Screening of nucleic acid agents via particle display
The present disclosure provides a method for identifying one or more nucleic acid agents, e.g., aptamers, having a desired property from a mixture of candidate nucleic acid agents. The method generally includes immobilizing the mixture of candidate nucleic acid agents onto particles, wherein only a subset of the candidate nucleic acid agents are immobilized on any one of the particles, and wherein the subset is present in multiple copies. The particles are exposed to a target, and particles including candidate nucleic acid agents having the desired property are isolated. In this way, one or more nucleic acid agents having the desired property may be identified. Related compositions and nucleic acid agents identified as having one or more desired properties are also provided.
1. A method for screening a mixture of candidate aptamer sequences, the method comprising:
exposing a plurality of aptamer particles to a target, wherein each of the aptamer particles is immobilized with only a subset of the candidate aptamer sequences, and wherein the subset is present in multiple copies;
quantitating a signal for each of the aptamer particles, wherein the signal, when present, is indicative of a desired property between the candidate aptamer sequence bound to each aptamer particle and the target; and
sorting each of the aptamer particles based on the quantitated signal for each aptamer particle.
2. The screening method of claim 1 , wherein the target is a protein target or a small molecule target.
3. The screening method of claim 1 , wherein the candidate aptamer sequences are DNA sequences.
4. The screening method of claim 1 , wherein one or more of the candidate aptamer sequences comprises a molecule conjugated thereto, wherein the molecule conjugated thereto is a small molecule, a fluorophore, a peptide, or an siRNA.
5. The screening method of claim 1 , wherein the desired property is a target binding activity or a target-binding induced activity.
6. The screening method of claim 5 , wherein the target binding activity is affinity, specificity or bi-specificity.
7. The screening method of claim 6 , wherein the target binding activity is specificity, the screening method comprises exposing the plurality of particles to a first target and a second target, and wherein the candidate aptamer sequences having the desired property exhibit a specific binding affinity for either the first target or the second target but not both.
8. The screening method of claim 6 , wherein the target binding activity is bi-specificity, the screening method comprises exposing the plurality of particles to a first target and a second target, and wherein the candidate aptamer sequences having the desired property exhibit a specific binding affinity for both the first and second target.
9. The screening method of claim 1 , wherein the plurality of particles comprises from 1×10 2 to 1×10 14 particles.
10. The screening method of claim 1 , wherein the sequence diversity of the mixture is from 1×10 2 to 1×10 14 .
11. The screening method of claim 1 , wherein each of the particles of the plurality of particles comprises from 1×10 2 to 1×10 10 candidate aptamer sequences bound thereto.
12. The screening method of claim 1 , wherein the sequence diversity of the subset of the candidate aptamer sequences immobilized on any one of the plurality of particles is from 1 to 106.
13. The screening method of claim 12 , wherein the sequence diversity of the subset of the candidate aptamer sequences immobilized on any one of the plurality of particles is 1.
14. The screening method of claim 1 , wherein the particle or particles that comprise one or more candidate aptamer sequences having the desired property are modified as a result of the desired property following exposure to the target, which modification allows the particle or particles that comprise the more candidate aptamer sequences having the desired property to be isolated, wherein the modification results in a physically detectable change, a chemically detectable change, or an optically detectable change.
15. The screening method of claim 1 , wherein the sorting step comprises sorting the plurality of particles using fluorescence activated cell sorting (FACS).
16. The method of claim 1 , further comprising isolating a particle or particles from the plurality of particles, wherein the isolated particle or particles comprise one or more candidate aptamer sequences having the desired property.
17. The method of claim 16 , further comprising identifying one or more aptamer sequences having the desired property from the isolated particle or particles.
18. The screening method of claim 17 further comprising introducing one or more mutations into the more aptamer sequences having the desired property.
19. The screening method of claim 17 , further comprising a step of amplifying the sequences of the one or more aptamer sequences identified as having the desired property, and iteratively repeating one or more of the exposing, isolating, identifying, and amplifying steps.