Parallel Proximity Ligation Event Analysis
First Claim
1. A composition comprising a binding partner attached to a forked adapter molecule.
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Accused Products
Abstract
The present invention describes compositions and methods showing that the spatial proximity of intracellular components may be related to their ability to cooperate in intracellular biochemical reactions. In some embodiments, the present invention contemplates a variety of nucleic acid barcoded binding partners capable of determining the spatial proximity of intracellular components as determined by ligation of their respective nucleotide barcodes. As such, an intracellular component contact map may be constructed to fingerprint specific physiological and/or pharmacological intracellular conditions.
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Citations
30 Claims
- 1. A composition comprising a binding partner attached to a forked adapter molecule.
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8. A composition comprising a nucleic acid sequence having a 3′
- -5′
first strand and a 5′
-3′
second strand, wherein said first strand 3′
end is attached to a first binding partner and said second strand 3′
end is attached to a second binding partner. - View Dependent Claims (9, 10, 11, 12, 13)
- -5′
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14. A method, comprising:
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a) providing; i) a first binding partner having affinity for a first intracellular component, wherein said first binding partner is attached to a first unique nucleotide barcode sequence; ii) a second binding partner having affinity for a second intracellular component, wherein said second binding partner is attached to a second unique nucleotide barcode sequence; iii) a biological cell sample comprising said first and second intracellular components; and b) contacting said first and second binding partners with said sample under conditions such that an asymmetric nucleotide barcode sequence is created. - View Dependent Claims (15, 16, 17, 18, 19, 20)
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21. A method, comprising:
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a) providing; i) a first single stranded nucleotide strand comprising a 3′
forked end, wherein said 3′
forked end comprises a first linker molecule;ii) a second single stranded nucleotide strand comprising a 5′
forked end, wherein said second strand is complementary to said first strand; andiii) a binding partner comprising a second linker molecule, wherein said second linker molecule is capable of conjugating with said first linker molecule; b) contacting said binding partner with said first single stranded nucleotide strand under conditions such that said first linker molecule conjugates with said second linker molecule; and c) hybridizing said second strand with said first strand. - View Dependent Claims (22, 23)
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24. A method, comprising:
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a) providing; i) a first single stranded nucleotide strand comprising a 3′
forked end, wherein said 3′
forked end comprises a first linker molecule;ii) a second single stranded nucleotide strand comprising a 5′
forked end, wherein said second strand is complementary to said first strand; andiii) a binding partner comprising a second linker molecule, wherein said second linker molecule is capable of conjugating with said first linker molecule; c) hybridizing said second strand with said first strand to create a forked adapter molecule; and b) contacting said forked adapter molecule with said binding partner under conditions such that said first linker molecule conjugates with said second linker molecule. - View Dependent Claims (25, 26)
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27. A kit, comprising:
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a) a first container comprising a plurality binding partners, wherein each partner is attached to a different forked adapter molecule; b) a second container comprising a solution capable of fixing a biological cell sample; c) a third container comprising buffers and reagents capable of supporting binding of said binding partner to intracellular components of said fixed biological cell sample; and d) instructions describing how to identify said intracellular components bound to said binding partners. - View Dependent Claims (28, 29, 30)
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Specification