US-20260125412-A1 - NUCLEOTIDES WITH ALPHA-IMINO PHOSPHATE GROUPS AND BRIDGING SULFURS, AND METHODS OF SYNTHESIZING AND USING THE SAME

Abstract

Nucleotides with alpha-imino phosphate groups and bridging sulfurs, and methods of synthesizing and using the same, are provided herein. In some examples, a nucleotide may include a sugar, a nucleobase coupled to the sugar, an alpha-imino phosphate group, and a bridging sulfur coupling the alpha-imino phosphate group to the sugar.

Inventors

• Jean-Alexandre Richard
• Xiangyuan YANG
• Sharyuen Soh
• Jing Liang
• Deepti Sharma
• Yin Nah Teo
• Ramesh Neelakandan
• Sadeer Salam
• Min Yen Lee
• Daniel Hartoyo Lukamto
• Shi Yuan Jeow
• Xi Liew
• Jin Yong Neo
• Tsz Ying Yuen

Assignees

• ILLUMINA, INC.

Dates

Publication Date

20260507

Application Date

20251104

Claims (20)

1. 1 . A nucleotide, comprising: a sugar; a nucleobase coupled to the sugar, an alpha-imino phosphate group; a bridging sulfur coupling the alpha-imino phosphate group to the sugar.
2. 2 . The nucleotide of claim 1 , further comprising a sulfonyl group or an aryl group coupled to the alpha-imino phosphate group.
3. 3 . The nucleotide of claim 2 , further comprising a first functional group coupled to the alpha-imino phosphate group via the sulfonyl group or aryl group.
4. 4 . The nucleotide of claim 2 , wherein the aryl group is functionalized.
5. 5 . The nucleotide of claim 2 , further comprising a second functional group coupled to the nucleobase.
6. 6 . (canceled)
7. 7 . (canceled)
8. 8 . The nucleotide of claim 5 , wherein the second functional group further is coupled to the first functional group to form a loop.
9. 9 . The nucleotide of claim 5 , wherein the nucleobase comprises a purine analog or a pyrimidine analog.
10. 10 . The nucleotide of claim 1 , wherein the nucleobase comprises a purine, a pyrimidine, a purine analog, or a pyrimidine analog.
11. 11 . The nucleotide of claim 1 , wherein the sugar comprises ribose or deoxyribose.
12. 12 . The nucleotide of claim 1 , further comprising at least one phosphate group coupled to the alpha-imino phosphate group.
13. 13 . The nucleotide of claim 1 , wherein the alpha-imino phosphate group is part of a triphosphate group.
14. 14 . A kit, comprising: the nucleotide of claim 1 ; and a reagent for selectively cleaving the bond between the alpha-imino phosphate and the bridging sulfur.
15. 15 . The kit of claim 14 , wherein the reagent comprises an Ag(I) metal salt, Au(III) metal salt, Pd(II) metal salt, or Oxone.
16. 16 . The kit of claim 14 , further comprising a polymerase for incorporating the nucleotide into a polynucleotide.
17. 17 . A method for modifying a polynucleotide, the method comprising: using a polymerase to incorporate the nucleotide of claim 1 into a polynucleotide; and using a reagent to selectively cleave the bond between the alpha-imino phosphate and the bridging sulfur after the nucleotide is incorporated into the polynucleotide.
18. 18 . A method of modifying a nucleotide, the method comprising: installing a thiol group at a 5′ position of a sugar of the nucleotide; coupling a phosphor atom to the sulfur atom of the thiol group; and forming an alpha-imino phosphate group coupled to a sulfonyl group or an aryl group.
19. 19 . The method of claim 18 , wherein installing the thiol group comprises using a Mitsunobu reaction followed by reduction; and wherein forming the alpha-imino phosphate group includes using a phosphoramidite followed by a Staudinger reaction.
20. 20 . (canceled)

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Patent Application No. 63/716,875, filed Nov. 6, 2024 and entitled “NUCLEOTIDES WITH ALPHA-IMINO PHOSPHATE GROUPS AND BRIDGING SULFURS, AND METHODS OF SYNTHESIZING AND USING THE SAME,” the entire contents of which are incorporated by reference herein. FIELD This application relates to nucleotides. BACKGROUND Modified nucleoside triphosphates are key drivers of various sequencing technologies. For example, some sequencing technologies track the incorporation of fluorophore-labelled nucleotides into a polynucleotide. The sequence of the polynucleotide is determined by reading the emission from nucleotide-specific fluorophores during each incorporation cycle. It may be desirable to modify nucleotides to include different moieties. Traditional methods of installing modifications may use intermediates that are costly and involve multi-step syntheses. Moreover, extensive functionalization of triphosphate substrates carries a risk of phosphate chain degradation. Such degradation can lead to poor overall yields. SUMMARY Nucleotides with alpha-imino phosphate groups and bridging sulfurs, and methods of synthesizing and using the same, are provided herein. Some examples herein provide a nucleotide. The nucleotide may include a sugar; a nucleobase coupled to the sugar; an alpha-imino phosphate group; and a bridging sulfur coupling the alpha-imino phosphate group to the sugar. In some examples, the nucleotide may include a sulfonyl group or aryl group coupled to the alpha-imino phosphate group. In some examples, the nucleotide further may include a first functional group coupled to the alpha-imino phosphate group via the sulfonyl group or aryl group. In some examples, the aryl group is functionalized. In some examples, the nucleotide includes a second functional group coupled to the nucleobase. The second functional group may be of a same type as the first functional group. Or, the second functional group may be of a different type than the first functional group. In some examples, the second functional group further is coupled to the first functional group to form a loop. In some examples, the nucleobase includes a purine analog or a pyrimidine analog. In some examples, the nucleobase includes a purine, a pyrimidine, a purine analog, or a pyrimidine analog. In some examples, the sugar includes ribose or deoxyribose. In some examples, the nucleotide includes at least one phosphate group coupled to the alpha-imino phosphate group. In some examples, the alpha-imino phosphate group is part of a triphosphate group. Some examples herein provide a kit. The kit may include any of the nucleotides provided herein, and a reagent for selectively cleaving the bond between the alpha-imino phosphate and the bridging sulfur. In some examples, the reagent includes an Ag(I) metal salt, Au(III) metal salt, Pd(II) metal salt, or Oxone. In some examples, the kit further includes a polymerase for incorporating the nucleotide into a polynucleotide. Some examples herein provide a method for modifying a polynucleotide. The method may include using a polymerase to incorporate any of the nucleotides provided herein into a polynucleotide. The method may include using a reagent to selectively cleave the bond between the alpha-imino phosphate and the bridging sulfur after the nucleotide is incorporated into the polynucleotide. Some examples herein provide a method for modifying a polynucleotide. The method may include installing a thiol group at a 5′ position of a sugar of the nucleotide; coupling a phosphor atom to the sulfur atom of the thiol group; and forming an alpha-imino phosphate group coupled to a sulfonyl group or an aryl group. In some examples, installing the thiol group includes using a Mitsonobu reaction followed by reduction. In some examples, forming the alpha-imino phosphate group includes using a phosphoramidite. In some examples, forming the alpha-imino phosphate group includes using a Staudinger reaction. In some examples, the sulfonyl group or the aryl group is coupled to a first functional group. In some examples, the nucleotide includes a nucleobase including a second functional group. In some examples, the method further includes coupling the first functional group to the second functional group to form a loop. Some examples herein provide a method for modifying a polynucleotide. The method may include, in examples in which the sulfonyl group or the aryl group is coupled to a first functional group, coupling the first functional group to the second functional group to form a loop. It is to be understood that any respective features/examples of each of the aspects of the disclosure as described herein can be implemented together in any appropriate combination, and that any features/examples from any one or more of these aspects can be implemented together with any of the features of the other aspect(s) as described herein in any a