The present disclosure provides a range of methods for dense information storage in oligomeric constructs, such as peptides. Various methods of the present disclosure provide for information storage in oligomers and oligomer libraries, and information retrieval by subsequent oligomer sequencing or analysis. The present disclosure further provides methods for appending information to materials and molecules with analyzable oligomeric constructs.

This disclosure is directed to a method for sequencing protein and peptide. The method specifies the steps of providing a polypeptide that is immobilized on solid surfaces and binding a N-terminal amino acid (NTAA) of the polypeptide with a modification molecule. Further, the method requires contacting the polypeptide with a NTAA binding molecule with a DNA coding tag, transferring an information from the DNA coding tag of the NTAA binding molecule to a universal primer and then forming an extended DNA tag on the solid surfaces, and cleaving the N-terminal amino acid on the polypeptide. Then, step (b) through step (e) are cyclically repeated. Finally, extended DNA strains are decoding on the solid surfaces.

The invention describes methods and reagents useful for sequencing polypeptide molecules. The method comprises affixing a polypeptide to a substrate and contacting the polypeptide with a plurality of probes that selectively bind to a terminal amino acid or a terminal amino acid derivative. Probes bound to the polypeptide molecule are then identified before cleaving the terminal amino acid or terminal amino acid derivative of the polypeptide. Also provided are probe compositions comprising (a) a ClpS variant comprising at least 80% sequence identity to SEQ ID NO: 1, wherein the ClpS variant binds to an N-terminal amino acid or a N-terminal amino acid derivative with a different selectivity than a wild-type ClpS; and (b) a detectable label.

Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides methods of obtaining data during a degradation process of a polypeptide, and outputting a sequence representative of the polypeptide. In some aspects, the application provides amino acid recognition molecules having a shielding element that enhances photostability in polypeptide sequencing reactions.

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

The present disclosure relates to compositions of matter, methods, and systems for analyzing polymeric macromolecules, including polymeric macromolecules such as peptides, polypeptides, and proteins.

The invention describes methods and reagents useful for sequencing polypeptide molecules. The method comprises affixing a polypeptide to a substrate and contacting the polypeptide with a plurality of probes. Each probe selectively binds to an N-terminal amino acid or an N-terminal amino acid derivative. Probes bound to the polypeptide molecule are then identified before cleaving the N-terminal amino acid or N-terminal amino acid derivative of the polypeptide. Also provided are methods for the sequencing a plurality of polypeptide molecules in a sample and probes specific for N-terminal amino acids or N-terminal amino acid derivatives.

Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides amino acid recognition molecules, such as amino acid binding proteins and fusion polypeptides thereof. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.

There is provided amino acid recognizers with improved binding properties, allowing for more structural information to be obtained from polypeptides based on the kinetics of on-off binding between recognizer and polypeptide. An amino acid recognizer may comprise an amino acid binding protein with an engineered binding pocket having one or more modifications relative to a homologous protein. The modified binding pocket may increase the number of interactions formed between the binding pocket and an amino acid ligand as compared to an unmodified binding pocket of the homologous protein, increase the number of types of amino acid ligands capable of being detectably bound as compared to an unmodified binding pocket of the homologous protein, and improve the kinetics of binding (e.g., K.sub.D, k.sub.off, k.sub.on) toward one or more types of amino acid ligands, which advantageously increases the amount of, or confidence in, structural information that may be derived from polypeptide analysis.

Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides methods of obtaining data during a degradation process of a polypeptide, and outputting a sequence representative of the polypeptide. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.