. B. et al. (Jul. 1, 1997). “Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes,” [cited by applicant]
Rosenblum, B.B. et al. (Nov. 1, 1997). “New dye-labeled terminators for improved DNA sequencing patterns,” [cited by applicant]
Ruparel, H. et al. (Apr. 26, 2005, e-published Apr. 13, 2005). “Design and synthesis of a 3′-0-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis,” [cited by applicant]
Shen, S. et al. (Feb. 9, 2017). “Near-infrared probes based on fluorinated Si-rhodamine for live cell imaging,” [cited by applicant]
Smith T. F. et al. (Dec. 1981, e-published Sep. 3, 2004). “Comparison of biosequences,” [cited by applicant]
Wu, J. et al. (Oct. 16, 2007, e-published Oct. 8, 2007). “3′-O-modified nucleotides as reversible terminators for pyrosequencing,” [cited by applicant]
Xu, H. et al. (May 19, 2016). “Cellular thermal shift and clickable chemical probe assays for the determination of drug-target engagement in live cells,” [cited by applicant]
Zhu, Z. et al. (Aug. 25, 1994). “Directly labeled DNA probes using fluorescent nucleotides with different length linkers,” [cited by applicant]