US 12,467,049 B2
Methods and kits using nucleic acid encoding and/or label
Mark S. Chee, Encinitas, CA (US); Kevin L. Gunderson, Encinitas, CA (US); Michael Phillip Weiner, San Diego, CA (US); Lei Shi, San Diego, CA (US); and Norihito Muranaka, San Diego, CA (US)
Filed by Encodia, Inc., San Diego, CA (US)
Filed on Aug. 9, 2024, as Appl. No. 18/799,749.
Application 18/799,749 is a continuation of application No. 18/125,075, filed on Mar. 22, 2023, granted, now 12,129,463.
Application 18/125,075 is a continuation of application No. 16/760,032, abandoned, previously published as PCT/US2018/058583, filed on Oct. 31, 2018.
Claims priority of provisional application 62/582,916, filed on Nov. 7, 2017.
Claims priority of provisional application 62/579,840, filed on Oct. 31, 2017.
Prior Publication US 2025/0051756 A1, Feb. 13, 2025
Int. Cl. C12N 15/10 (2006.01); C12Q 1/6804 (2018.01); G01N 33/68 (2006.01)
CPC C12N 15/1065 (2013.01) [C12Q 1/6804 (2013.01); G01N 33/68 (2013.01); G01N 2458/10 (2013.01)] 29 Claims
OG exemplary drawing
 
1. A method for analyzing a polypeptide, comprising:
(a) contacting (i) a plurality of fragments of a polypeptide, wherein each fragment is associated directly or indirectly with a recording tag, with (ii) a plurality of binding agents, wherein the recording tags comprise a common barcode, wherein each binding agent comprises a binding moiety and a coding tag comprising identifying information regarding the binding moiety, wherein the binding moiety is capable of binding to one or more amino acids of a fragment of the plurality of fragments, or capable of binding to the one or more amino acids modified by a functionalizing reagent, and wherein each fragment and/or its associated recording tag, or each binding agent, is immobilized directly or indirectly on a substrate;
(b) for each fragment of the plurality of fragments, allowing transfer of information between (i) the recording tag associated with the fragment and (ii) the coding tag of a binding agent of the plurality of binding agents, upon binding between the binding moiety of the binding agent and the one or more amino acids of the fragment, thereby generating an extended recording tag, an extended coding tag, or a di-tag construct for each fragment of the plurality of fragments, wherein the extended recording tag, the extended coding tag, or the di-tag construct comprises nucleic acid sequence information of the common barcode and the identifying information regarding the binding moiety; and
(c) analyzing nucleic acid sequence of the extended recording tag, the extended coding tag, or the di-tag construct to obtain at least partial amino acid sequence information of each fragment of the plurality of fragments and a nucleic acid sequence of the common barcode, and combining the at least partial amino acid sequence information of each fragment of the plurality of fragments using the nucleic acid sequence information of the common barcode to obtain amino acid sequence information regarding the polypeptide.