	US 11,782,062 B2
	Kits for analysis using nucleic acid encoding and/or label
Mark S. Chee, Encinitas, CA (US); John M. Beierle, San Diego, CA (US); Norihito Muranaka, San Diego, CA (US); Kevin L. Gunderson, Encinitas, CA (US); Michael Phillip Weiner, San Diego, CA (US); Lei Shi, San Diego, CA (US); Robert C. James, San Diego, CA (US); and Luca Monfregola, San Diego, CA (US)
Assigned to Encodia, Inc., San Diego, CA (US)
Filed by Encodia, Inc., San Diego, CA (US)
Filed on Feb. 8, 2023, as Appl. No. 18/166,461.
Application 18/166,461 is a continuation of application No. 17/819,263, filed on Aug. 11, 2022.
Application 17/819,263 is a continuation of application No. 16/760,028, granted, now 11,513,126, issued on Nov. 29, 2022, previously published as PCT/US2018/058565, filed on Oct. 31, 2018.
Claims priority of provisional application 62/583,448, filed on Nov. 8, 2017.
Claims priority of provisional application 62/582,312, filed on Nov. 6, 2017.
Claims priority of provisional application 62/579,844, filed on Oct. 31, 2017.
Prior Publication US 2023/0236198 A1, Jul. 27, 2023
Int. Cl. C40B 70/00 (2006.01); G01N 33/68 (2006.01); C40B 40/10 (2006.01)

CPC G01N 33/6842 (2013.01) [C40B 40/10 (2013.01); C40B 70/00 (2013.01); G01N 33/6845 (2013.01)]

24 Claims

1. A method for analyzing a polypeptide, comprising:

(a) contacting the polypeptide with a first binding agent,

wherein the polypeptide is associated with a nucleic acid recording tag joined to a support,

wherein the first binding agent is associated with a first nucleic acid coding tag that comprises identifying information regarding the first binding agent, and

wherein the first binding agent binds to a terminal amino acid (TAA) or a modified TAA of the polypeptide;

(b) transferring the identifying information regarding the first binding agent from the first nucleic acid coding tag to the nucleic acid recording tag to generate a first order extended nucleic acid recording tag on the support, and/or transferring sequence information of the nucleic acid recording tag to the first nucleic acid coding tag to generate an extended first nucleic acid coding tag;

(c) cleaving the polypeptide to generate a cleaved polypeptide, thereby removing the TAA or the modified TAA to expose a new TAA, and, optionally, modifying the new TAA to yield a newly modified TAA;

(d) contacting the cleaved polypeptide with a second binding agent,

wherein the second binding agent is associated with a second nucleic acid coding tag that comprises identifying information regarding the second binding agent, and

wherein the second binding agent binds to the new TAA or the newly modified TAA;

(e) transferring the identifying information regarding the second binding agent from the second nucleic acid coding tag to the first order extended nucleic acid recording tag to generate a second order extended nucleic acid recording tag on the support, and/or transferring sequence information of the nucleic acid recording tag to the second nucleic acid coding tag to generate an extended second nucleic acid coding tag; and

(f) analyzing the second order extended nucleic acid recording tag and/or analyzing the extended first and extended second nucleic acid coding tags, wherein the analyzing comprises a sequencing method, to obtain the identifying information regarding the first binding agent and the identifying information regarding the second binding agent, thereby providing information regarding an amino acid sequence of the polypeptide.