Nucleic acid delivery scaffolds

Patent metadata

Field	Value
Publication number	US-2025188521-A1
Application number	US-202318844864-A
Country	US
Kind code	A1
Filing date	Mar 9, 2023
Priority date	Mar 10, 2022
Publication date	Jun 12, 2025
Grant date	—

Abstract

Arrays are an important tool in biomedical research, providing a platform that arranges biological samples and enables high-throughput analyses. Delivering breakthroughs in proteomics, multiplexed immunoassays, and complex genomic analyses, arrays (e.g., microarrays and nanoarrays) can be designed to host thousands, millions, or even billions, of features that are subjected to simultaneous reaction conditions. Disclosed herein, inter alia, are degradable nanoparticles, nanoarrays, and methods of use thereof.

First claim

1 .- 79 . (canceled)

80 . A particle comprising:
a metal-organic framework (MOF) core comprising a Zeolitic Imidazolate Framework (ZIF) core, Isoreticular Metal-Organic Framework (IR-MOF) core, Porous Coordination Network (PCN) core, Materials Institute Lavoisier (MIL) MOF core, Porous Coordination Polymer (PCP) core, or University of Oslo (UiO) MOF core; a polymer shell surrounding the MOF core, wherein the polymer shell comprises polymerized units of polyacrylamide (AAm), poly-N-isopropylacrylamide, poly N-isopropylpolyacrylamide, sulfobetaine acrylate (SBA), carboxybetaine acrylate (CBA), phosphorylcholine acrylate (PCA), sulfobetaine methacrylate (SBMA), carboxybetaine methacrylate (CBMA), phosphorylcholine methacrylate (PCMA), polyethylene glycol acrylate, methacrylate, polyethylene glycol (PEG)-thiol/PEG-acrylate, acrylamide/N,N′-bis(acryloyl)cystamine (BACy), PEG/polypropylene oxide (PPO), polyacrylic acid, poly(hydroxyethyl methacrylate) (PHEMA), poly(methyl methacrylate) (PMMA), poly(N-isopropylacrylamide) (PNIPAAm), poly(lactic acid) (PLA), poly(lactic-co-glycolic acid) (PLGA), polycaprolactone (PCL), poly(vinylsulfonic acid) (PVSA), poly(L-aspartic acid), poly(L-glutamic acid), polylysine, agar, agarose, alginate, heparin, alginate sulfate, dextran sulfate, hyaluronan, pectin, carrageenan, gelatin, chitosan, cellulose, collagen, glicydyl methacrylate (GMA), glicydyl methacrylate (GMA) azide, hydroxyethylmethacrylate (HEMA), hydroxyethylacrylate (HEA), hydroxypropylmethacrylate (HPMA), polyethylene glycol methacrylate (PEGMA), polyethylene glycol acrylate (PEGA), isocyanatoethyl methacrylate (IEM), or a copolymer thereof; and a plurality of oligonucleotide moieties, wherein each oligonucleotide moiety is covalently attached to the polymer shell via a bioconjugate linker, wherein the bioconjugate linker is formed via a reaction between the polymer shell comprising a first bioconjugate reactive moiety and the oligonucleotide moiety comprising a second bioconjugate reactive moiety.

81 . The particle of claim 79 , wherein the plurality of oligonucleotide moieties comprises comprising a first plurality of oligonucleotide moieties and a second plurality of oligonucleotide moieties.

82 . The particle of claim 79 , wherein the particle is non-covalently attached to a solid support.

83 . The particle of claim 81 , wherein the solid support comprises polymerized units of alkoxysilyl polymers.

84 . The particle of claim 79 , wherein the MOF core is a Zeolitic Imidazolate Framework 8 (ZIF-8) core or a UiO-66 MOF core.

85 . The particle of claim 79 , wherein the polymer shell is permeable to a polymerase.

86 . The particle of claim 79 , wherein the polymer shell is permeable to an amplification reaction mixture and/or a sequencing reaction mixture.

87 . The particle of claim 79 , wherein the polymer shell comprises polymerized units of a) polyethylene glycol methaciylate (PEGMA) and glicydyl methacrylate (GMA), b) polyethylene glycol methacrylate (PEGMA) and isocyanatoethyl nthacrylate (IEM), or c) polyethylene glycol methacrylate (PEGMA) and glicydyl methacrylate (GMA) azide.

88 . The particle of claim 79 , wherein the polymer shell comprises polymerized units of polyethylene glycol methaciylate (PEGMA) and glicydyl methacrylate (GMA) azide.

89 . The particle of claim 79 , wherein the polymer shell comprises a ratio of GMA azide to PEGMA that is about1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7 or about 1:8.

90 . The particle of claim 79 , wherein each oligonucleotide moiety is about 10 to about 250 nucleotides in length.

91 . The particle of claim 79 , wherein two or more oligonucleotide moieties comprises a cleavable site.

92 . The particle of claim 79 , wherein two or more oligonucleotide moieties are capable of hybridizing to a complementary sequence of a template nucleic acid.

93 . The particle of claim 79 , wherein the first bioconjugate reactive moiety is an amine moiety, azide moiety, alkyne moiety, dibenzocyclooctyne (DBCO) moiety, epoxy moiety, or isocyanate moiety; and the second bioconjugate reactive moiety is an amine moiety, azide moiety, alkyne moiety, dibenzocyclooctyne (DBCO) moiety, epoxy moiety, or isocyanate moiety, wherein the second bioconjugate reactive moiety is different than the first bioconjugate reactive moiety.

94 . A method of attaching an oligonucleotide to a solid support, said method comprising:
contacting the solid support with a particle comprising a degradable particle core and a polymer shell attached to said degradable particle core, wherein said polymer shell comprises a first bioconjugate reactive moiety covalently linked to said polymer shell; contacting the particle with a degrading agent thereby decomposing the degradable particle core and forming a polymer composition attached to solid support; and contacting the first bioconjugate reactive moiety with an oligonucleotide comprising a second bioconjugate reactive moiety and forming a bioconjugate linker, thereby attaching the oligonucleotide to the solid support.

95 . The method of claim 93 , further comprising hybridizing a target polynucleotide to said oligonucleotide and extending with a polymerase said oligonucleotide to form a complement of the target polynucleotide.

96 . The method of claim 94 , further comprising amplifying said complement of the target polynucleotide.

97 . The method of claim 93 , further comprising sequencing the target polynucleotide or a complement thereof.

Assignees

• Singular Genomics Systems Inc

Inventors

• Kalaj Mark
• Witters Daan

Classifications

• C12Q1/6869

  Methods for sequencing · CPC title

• C12Q1/6834 Primary

  Enzymatic or biochemical coupling of nucleic acids to a solid phase · CPC title

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title