# US 10,767,278 B2 · Chemically encoded spatially addressed library screening platforms

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- Number: US 10,767,278 B2
- Document ID: US10767278B2
- Status: Granted
- Kind: B2
- Application number: 16/555,531
- Filed: 2019-08-29
- Published: 2019-12-26
- Granted: 2020-09-08
- Earliest claimed: 2015-02-24
- Assignees: City of Hope
- Applicants: City of Hope
- Inventors: Jacob Berlin; Gregory Copeland; Kathleen Elison; Hurik Muradyan
- Web page: https://patentgrep.com/patent/US10767278B2

## CPC

- C40B 50/16: involving encoding steps
- C12N 15/1065: {Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags}
- C40B 40/10: Libraries containing peptides or polypeptides, or derivatives thereof
- C40B 70/00: Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
- G01N 33/54313: {the carrier being characterised by its particulate form}
- G01N 33/54326: {Magnetic particles}
- G01N 33/54346: {Nanoparticles}
- G01N 33/54353: {with ligand attached to the carrier via a chemical coupling agent (coatings G01N33/54393)}
- B82Y 5/00: Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- B82Y: SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES

## Abstract

Provided herein are encoded split pool libraries useful, inter alia, for forming highly diverse and dense arrays for screening and detection of a variety of molecules.

## Claims

### Claim 1

A method comprising:
(i) attaching a microparticle to a solid support, thereby forming an immobilized microparticle, wherein said immobilized microparticle is further covalently attached to:
(a) a ligand domain through a first linker; and
(b) a nucleic acid domain through a second linker;
wherein said second linker comprises an acyl group, a sulfonamide group, or a photocleavable group, and
wherein said second linker is cleavable and said first linker is not cleavable under a condition that said second linker is cleavable; and
(ii) performing a decoding procedure on the nucleic acid domain, thereby identifying the composition of the ligand domain and its location on said solid support.

### Claim 2 (depends on 1)

The method of claim 1, further comprising cleaving said second linker of the microparticle, thereby forming a cleaved microparticle.

### Claim 3 (depends on 2)

The method of claim 2, further comprising binding a ligand binder to said ligand domain of said cleaved microparticle, thereby forming a bound ligand binder.

### Claim 4 (depends on 3)

The method of claim 3, further comprising identifying a location of said bound ligand binder on said solid support, thereby detecting said ligand binder.

### Claim 5 (depends on 1)

The method of claim 1, wherein said ligand domain comprises a removable protecting moiety covalently attached to a reactive moiety, wherein said removable protecting moiety prevents the ligand domain from binding a ligand binder.

### Claim 6 (depends on 5)

The method of claim 5, further comprising chemically removing said removable protecting moiety, thereby forming a deprotected microparticle.

### Claim 7 (depends on 6)

The method of claim 6, further comprising binding a ligand binder to said ligand domain of said deprotected microparticle, thereby forming a bound ligand binder.

### Claim 8 (depends on 7)

The method of claim 7, further comprising identifying a location of said bound ligand binder on said solid support, thereby detecting said ligand binder.

### Claim 9 (depends on 6)

The method of claim 6, further comprising reacting said reactive moiety with a domain capable of binding a ligand binder, thereby forming a reacted microparticle.

### Claim 10 (depends on 9)

The method of claim 9, further comprising binding a ligand binder to said ligand domain of said reacted microparticle, thereby forming a bound ligand binder.

### Claim 11 (depends on 10)

The method of claim 10, further comprising identifying a location of said bound ligand binder on said solid support, thereby detecting said ligand binder.

### Claim 12 (depends on 1)

The method of claim 1, wherein said ligand domain is selected from the group consisting of a small molecule, a peptide, and a protein.

### Claim 13 (depends on 1)

The method of claim 1, wherein said second linker is a photocleavable linker, an acid labile linker, or an alkali labile linker.

### Claim 14

A method comprising:
(i) providing a solid support comprising a plurality of wells;
(ii) attaching a plurality of microparticles to said plurality of wells to form an ordered array of a plurality of immobilized microparticles, wherein each of said plurality of immobilized microparticles is further covalently attached to:
(a) a ligand domain through a first linker; and
(b) a nucleic acid domain through a second linker;
wherein said second linker comprises an acyl group, a sulfonamide group, or a photocleavable group, and
wherein said second linker is cleavable and said first linker is not cleavable under a condition that said second linker is cleavable; and
(iii) performing a decoding procedure on the nucleic acid domain of each of said plurality of microparticles, thereby identifying the composition of the corresponding ligand domain and its location on said solid support.

### Claim 15 (depends on 14)

The method of claim 14, wherein the decoding procedure comprises sequencing the nucleic acid domain of each of said plurality of microparticles by hybridization or enzymatic-based sequencing procedures.

### Claim 16 (depends on 14)

The method of claim 14, further comprising cleaving said second linker of each of said plurality of microparticles, thereby forming a cleaved ordered array.

### Claim 17 (depends on 16)

The method of claim 16, further comprising binding ligand binders to the ligand domain of each of said plurality of immobilized microparticles, thereby forming a plurality of bound ligand binders.

### Claim 18 (depends on 17)

The method of claim 17, further comprising identifying the locations of said plurality of bound ligand binders on said solid support, thereby detecting said plurality of ligand binders.

### Claim 19 (depends on 14)

The method of claim 14, wherein said ligand domain is selected from the group consisting of a small molecule, a peptide, and a protein.

### Claim 20 (depends on 14)

The method of claim 14, wherein said ordered array includes at least about 10,000 microparticles per square millimeter.

### Claim 21 (depends on 14)

The method of claim 14, wherein said second linker is a photocleavable linker, an acid labile linker, or an alkali labile linker.

### Claim 22 (depends on 14)

The method of claim 14, wherein said ligand domain of each of said plurality of immobilized microparticles comprises a removable protecting moiety covalently attached to a reactive moiety, wherein said removable protecting moiety prevents the ligand domain from binding a ligand binder.

### Claim 23 (depends on 22)

The method of claim 22, further comprising chemically removing said removable protecting moiety of each of said plurality of immobilized microparticles, thereby forming a plurality of deprotected microparticles.

### Claim 24 (depends on 23)

The method of claim 23, further comprising binding a ligand binder to said ligand domain of each of said plurality of deprotected microparticles, thereby forming a plurality of bound ligand binders.

### Claim 25 (depends on 24)

The method of claim 24, further comprising identifying the locations of each of said plurality of bound ligand binders on said solid support, thereby detecting said plurality of ligand binders.

### Claim 26 (depends on 23)

The method of claim 23, further comprising reacting each of said reactive moieties with a domain capable of binding a ligand binder, thereby forming a plurality of reacted microparticles.

### Claim 27 (depends on 26)

The method of claim 26, further comprising binding a ligand binder to said ligand domain of said plurality of reacted microparticles, thereby forming a plurality of bound ligand binders.

### Claim 28 (depends on 27)

The Method of claim 27, further comprising identifying the locations of each of said plurality of bound ligand binders on said solid support, thereby detecting said plurality of ligand binders.