Granted Patent
B2
US 12,292,446 · App. 18/787,946 · Granted May 6, 2025
Kits for analysis using nucleic acid encoding and/or label
Inventors:
Mark S. Chee (Encinitas, CA); John M. Beierle (San Diego, CA); Norihito Muranaka (San Diego, CA); Kevin L. Gunderson (Encinitas, CA); Michael Phillip Weiner (San Diego, CA); Lei Shi (San Diego, CA); Robert C. James (San Diego, CA); Luca Monfregola (San Diego, CA)
Assignee:
ENCODIA, INC.
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Abstract
Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.
Claims (26)
1. A kit for analyzing a polypeptide, comprising:
(a) a functionalizing reagent that reacts with an N-terminal amino acid (NTAA) of the polypeptide to generate a functionalized NTAA of the polypeptide;
(b) one or more nucleic acid recording tags configured to associate directly or indirectly with the polypeptide or with a component of the polypeptide obtained by a cleavage of the functionalized NTAA of the polypeptide, wherein each of the one or more nucleic acid recording tags comprises a unique molecular identifier (UMI); and
(c) one or more binding agents each comprising:
(i) a binding moiety that binds to the functionalized NTAA of the polypeptide or the component of the polypeptide obtained by the cleavage of the functionalized NTAA of the polypeptide; and
(ii) a nucleic acid coding tag attached to the binding moiety and comprising a barcode sequence that comprises identifying information regarding the binding moiety;
wherein the one or more nucleic acid recording tags and the one or more nucleic acid coding tags are configured to allow transfer of sequence information of the barcode sequence and/or the UMI by ligation or primer extension, upon binding between each binding agent and the functionalized NTAA of the polypeptide or the component of the polypeptide, thereby generating one or more extended nucleic acid constructs each comprising the barcode sequence or a complement thereof and the UMI or a complement thereof.
2. The kit of claim 1 , wherein the component of the polypeptide comprises one or more amino acid residues of the polypeptide.
3. The kit of claim 1 , wherein the component of the polypeptide comprises one or more terminal amino acid residues of the polypeptide.
4. The kit of claim 1 , wherein the component of the polypeptide is an N-terminal amino acid (NTAA) residue.
5. The kit of claim 1 , which is for analyzing 1,000,000 or more polypeptide molecules.
6. The kit of claim 1 , further comprising an instruction for using the kit in high throughput polypeptide analysis.
7. The kit of claim 1 , comprising three or more different binding agents.
8. The kit of claim 1 , wherein at least one of the one or more binding agents is capable of binding to a terminal amino acid residue of the polypeptide.
9. The kit of claim 1 , wherein the component of the polypeptide comprises a modified or functionalized amino acid residue of the polypeptide.
10. The kit of claim 1 , further comprising an eliminating reagent for removing the functionalized NTAA residue to expose its immediately adjacent amino acid residue, as a second NTAA.
11. The kit of claim 1 , wherein the polypeptide or the component of the polypeptide is immobilized on a solid support.
12. The kit of claim 1 , further comprising a solid support, wherein the one or more nucleic acid recording tags are configured to be: covalently immobilized directly or indirectly to the solid support; or associated with the polypeptide immobilized on the solid support.
13. The kit of claim 12 , wherein the solid support is a bead.
14. The kit of claim 12 , wherein the solid support comprises a plurality of nucleic acid hairpins immobilized on the solid support and configured to capture via hybridization the one or more nucleic acid recording tags associated with the polypeptide.
15. The kit of claim 1 , wherein each of the one or more nucleic acid recording tags further comprises a sample barcode.
16. The kit of claim 1 , further comprising a reagent for transferring sequence information of the barcode sequence and/or the UMI by ligation between the one or more nucleic acid recording tags and the one or more nucleic acid coding tags.
17. The kit of claim 1 , further comprising a reagent for transferring sequence information of the barcode sequence and/or the UMI by primer extension of the one or more nucleic acid recording tags and/or the one or more nucleic acid coding tags.
18. The kit of claim 1 , wherein each of the one or more nucleic acid recording tags and each of the one or more nucleic acid coding tags comprise complementary spacer sequences.
19. The kit of claim 1 , wherein each nucleic acid coding tag attached to the binding moiety further comprises a cycle-specific barcode.
20. The kit of claim 1 , wherein the one or more nucleic acid recording tags are configured to be covalently attached directly or indirectly to the polypeptide or to the component of the polypeptide.
Assignments (4)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded May 18, 2026
From: ENCODIA, INC.
To: 2026 DF PEPTIDE ACQUISITION LLC
Reel/Frame 075642/0658 →
NON-RECOURSE ASSIGNMENT OF INTELLECTUAL PROPERTY SECURITY AGREEMENT
Recorded Jan 30, 2026
From: FIRST-CITIZENS BANK & TRUST COMPANY
To: DF PEPTIDE ACQUISITION LLC
Reel/Frame 074539/0609 →
SECURITY INTEREST
Recorded Oct 21, 2025
From: ENCODIA, INC.
To: FIRST-CITIZENS BANK & TRUST COMPANY
Reel/Frame 073175/0335 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Aug 6, 2024
From: CHEE, MARK S.; BEIERLE, JOHN M.; MURANAKA, NORIHITO; GUNDERSON, KEVIN L.; WEINER, MICHAEL PHILLIP; SHI, LEI; JAMES, ROBERT C.; MONFREGOLA, LUCA
To: ENCODIA, INC.
Reel/Frame 068199/0961 →
Continuity (6)
Continuation
16760028
Provisional Application
62583448
· Nov 8, 2017
Provisional Application
62582312
· Nov 6, 2017
Provisional Application
62579844
· Oct 31, 2017
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