Granted Patent
B2
US 12,517,133 · App. 18/660,053 · Granted Jan 6, 2026
Macromolecule analysis employing nucleic acid encoding
Inventors:
Mark S. Chee (Encinitas, CA); Kevin L. Gunderson (Encinitas, CA); Michael Phillip Weiner (San Diego, CA)
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Abstract
A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
Claims (33)
1 . A method of analyzing a polypeptide of a spatial sample, the method comprising:
(a) attaching the polypeptide to a nucleic acid recording tag within the spatial sample;
(b) contacting the spatial sample with an array of spatial barcode molecules, wherein each of the spatial barcode molecules comprises a nucleic acid sequence that reflects a spatial position of the spatial barcode molecule within the array and further comprises a nucleic acid sequence configured to hybridize with a portion of the nucleic acid recording tag;
(c) cleaving spatial barcode molecules from the array and allowing them to diffuse into the spatial sample and hybridize to the nucleic acid recording tag attached to the polypeptide within the spatial sample;
(d) generating an extended nucleic acid recording tag attached to the polypeptide by transferring information of a hybridized spatial barcode molecule to the nucleic acid recording tag attached to the polypeptide; and
(e) analyzing the extended nucleic acid recording tag, wherein the analyzing comprises a nucleic acid sequencing method, to obtain information about location of the polypeptide within the spatial sample.
2 . The method of claim 1 , further comprising analyzing at least a portion of a sequence of the polypeptide attached to the extended nucleic acid recording tag.
3 . The method of claim 1 , further comprising fragmenting, before step (e), the polypeptide attached to the extended nucleic acid recording tag, thereby generating a peptide attached to the extended nucleic acid recording tag.
4 . The method of claim 3 , further comprising extracting the peptide attached to the extended nucleic acid recording tag from the spatial sample into a solution.
5 . The method of claim 4 , further comprising analyzing at least a portion of an amino acid sequence of the extracted peptide attached to the extended nucleic acid recording tag.
6 . The method of claim 5 , wherein the sequence of the peptide attached to the extended nucleic acid recording tag is analyzed by:
(a) binding the peptide with a binding agent, wherein the binding agent comprises a coding tag with identifying information regarding the binding agent; and
(b) transferring the identifying information of the coding tag to the extended nucleic acid recording tag attached to the peptide to generate a further extended recording tag,
wherein the further extended recording tag is analyzed using the nucleic acid sequencing method to obtain the identifying information regarding the binding agent and the information about location of the polypeptide within the spatial sample.
7 . The method of claim 1 , wherein the extended nucleic acid recording tag is generated using a polymerase extension.
8 . The method of claim 3 , wherein the polypeptide is fragmented with a protease.
9 . The method of claim 1 , wherein the spatial sample is a tissue slice.
10 . The method of claim 9 , wherein the tissue slice is fixed and permeabilized.
11 . A method of analyzing a polypeptide of a spatial sample, the method comprising:
(a) attaching the polypeptide to a nucleic acid recording tag within the spatial sample;
(b) contacting the spatial sample with an array of spatial barcode molecules, wherein each of the spatial barcode molecules comprises a nucleic acid sequence that reflects a spatial position of the spatial barcode molecule within the array and further comprises a nucleic acid sequence configured to hybridize with a portion of the nucleic acid recording tag;
(c) fragmenting the polypeptide attached to the nucleic acid recording tag, thereby generating a peptide attached to the nucleic acid recording tag, and allowing the peptide and the attached nucleic acid recording tag to diffuse to the array and hybridize to one of the spatial barcode molecules within the array;
(d) generating an extended nucleic acid recording tag attached to the peptide by transferring information of the hybridized spatial barcode molecule to the nucleic acid recording tag attached to the peptide; and
(e) analyzing the extended nucleic acid recording tag, wherein the analyzing comprises a nucleic acid sequencing method, to obtain information about location of the polypeptide within the spatial sample.
12 . The method of claim 11 , further comprising analyzing at least a portion of a sequence of the polypeptide attached to the extended nucleic acid recording tag.
13 . The method of claim 12 , wherein the sequence of the peptide attached to the extended nucleic acid recording tag is analyzed by:
(a) binding the peptide with a binding agent, wherein the binding agent comprises a coding tag with identifying information regarding the binding agent; and
(b) transferring the identifying information of the coding tag to the extended nucleic acid recording tag attached to the peptide to generate a further extended recording tag,
wherein the further extended recording tag is analyzed using the nucleic acid sequencing method to obtain the identifying information regarding the binding agent and the information about location of the polypeptide within the spatial sample.
14 . The method of claim 11 , wherein the extended nucleic acid recording tag is generated using a polymerase extension.
15 . The method of claim 11 , wherein the polypeptide is fragmented with a protease.
16 . The method of claim 11 , wherein the spatial sample is a tissue slice.
17 . The method of claim 16 , wherein the tissue slice is fixed and permeabilized.
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 May 24, 2024
From: CHEE, MARK S.; GUNDERSON, KEVIN L.; WEINER, MICHAEL PHILLIP
To: ENCODIA, INC.
Reel/Frame 067524/0701 →
Continuity (6)
Continuation
16098436
Provisional Application
62376886
· Aug 18, 2016
Provisional Application
62339071
· May 19, 2016
Provisional Application
62330841
· May 2, 2016
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