Nucleic acid complexes for screening barcoded compounds
The invention provides compositions comprising nucleic acid complexes for use in screening compounds based on their ability to modulate binding interactions, wherein the compounds are barcoded.
1 . A method comprising
contacting (1) a nucleic acid complex conjugated to a first binding partner and a second binding partner with (2) a candidate ligand conjugated to a nucleic acid barcode,
isolating a nucleic acid complex having the first binding partner bound to (a) the second binding partner and (b) the candidate ligand, and
identifying the candidate ligand bound to the first binding partner by nucleic acid sequencing of the nucleic acid barcode,
wherein the nucleic acid complex comprises a single-stranded scaffold nucleic acid hybridized to a plurality of single-stranded oligonucleotides, wherein a first single-stranded oligonucleotide in the plurality is linked to the first binding partner and a second single-stranded oligonucleotide in the plurality is linked to the second binding partner, and
wherein the first binding partner and the second binding partner do not bind to each other unless the candidate ligand is bound to the first binding partner.
2 . The method of claim 1 , wherein identifying the candidate ligand comprises nucleic acid amplification of the nucleic acid barcode.
3 . The method of claim 1 , wherein the candidate ligand is in solution.
4 . The method of claim 1 , wherein the candidate ligand is linked to a third single-stranded oligonucleotide in the nucleic acid complex.
5 . The method of claim 1 , further comprising covalently attaching the candidate ligand to the first binding partner after the contacting step.
6 . A method comprising
contacting (1) a plurality of nucleic acid complexes each conjugated to a first binding partner and a second binding partner with (2) a plurality of candidate ligands each conjugated to a distinct/unique nucleic acid barcode,
physically separating (1) nucleic acid complexes having the first binding partner bound to the second binding partner and to the candidate ligand from (2) other nucleic acid complexes, and
identifying the candidate ligand bound to the first binding partner by nucleic acid sequencing of the nucleic acid barcode,
wherein each nucleic acid complex comprises a single-stranded scaffold nucleic acid hybridized to a plurality of single-stranded oligonucleotides, wherein a first single-stranded oligonucleotide in the plurality is linked to the first binding partner and a second single-stranded oligonucleotide in the plurality is linked to the second binding partner,
wherein the first binding partner and the second binding partner do not bind to each other unless the candidate ligand is bound to the first binding partner.
7 . The method of claim 6 , wherein the nucleic acid complexes are identical to each other.
8 . The method of claim 6 , wherein the plurality of candidate ligands is a library of candidate ligands.
9 . A method comprising
contacting a target with a candidate ligand conjugated to a nucleic acid barcode, wherein the target and optionally the candidate ligand are bound to a nucleic acid complex that is further bound to an active-target-specific binding partner and an inactive-target-specific binding partner,
isolating a target bound to a candidate ligand and an active-target-specific binding partner, and
identifying the candidate ligand bound to the target by nucleic acid sequencing of the nucleic acid barcode,
wherein the nucleic acid complex comprises a single-stranded scaffold nucleic acid hybridized to a plurality of single-stranded oligonucleotides, wherein a first single-stranded oligonucleotide is linked to the target and a second single-stranded oligonucleotide is linked to the active-target-specific binding partner,
wherein the target does not bind to the active-target-specific binding partner in the absence of the candidate ligand.
10 . The method of claim 9 , wherein the candidate ligand is linked to a third single-stranded oligonucleotide in the nucleic acid complex.
11 . The method of claim 9 , wherein the candidate ligand is in solution.
12 . The method of claim 9 , wherein the candidate ligand is covalently linked to the target to which it is bound prior to isolating.
13 . The method of claim 9 , wherein the target is covalently linked to the bound active-target-specific binding partner prior to isolating.
14 . A method comprising
contacting (1) a nucleic acid complex conjugated to a first binding partner and a second binding partner with (2) a candidate ligand conjugated to a nucleic acid barcode, wherein the first binding partner has affinity for the second binding partner in the absence of the candidate ligand,
isolating a nucleic acid complex having the first binding partner bound to the candidate ligand and not bound to the second binding partner, and
identifying the candidate ligand bound to the first binding partner by nucleic acid sequencing of the nucleic acid barcode,
wherein the nucleic acid complex comprises a single-stranded scaffold nucleic acid hybridized to a plurality of single-stranded oligonucleotides, wherein a first single-stranded oligonucleotide in the plurality is linked to the first binding partner and a second single-stranded oligonucleotide in the plurality is linked to the second binding partner,
wherein the second binding partner and the candidate ligand are different from each other.
15 . The method of claim 14 , wherein wherein identifying the candidate ligand comprises nucleic acid amplification of the nucleic acid barcode.
16 . The method of claim 14 , wherein the candidate ligand is in solution.
17 . The method of claim 14 , wherein the candidate ligand is linked to a third single-stranded oligonucleotide in the nucleic acid complex.
18 . The method of claim 14 , further comprising covalently attaching the candidate ligand to the first binding partner after the contacting step.
19 . The method of claim 14 , wherein the first binding partner is directly bound to the second binding partner prior to contact with the candidate ligand, and upon direct binding to the candidate ligand the first binding partner dissociates from the second binding partner.