DNA-glycan conjugates and methods of use

Patent metadata

Field	Value
Publication number	US-11884961-B2
Application number	US-201816617756-A
Country	US
Kind code	B2
Filing date	Jun 1, 2018
Priority date	Jun 2, 2017
Publication date	Jan 30, 2024
Grant date	Jan 30, 2024

Abstract

Provided herein are DNA-glycan conjugates that include a glycan and a covalently attached polynucleotide. The polynucleotide includes a plurality of modules. Each module includes a nucleotide string, and the plurality of modules includes a monomer module that corresponds to each carbohydrate monomer present in the DNA-glycan conjugate, and a linkage module that corresponds to each glycosidic linkage present between each carbohydrate monomer in the DNA-glycan conjugate. The nucleotide sequence of the plurality of modules corresponds to the glycan structure. Also provided herein are methods for making and using the DNA-glycan conjugates. Further provided is a computer-implemented method for translating data from a nucleotide sequence to a glycan structure, a system for converting data from a glycan structure to a nucleotide sequence, and a system for translating data from a nucleotide sequence to a glycan structure.

First claim

What is claimed is:

1. A DNA-glycan conjugate comprising:
a glycan comprising a glycan structure of at least two carbohydrate monomers,
wherein each carbohydrate monomer is attached to at least one other carbohydrate monomer by a glycosidic linkage; and

a polynucleotide covalently attached to the glycan, the polynucleotide comprising a plurality of modules, each module comprising a nucleotide string,
wherein the plurality of modules comprises:
a monomer module identifying each carbohydrate monomer present in the DNA-glycan conjugate, and
a linkage module identifying each glycosidic linkage present between each carbohydrate monomer in the DNA-glycan conjugate,

wherein the nucleotide sequence of the plurality of modules corresponds to the glycan structure.

2. The DNA-glycan conjugate of claim 1 , wherein each carbohydrate monomer is selected from the group consisting of All, AllNAc, AllN, AllA, Alt, AltNAc, AltN, AltA, Glc, GlcNAc, GlcN, GlcA, Man, ManNAc, ManN, ManA, GpL, GulNAc, GulN, GulA, Ido, IdoNAc, IdoN, IdoA, Gal, GalNAc, GalN, GalA, Tal, TalNAc, TalN, TalA, Tag, TagA, Hep, DDManHep, Dha, LDManHep, Fuc, FucNAc, FucN, Qui, QuiNAc, QuiN, Rha, RhaNAc, RhaN, Tyv, Oli, Par, Dig, 6dAlt, 6dTal, Abe, Api, Col, Neu5Ac, Neu5GC, Kdn, Kdo, Mur, MurNAc, MurNGc, Sia, Neu, Fru, Sor, Psi, Rib, Ara, Xyl, or Lyx.

3. The DNA-glycan conjugate of claim 1 , wherein each linkage module identifies a glycosidic linkage that comprises an anomeric configuration and linkage position of each glycosidic linkage, the glycosidic linkage selected from: a1-1, a1-2, a1-3, a1-4, a1-5, a1-6, a1-7, a1-8, a2-1, a2-2, a2-3, a2-4, a2-5, a2-6,a2-7, a2-8, b1-1, b1-2, b1-2, b1-4, b1-5, b1-6, b1-7, b1-8, a?, b?, ?1, ?2, ?2, ?4, ?5, ?6, ?7, ?8, ??,), and (, wherein ? means i) the position or configuration of the anomeric carbon of a monomer is not characterized or (ii) the linkage position between the anomeric carbon of the monomer and the carbon bearing the connecting oxygen of the following monomer is not characterized.

4. The DNA-glycan conjugate of claim 1 , wherein the glycan comprises a sequence of at least 3 carbohydrate monomers,
wherein at least 2 of the carbohydrate monomers are joined by a branch, and
wherein the plurality of modules further comprises a branch beginning module and a branch ending module identifying each branch present in the DNA-glycan conjugate.

5. The DNA-glycan conjugate of claim 4 , wherein the branch linkage is selected from: a1-1, a1-2, a1-3, a1-4, a1-5, a1-6, a1-7, a1-8, a2-1, a2-2, a2-3, a2-4, a2-5, a2-6,a2-7, a2-8, b1-1, b1-2, b1-2, b1-4, b1-5, b1-6, b1-7, b1-8, a?, b?, ?1, ?2, ?2, ?4, ?5, ?6, ?7, ?8, ??,), and (, wherein ? means i) the position or configuration of the anomeric carbon of a monomer is not characterized or (ii) the linkage position between the anomeric carbon of the monomer and the carbon bearing the connecting oxygen of the following monomer is not characterized.

6. The DNA-glycan conjugate of claim 1 , wherein a carbohydrate monomer comprises a modification, and
wherein the plurality of modules further comprises a modification module identifying each modification present in the DNA-glycan conjugate.

7. The DNA-glycan conjugate of claim 6 , wherein each modification is selected from 2Y, 4Y, 7Y, 8Y, ?Y, 20H, 40H, 70H, 80H, ?OH, 2V, 4V, 7V, 8V, ?V, 2S, 4S, 7S, 8S, ?S, 2P, 4P, 7P, 8P, ?P, 2J, 4J, 7J, 8J, ?J, 2NAc, 4NAc, 7NAc, 8NAc, ?Nac, 2Ac, 4Ac, 7Ac, 8Ac, ?Ac, 2COOH, 4COOH, 7COOH, 8COOH, ?COOH, 2IN, 3IN, 7IN, 81N, ?IN, 2EE, 4EE, 7EE, 8EE, ?EE, 2EH, 4EH, 7EH, 8EH, ?EH, 2Q, 4Q, 7Q, 8Q, ?Q, 2QS, 4QS, 7QS, 8QS, ?QS, 2PYR, 4PYR, 7PYR, 8PYR, ?PYR, 2ECO, 4ECO, TECO, 8ECO, ?ECO, 2PC, 4PC, 7PC, 8PC, ?PC, 2PE, 4PE, 7PE, 8PE, ?PE, 2ME, 3ME, 4ME, 7ME, 8ME, ?ME, and 3 S, wherein “?” means the position of the modification is not characterized.

8. A kit for identifying a DNA-glycan conjugate bound to a glycan-binding compound, comprising in separate containers:
the DNA-glycan conjugate of claim 1 ; and
primers for amplification of the polynucleotide of the DNA-glycan conjugate.

9. A kit for determining whether a specific glycan associated with a blood group is present in a sample, comprising in separate containers:
DNA-glycan conjugates of claim 1 , wherein separate DNA-glycan conjugates comprise glycans that comprise a blood group selected from A blood group, B blood group, the O group, blood group P, blood group p1, blood group Pk, blood group FORS1, blood group LKE, blood group I, and blood group I; and
primers for amplification of the polynucleotides of the DNA-glycan conjugates.

10. A composition of at least two populations of DNA-glycan conjugates, wherein each population of DNA-glycan conjugate is different and comprises the structure of the DNA-glycan conjugate of claim 1 .

11. A library comprising the DNA-glycan conjugate of claim 1 and at least two different DNA-glycan conjugates, wherein each of the at least two different DNA-glycan conjugates comprise:
a glycan comprising a glycan structure of at least two carbohydrate monomers,
wherein each carbohydrate monomer is attached to at least one other carbohydrate monomer by a glycosidic linkage; and
a polynucleotide covalently attached to the glycan, the polynucleotide comprising a plurality of modules, each module comprising a nucleotide string,
wherein the plurality of modules comprises:
a monomer module identifying each carbohydrate monomer present in the DNA-glycan conjugate, and
a linkage module identifying each glycosidic linkage present between each carbohydrate monomer in the DNA-glycan conjugate,

wherein the nucleotide sequence of the plurality of modules corresponds to the glycan structure.

12. A method for identifying a glycan-binding compound, the method comprising:
contacting a portion of a sample suspected of comprising one or more glycan-binding compounds with the DNA-glycan conjugate of claim 1 to result in a mixture, wherein the sample is suspected of comprising a glycan-binding compound that will bind the DNA-glycan conjugate, and wherein the contacting is under conditions suitable for binding of the glycan-binding compound and the DNA-glycan conjugate to form a complex; and
identifying any DNA-glycan conjugate bound to the glycan-binding compound.

13. The method of claim 12 wherein the sample does not comprise a glycan-binding compound that will bind a DNA-glycan conjugate present in the mixture.

14. The method of claim 12 wherein the sample comprises a biological sample.

15. The method of claim 14 wherein the biological sample comprises blood.

16. The method of claim 12 wherein the glycan-binding compound comprises a protein.

17. The method of claim 16 wherein the protein comprises an antibody.

18. The method of claim 12 wherein the identifying comprises determining the nucleotide sequence of the polynucleotide attached to the DNA-glycan conjugate bound to the glycan-binding compound.

19. A method for identifying a glycan-binding compound, the method comprising:
contacting a sample suspected of comprising a plurality of glycan-binding compounds with a plurality of the DNA-glycan conjugates of claim 1 to result in a mixture, wherein the sample is suspected of comprising at least one glycan-binding compound that will bind a DNA-glycan conjugate of the plurality of the DNA-glycan conjugates, and wherein the contacting is under conditions suitable for binding a glycan-binding compound of the sample to a DNA-glycan conjugate of the plurality of the DNA-glycan conjugates; and
identifying any DNA-glycan conjugates bound to glyca

Assignees

• Univ Georgia State Res Found

Inventors

• Wang Peng George
• Song Jing
• Kondengaden Muhammed Shukkoor
• Parameswaran Aishwarya

Classifications

• C12Q1/6804 Primary

  Nucleic acid analysis using immunogens (immunoassay G01N33/53) · CPC title

• G01N33/5308

  for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites · CPC title

• G01N33/80

  involving blood groups or blood types {or red blood cells (white blood cells G01N33/56972)} · CPC title

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• G16B40/20

  Supervised data analysis · CPC title