IP Library Granted Patent US 12,281,137
Granted Patent B2
US 12,281,137 · App. 18/112,952 · Granted Apr 22, 2025

Method for the site-specific enzymatic labelling of nucleic acids in vitro by incorporation of unnatural nucleotides

Inventors: Floyd E. Romesberg (La Jolla, CA); Denis A. Malyshev (Solana Beach, CA); Lingjun Li (San Diego, CA); Thomas Lavergne (Le Versoud, FR); Zhengtao Li (Pudong new district, CN)
Assignee: The Scripps Research Institute
C07H19/24C07H19/00C07H21/00C07H21/04C12N9/22C12N15/1024C12P19/34C12Q1/6832
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Quick Facts
Patent No.
US 12,281,137
App. No.
18/112,952
Granted
Apr 22, 2025
Kind
B2
Abstract

Provided herein are analogs of unnatural nucleotides bearing predominantly hydrophobic nucleobase analogs that form unnatural base pairs during DNA polymerase-mediated replication of DNA or RNA polymerase-mediated transcription of RNA. In this manner, the unnatural nucleobases can be introduced in a site-specific way into oligonucleotides (single or double stranded DNA or RNA), where they can provide for site-specific cleavage, or can provide a reactive linker than can undergo functionalization with a cargo-bearing reagent by means of reaction with a primary amino group or by means of click chemistry with an alkyne group of the unnatural nucleobase linker.

Claims (50)

1. A nucleobase pair comprising a first nucleobase analog having the structure β9b, and a second nucleobase analog having any of the structures α15a or α15b:

wherein each X is independently carbon or nitrogen,

wherein each R 1 is independently hydrogen, alkyl group, a reactive linker comprising a reactive center a linker coupled to a cargo,

wherein each R 2 is optional and when present is independently hydrogen, alkyl, alkenyl, alkynyl, methoxy, methanethiol, methaneseleno, halogen, cyano, azide, nitro group, a reactive linker comprising a reactive center, or a linker coupled to a cargo,

wherein each Y is independently sulfur, oxygen, selenium, or a secondary amine,

wherein each E is independently oxygen, sulfur or selenium,

and the wavy line indicates a point of bonding to a ribosyl, deoxyribosyl, or dideoxyribosyl moiety or an analog thereof, wherein the ribosyl, deoxyribosyl, or dideoxyribosyl moiety, or analog thereof is in free form, is bound to a mono-phosphate, diphosphate, triphosphate, α-thiotriphosphate, β-thiophosphate, or γ-thiophosphate group, or is included in an RNA or a DNA or in an RNA analog or a DNA analog.

2. A double-stranded oligonucleotide comprising the nucleobase pair of claim 1 .

3. The nucleobase pair of claim 1 , wherein the ribosyl, deoxyribosyl, or dideoxyribosyl moiety or analog thereof is included in an RNA.

4. The nucleobase pair of claim 1 , wherein the ribosyl, deoxyribosyl, or dideoxyribosyl moiety or analog thereof is included in a DNA.

5. The nucleobase pair of claim 1 , wherein each X in structure β9b is carbon.

6. The nucleobase pair of claim 1 , wherein each R 2 in structure β9b is hydrogen.

7. The nucleobase pair of claim 1 , wherein Y is sulfur.

8. The nucleobase pair of claim 7 , wherein E in structure β9b is sulfur.

9. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

10. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

11. The nucleobase pair of claim 1 , wherein each X in structure α15b and α15a is carbon.

12. The nucleobase pair of claim 1 , wherein the second nucleobase analog has the structure α15b.

13. The nucleobase pair of claim 12 , wherein R 1 in structure α15b is methyl.

14. The nucleobase pair of claim 13 , wherein E in structure α15b is oxygen.

15. The nucleobase pair of claim 12 , wherein each R 2 in structure α15b is hydrogen.

16. The nucleobase pair of claim 12 , wherein the second nucleobase analog is

17. The nucleobase pair of claim 1 , wherein the second nucleobase analog has the structure α15a.

18. The nucleobase pair of claim 17 , wherein at least one R 2 is CN.

19. The nucleobase pair of claim 17 , wherein R 1 in structure α15a is methyl.

20. The nucleobase pair of claim 19 , wherein E in structure α15a is oxygen.

21. The nucleobase pair of claim 17 , wherein the second nucleobase analog is

22. The nucleobase pair of claim 1 , wherein the second nucleobase analog has any of the structures

wherein each R is independently hydrogen, or the reactive linker.

23. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

24. The nucleobase pair of claim 23 , wherein the second nucleobase analog is

25. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

and the second nucleobase analog is

26. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

and the second nucleobase analog is

27. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

and the second nucleobase analog is

28. The nucleobase pair of claim 1, 7, or 8 , wherein at least one R 2 in structure β9b is halogen.

29. The nucleobase pair of claim 8 , wherein each X in structure β9b is carbon.

30. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

31. The nucleobase pair of claim 1 , wherein the first nucleobase analog is

and the second nucleobase analog is

32. A nucleobase pair comprising a first nucleobase analog having the structure

and a second nucleobase analog having the structure

wherein the wavy line indicates a point of bonding to a ribosyl, deoxyribosyl, or dideoxyribosyl moiety, wherein the ribosyl, deoxyribosyl, or dideoxyribosyl moiety (i) has its 5′-hydroxy group in free form or bound to a mono-phosphate, diphosphate, triphosphate, α-thiotriphosphate, β-thiophosphate, γ-thiophosphate group, or (ii) is included in an RNA or a DNA.

33. A nucleobase pair comprising a first nucleobase analog having the structure

and a second nucleobase analog having the structure

wherein the wavy line indicates a point of bonding to a ribosyl, deoxyribosyl, or dideoxyribosyl moiety, wherein the ribosyl, deoxyribosyl, or dideoxyribosyl moiety (i) has its 5′-hydroxy group in free form or bound to a mono-phosphate, diphosphate, triphosphate, α-thiotriphosphate, β-thiophosphate, or γ-thiophosphate group, or (ii) is included in an RNA or a DNA.

34. A double-stranded oligonucleotide comprising the nucleobase pair of claim 32 .

35. A double-stranded oligonucleotide comprising the nucleobase pair of claim 33 .

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 22, 2023
From: ROMESBERG, FLOYD E.; MALYSHEV, DENIS A.; LI, LINGJUN; LAVERGNE, THOMAS; LI, ZHENGTAO
To: THE SCRIPPS RESEARCH INSTITUTE
Reel/Frame 062773/0013 →
Continuity (4)
Division 16518715 · Jul 22, 2019
Division 14910203
Provisional Application 61863649 · Aug 8, 2013
Related Publication 20240101590A1 · Mar 28, 2024
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