# US 11,993,807 B2 · Affinity reagents having enhanced binding and detection characteristics > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 11,993,807 B2 - Document ID: US11993807B2 - Status: Granted - Kind: B2 - Application number: 18/179,924 - Filed: 2023-03-07 - Published: 2023-08-31 - Granted: 2024-05-28 - Earliest claimed: 2020-11-11 - Assignees: Nautilus Subsidiary, Inc. - Applicants: Nautilus Subsidiary, Inc. - Inventors: Tural Aksel; Torri Rinker; Markus Burns; Michael Dorwart; Rachel Galimidi; Dmitriy Gremyachinskiy; Stephen Hendricks; Elvis Ikwa; Gregory Kapp; Joshua Simon Klein; Julia Robinson; Cassandra Stawicki; Sonal Tonapi; Parag Mallick - Web page: https://patentgrep.com/patent/US11993807B2 ## CPC - C12Q 1/6811: Selection methods for production or design of target specific oligonucleotides or binding molecules - C12Q 1/6832: Enhancement of hybridisation reaction - C12Q 1/6834: Enzymatic or biochemical coupling of nucleic acids to a solid phase - C12Q 1/6876: Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract An affinity reagent, having: (a) a retaining component such as a structured nucleic acid particle; and (b) one or both of (i) one or more label components attached to the retaining component, and (ii) one or more binding components attached to the retaining component. ## Claims ### Claim 1 A method of detecting an analyte, comprising: (a) contacting an array of analytes with a detectable probe, wherein the array of analytes comprises individual analytes each attached to sites that are physically isolated from all other analytes in the array of analytes, wherein the detectable probe comprises: (i) a retaining component comprising nucleic acid origami, (ii) two or more label components attached to the retaining component, and (iii) two or more binding components attached to the retaining component, wherein the two or more binding components recognize the same epitope of the analyte, wherein the detectable probe binds to the analyte via non-covalent binding of at least one of the two or more binding components to the epitope; and (b) acquiring signals from the two or more label components of the detectable probe bound to the analyte, thereby detecting the analyte. ### Claim 2 (depends on 1) The method of claim 1, wherein the nucleic acid origami comprises a scaffold nucleic acid and a staple nucleic acid hybridized to two regions of the scaffold nucleic acid, wherein the two regions of the scaffold nucleic acid are separated by an intervening region that does not hybridize to the staple nucleic acid. ### Claim 3 (depends on 2) The method of claim 2, wherein the scaffold nucleic acid comprises a circular nucleic acid. ### Claim 4 (depends on 2) The method of claim 2, wherein the nucleic acid origami comprises a plurality of staple nucleic acids hybridized to the scaffold nucleic acid. ### Claim 5 (depends on 1) The method of claim 1, wherein the two or more label components comprise fluorophores that emit fluorescence at the same wavelength, and wherein the signals comprise the fluorescence. ### Claim 6 (depends on 5) The method of claim 5, wherein the retaining component maintains the at least two label components at a spacing of at least 15 nm. ### Claim 7 (depends on 1) The method of claim 1, wherein the analyte is attached to the site via a structured nucleic acid particle. ### Claim 8 (depends on 1) The method of claim 1, wherein the analyte comprises a polypeptide. ### Claim 9 (depends on 8) The method of claim 8, wherein the epitope is a trimer amino acid sequence. ### Claim 10 (depends on 8) The method of claim 8, wherein the epitope is a tetramer amino acid sequence. ### Claim 11 (depends on 8) The method of claim 8, wherein the polypeptide is denatured. ### Claim 12 (depends on 1) The method of claim 1, wherein the two or more binding components comprise antibodies or functional fragments thereof. ### Claim 13 (depends on 1) The method of claim 1, wherein the two or more binding components comprise nucleic acid aptamers. ### Claim 14 (depends on 1) The method of claim 1, wherein the structures of the two or more binding components are the same. ### Claim 15 (depends on 1) The method of claim 1, wherein the sites are separated by at least 100 nm. ### Claim 16 (depends on 1) The method of claim 1, wherein the detectable probe is bound to the analyte via non-covalent binding of only one binding component of the two or more binding components to the epitope. ### Claim 17 (depends on 1) The method of claim 1, wherein the retaining component comprises a first nucleic acid sequence that is complementary to a nucleic acid that is coupled to one of the binding components. ### Claim 18 (depends on 17) The method of claim 17, wherein the retaining component further comprises a second nucleic acid sequence that is complementary to a nucleic acid that is coupled to one of the label components, wherein the first nucleic acid sequence differs from the second nucleic acid sequence. ### Claim 19 (depends on 1) The method of claim 1, wherein the array of analytes comprises at least 1×104 different analytes each attached to sites that are physically isolated from all other analytes in the array of analytes. ### Claim 20 (depends on 1) The method of claim 1, wherein the structures of the two or more label components are the same. ### Claim 21 (depends on 1) The method of claim 1, further comprising: (c) contacting the array of analytes with a second detectable probe, wherein the second detectable probe comprises: (i) a second retaining component comprising nucleic acid origami, (ii) a second label component attached to the second retaining component, and (iii) a second binding component attached to the second retaining component, wherein the second binding component of the second detectable probe is different from the two or more binding components of the detectable probe, wherein the second detectable probe binds to the analyte via non-covalent binding of the second binding component to an epitope of the analyte; and (d) acquiring signals from the second label component of the second detectable probe bound to the analyte, thereby detecting the analyte. ### Claim 22 (depends on 21) The method of claim 21, further comprising, prior to step (c), removing the detectable probe of step (a) from the analyte. ### Claim 23 (depends on 22) The method of claim 22, wherein the analyte comprises a polypeptide and wherein the method further comprises (e) identifying the polypeptide based on the detecting of steps (b) and (d).