Macromolecule analysis employing nucleic acid encoding
Inventors
Chee, Mark S. • Gunderson, Kevin L. • Weiner, Michael Phillip
Assignees
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Publication Number
US-11959922-B2
Publication Date
2024-04-16
Expiration Date
Abstract
A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
Core Innovation
The invention relates to a composition that enables cyclic/macromolecule analysis of covalently attached peptide molecules associated with nucleic-acid tags. One or more solid supports each include at least 100,000 peptide molecules covalently attached, with at least 100 different peptides, and adjacent peptide molecules spaced at an average distance of about 50 nm or greater. The nucleic-acid tagging provides an information-bearing linkage between peptides on the solid support and recording tags for later reconstruction.
A plurality of binding agents is bound to the peptide molecules, and the plurality comprises at least 3 different binding agents. Each binding agent is selective for a different peptide component and is bound to an N-terminal amino acid (NTAA) residue or a C-terminal amino acid (CTAA) residue of a peptide molecule. This NTAA/CTAA-selective binding transfers identifying information between nucleic-acid recording tags and coding tags through cyclic extensions, supporting peptide/protein sequence reconstruction including order and PTMs.
The document describes a nucleic-acid-encoded, highly-parallel digital macromolecule analysis platform in which peptide molecules are associated with nucleic acid tags and analyzed by partitioning, ligation, and barcode-based mapping. Emulsion partitioning, droplets, microwells, or separated surface regions are used to compartmentalize reactions and link compartment barcodes and UMIs with amino-acid code tags. The platform supports recording post-translational modifications and downstream sequencing readout using multiple sequencing technologies, including nanopore sequencing.
Claims Coverage
Independent claim clm-00001 defines a composition including nucleic-acid-tagged peptide molecules on covalently attached solid supports and a set of at least three NTAA/CTAA-selective binding agents. The claim requires multiple peptides, at least 100 different peptides, spacing between adjacent peptide molecules, and a plurality of binding agents selective for different peptide terminal components.
Nucleic-acid-tagged peptide molecules on spaced covalent solid supports
One or more solid supports wherein each solid support comprises at least 100,000 peptide molecules covalently attached to the solid support, each peptide molecule associated with a nucleic acid tag, wherein the peptide molecules comprise molecules of at least 100 different peptides, and wherein adjacent peptide molecules are spaced apart at an average distance of about 50 nm or greater.
At least three NTAA/CTAA-selective binding agents for different terminal components
A plurality of binding agents each bound to one of the peptide molecules, wherein the plurality comprises at least 3 different binding agents, wherein each of the at least 3 different binding agents is bound to a N-terminal amino acid (NTAA) residue or C-terminal amino acid (CTAA) residue of a peptide molecule and is selective for a different peptide component.
The inventive scope centers on large-scale covalently attached peptide arrays carrying nucleic-acid tags with controlled spacing, together with at least three binding agents that selectively bind different NTAA or CTAA residue components.
Stated Advantages
Documented Applications
No documented applications found
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