Macromolecule analysis employing nucleic acid encoding
Inventors
Chee, Mark • Gunderson, Kevin • Weiner, Michael Phillip
Assignees
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Publication Number
US-12123878-B2
Publication Date
2024-10-22
Expiration Date
Abstract
A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
Core Innovation
The invention provides a method for analyzing a plurality of different macromolecule analytes in which each macromolecule analyte is associated with a nucleic acid recording tag and the analyte and recording tag are joined to a single solid support. The method uses nucleic acid coding tags carried by binding agents, where each coding tag comprises identifying information regarding the binding agent.
Different binding agents are contacted to the macromolecule analytes in a controlled sequence. After a first binding agent binds a first macromolecule analyte, identifying information regarding the first binding agent is transferred from the nucleic acid coding tag to the nucleic acid recording tag to generate a first order extended recording tag joined to the solid support, and additional binding agents transfer coding-tag identifying information to generate second order extended recording tags.
The method optionally repeats contacting and transferring for additional cycles so that an (n+2)th order extended recording tag is generated and represents the first macromolecule analyte. The analyzing comprises a sequencing method to obtain identifying information regarding the binding agents that bind to the first macromolecule analyte in each cycle, and the framework is compatible with nucleic-acid sequencing platforms and downstream processing of extended recording/coding tags, including library amplification, targeted enrichment (hybrid capture), and multiplexing.
Claims Coverage
Independent claim clm-00001 covers a cyclic, tag-based analyte analysis workflow that transfers identifying information from coding tags on sequentially bound binding agents into extended nucleic acid recording tags on a single solid support, followed by sequencing-based analysis of the extended recording tags. This claim includes 5 inventive features.
Single solid support with nucleic-acid recording tags
Providing a plurality of different macromolecule analytes, each associated with a nucleic acid recording tag, such that the plurality of different macromolecule analytes and the nucleic acid recording tags associated therewith are joined to a single solid support.
Coding-tagged binding agents and identifying-information transfer to extended recording tags
Contacting the plurality of different macromolecule analytes with a first plurality of binding agents each associated with a nucleic acid coding tag comprising identifying information regarding the binding agent; following binding of a first binding agent to a first macromolecule analyte, transferring identifying information regarding the first binding agent from the nucleic acid coding tag associated therewith to the nucleic acid recording tag associated with the first macromolecule analyte to generate a first order extended recording tag joined to the solid support.
Sequential binding and generating higher order extended recording tags
Contacting the plurality of different macromolecule analytes with a second plurality of binding agents each associated with a nucleic acid coding tag comprising identifying information regarding the binding agent; following binding of a second binding agent to the first macromolecule analyte, transferring identifying information regarding the second binding agent from the nucleic acid coding tag associated therewith to the first order extended recording tag to generate a second order extended recording tag joined to the solid support.
Cyclic repetition to generate (n+2)th order extended recording tags
Optionally repeating steps (d)-(e) for “n” additional cycles of contacting and transferring, wherein n is a natural number, and during each cycle transferring identifying information regarding the coding tag of each binding agent that binds to the first macromolecule analyte to generate an (n+2)th order extended recording tag joined to the solid support that represents the first macromolecule analyte.
Sequencing analysis to obtain per-cycle binding-agent identity information
Analyzing the second order extended recording tag or (n+2)th order extended recording tag, wherein analyzing comprises a sequencing method, and obtaining the identifying information regarding the binding agents that bind to the first macromolecule analyte in each cycle of contacting and transferring to provide information regarding the first macromolecule analyte.
Across independent claim clm-00001, the core inventive concept is constructing analyte-specific extended nucleic acid recording tags on a single solid support via sequential/cyclic transfer of binding-agent identifying information from coding tags, followed by sequencing-based analysis to derive binding-agent identity per cycle and thereby provide information about each analyte.
Stated Advantages
Enables obtaining identifying information regarding binding agents that bind to a macromolecule analyte in each cycle of contacting and transferring by analyzing extended recording tags using a sequencing method.
Supports analysis of a plurality of different macromolecule analytes by using nucleic acid recording tags and coding-tagged binding agents joined to a single solid support.
Provides a cyclic extended recording-tag framework that iteratively represents the first macromolecule analyte through sequential order extended recording tags.
Documented Applications
Nucleic-acid sequencing platforms and downstream processing of extended recording/coding tags, including library amplification, targeted enrichment (hybrid capture), and multiplexing.
Analyzing a plurality of different macromolecule analytes by generating extended recording tags and obtaining information regarding binding agents that bind to a first macromolecule analyte in each cycle using a sequencing method.
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