Macromolecule analysis employing nucleic acid encoding
Inventors
Chee, Mark S. • Gunderson, Kevin L. • Weiner, Michael Phillip
Assignees
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Publication Number
US-12235276-B2
Publication Date
2025-02-25
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 proteomics workflow that combines compartmentalization/partitioning with nucleic-acid recording and coding tags to analyze peptide-associated information. A peptide or a component of the peptide is associated with a nucleic acid recording tag comprising a barcode for the peptide, and binding agents each include a nucleic acid coding tag comprising an encoder sequence that comprises identifying information regarding the binding agent.
After binding between a binding agent and the peptide or a component, sequence information of the encoder sequence and/or the barcode for the peptide is transferred by ligation and/or primer extension between the nucleic acid coding tag of the binding agent and the nucleic acid recording tag of the peptide, thereby generating an extended nucleic acid construct. One or more additional binding cycles are performed by repeating binding and transfer, producing extended nucleic acid constructs that encode binding-agent identity across multiple cycles.
The extended nucleic acid constructs are analyzed by nucleic acid sequencing to obtain the identifying information regarding the binding agents bound during each binding cycle, thereby analyzing the peptide. The disclosed approach links compartment barcodes/UMIs and peptide signatures, including primary amino-acid sequence and/or amino-acid composition signatures, to map back to proteome subsets and to identify and quantitate proteins.
The document further describes terminal amino acid labeling (NTAA/CTAA) and mild NTAA cleavage strategies compatible with nucleic-acid encoding, and processing of extended recording/coding/di-tag libraries for sequencing. It also describes compartment tags with barcodes/UMIs that support cyclic binding, transfer, and analysis, including targeted enrichment of DNA-encoded libraries.
Claims Coverage
The independent claim set includes one independent claim (clm-00001). Across that independent claim, there are key inventive features centered on nucleic-acid recording/coding tags for peptides, cyclic transfer by ligation and/or primer extension, and nucleic-acid sequencing to recover identifying information per binding cycle.
Peptide-associated nucleic-acid recording tag and binding-agent nucleic-acid coding tag
A method in which a peptide or a component of the peptide is associated with a nucleic acid recording tag comprising a barcode for the peptide, and each binding agent comprises a nucleic acid coding tag comprising an encoder sequence that comprises identifying information regarding the binding agent.
Ligation and/or primer extension transfer to generate an extended nucleic-acid construct
Following binding between a binding agent and the peptide or the component, sequence information of the encoder sequence and/or the barcode for the peptide is transferred by ligation and/or primer extension between the nucleic acid coding tag of the binding agent and the nucleic acid recording tag of the peptide, thereby generating an extended nucleic acid construct comprising sequence information of the encoder sequence and the barcode for the peptide.
One or more additional binding cycles by repeating binding and transfer
Repeating the contacting, binding, and ligation or primer-extension-based transfer steps to perform one or more additional binding cycles for the peptide or another component of the peptide.
Sequencing analysis of extended nucleic-acid constructs to obtain identifying information per binding cycle
Analyzing the extended nucleic acid constructs by nucleic acid sequencing, and obtaining the identifying information regarding the binding agents bound to the peptide or to the components of the peptide during each binding cycle, thereby analyzing the peptide.
Claim coverage centers on cyclic peptide analysis using peptide-associated nucleic-acid recording tags and binding-agent nucleic-acid coding tags, with transfer of encoder and barcode sequence information via ligation and/or primer extension to form extended nucleic-acid constructs that are then sequenced to determine identifying information for binding agents across binding cycles.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
Interested in licensing this patent?