Methods for arbitrary peptide synthesis

1. A method comprising:

determining, with one or more computing units, an order that two or more types of charged tRNA are to be sequentially flowed to one or more first identifiable locations in a reaction chamber of a fluidic device; and

controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals.

2. The method of claim 1 , wherein controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals comprises:

synthesizing a target peptide by sequentially providing the two or more types of charged tRNA to the one or more identifiable locations at the one or more first identifiable time intervals.

3. The method of claim 1 , wherein two or more of the two or more types of charged tRNA have the same anti-codon and are charged with different amino acids.

4. The method of claim 1 , wherein two or more of the two or more types of charged tRNA have one or more of different anti-codons or different tRNA and are charged with the same amino acid.

5. The method of claim 1 , wherein the one or more first identifiable time intervals are based on one or more of a predicted rate of incorporation of one or more amino acids into one or more peptides, a predicted rate of activity of one or more ribosome-based assemblers, a predicted rate of translocation of one or more nucleic acids, or a predicted release rate for tRNA.

6. The method of claim 1 , wherein the one or more first identifiable time intervals are from approximately 0.001 seconds to approximately 0.1 seconds.

7. The method of claim 1 , wherein the one or more first identifiable time intervals are approximately 0.01 seconds.

8. The method of claim 1 , further comprising:

monitoring one or more of amino acid incorporation into one or more peptides, ribosome-based assembler activity, nucleic acid translocation, or tRNA release.

9. The method of claim 8 , wherein the one or more first identifiable time intervals are based on one or more of the amino acid incorporation into the one or more peptides, the ribosome-based assembler activity, the nucleic acid translocation, or the tRNA release.

10. The method of claim 8 , wherein controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals comprises:

sequentially providing the two or more types of charged tRNA to the one or more identifiable locations at the one or more first identifiable time intervals at least partially based on availability of one or more nucleic acid codons.

11. The method of claim 1 , further comprising:

monitoring one or more of presence or absence, concentration, or composition of one or more of the two or more types of charged tRNA or one or more tRNA.

12. The method of claim 11 , wherein the one or more first identifiable time intervals are based on the concentrations of one or more of the two or more types of charged tRNA or the one or more tRNA.

13. The method of claim 11 , wherein the one or more first identifiable time intervals are based on one or more of presence or absence of one or more of the two or more types of charged tRNA or the one or more tRNA.

14. The method of claim 11 , wherein the one or more first identifiable time intervals are based on one or more of presence or absence of one or more anti-codons on one or more of the two or more types of charged tRNA or the one or more tRNA.

15. The method of claim 1 , wherein the two or more types of charged tRNA are charged with one or more natural, one or more unnatural, or one or more arbitrary amino acids.

16. The method of claim 1 , further comprising:

charging the two or more tRNA with one or more natural amino acids, one or more arbitrary amino acids, or one or more unnatural amino acids.

17. The method of claim 1 , wherein controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals comprises:

providing one or more first charged tRNA to the one or more identifiable locations;

providing one or more second charged tRNA to the one or more identifiable locations; and

optionally repeating.

18. The method of claim 17 , wherein the one or more first charged tRNA is a different type from the one or more second charged tRNA.

19. The method of claim 1 , wherein controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals comprises:

sequentially providing the two or more types charged tRNA to the one or more identifiable locations at the one or more first identifiable time intervals, wherein the one or more identifiable locations contains one or more ribosome-based assemblers.

20. The method of claim 19 , wherein sequentially providing the two or more types of charged tRNA to the one or more identifiable locations at the one or more first identifiable time intervals comprises:

sequentially providing the two or more types of charged tRNA to the one or more identifiable locations at the one or more first identifiable time intervals, wherein the one or more identifiable locations contains the one or more ribosome-based assemblers co-localized with one or more nucleic acids having a defined protein coding sequence.

21. The method of claim 20 , wherein sequentially providing the two or more types of charged tRNA to the one or more identifiable locations at the one or more first identifiable time intervals comprises:

sequentially providing the two or more types of charged tRNA in the determined order to the one or more identifiable locations at the one or more first identifiable time intervals, wherein the the determined order is at least partially determined based on the defined protein coding sequence of the one or more nucleic acids.

22. The method of claim 1 , wherein controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals comprises:

sequentially providing the two or more types of charged tRNA to one or more receptacles at the one or more identifiable locations at the one or more first identifiable time intervals.

23. The method of claim 22 , wherein sequentially providing the two or more types of charged tRNA to one or more receptacles at the one or more identifiable locations at the one or more first identifiable time intervals comprises:

sequentially providing the two or more types of charged tRNA to the one or more receptacles at the one or more identifiable locations at the one or more first identifiable time intervals, wherein the one or more receptacles contains one or more ribosome-based assemblers.

24. The method of claim 23 , sequentially providing the two or more types of charged tRNA to the one or more receptacles at the one or more identifiable locations at the one or more first identifiable time intervals, wherein the one or more receptacles contains one or more ribosome-based assemblers comprises:

sequentially providing the two or more types of charged tRNA to the one or more receptacles at the one or more identifiable locations at the one or more first identifiable time intervals, wherein the one or more receptacles contains the one or more ribosome-based assemblers co-localized with one or more nucleic acids having a defined protein coding sequence.

25. The method of claim 24 , wherein sequentially providing the two or more types of charged tRNA to the one or more receptacles at the one or more identifiable locations at the one or more first identifiable time intervals comprises:

sequentially providing the two or more types of charged tRNA in the determined order to the one or more receptacles at the one or more identifiable locations at the one or more first identifiable time intervals, wherein the determined order is at least partially determined based on the defined protein coding sequence of the one or more nucleic acids.

26. The method of claim 1 , wherein individually sequentially flowing the two or more types of charged tRNA to the one or more identifiable locations at the one or more first identifiable time intervals comprises:

sequentially providing two or more charged anti-stop codon tRNA to an identifiable location.

27. The method of claim 26 , wherein the two or more charged anti-stop codon tRNA are charged with one or more natural amino acids or one or more unnatural amino acids.

28. The method of claim 26 , further comprising:

charging one or more anti-stop codon tRNA with one or more natural amino acids or one or more unnatural amino acids.

29. The method of claim 1 , further comprising:

selecting the two or more types charged tRNA.

30. The method of claim 29 , wherein selecting the two or more types of charged tRNA comprises:

selecting the two or more charged tRNA at least partially based on a target peptide sequence.

31. The method of claim 29 , wherein selecting the two or more types of charged tRNA comprises:

selecting the two or more types of charged tRNA at least partially based on a nucleic acid protein coding sequence.

32. A method of extra-cellular peptide synthesis comprising:

determining, with one or more computing units, an order that two or more types of charged tRNA are to be sequentially flowed to one or more first identifiable locations in a reaction chamber of a fluidic device; and

controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals in vitro.

33. A method comprising:

determining an assembly order with one or more computing units; and

controlling the operation of a fluidic device with the one or more computing units so that two or more types of charged tRNA are individually sequentially flowed according to the assembly order in one or more channels of the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals.

34. The method of claim 1 , further comprising:

receiving data representative of at least one of a target peptide structure or charged tRNA sequences; and

wherein determining, with one or more computing units, an order that two or more types of charged tRNA are to be sequentially flowed to one or more first identifiable locations in a reaction chamber of a fluidic device is based at least partially on the data.

35. The method of claim 1 , wherein controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals includes:

flowing the two or more types of charged tRNA from at least one tRNA reservoir to the reaction chamber via one or more tRNA ports.

36. The method of claim 35 , wherein the reaction chamber is part of a microchip.

37. The method of claim 1 , wherein controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined order through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals includes:

sequentially flowing the two or more types of charged tRNA through the reaction chamber having one or more ribosome-based assemblers fixed therein.

38. The method of claim 32 , further comprising:

receiving data representative of at least one of a target peptide structure or charged tRNA sequences; and

wherein determining, with one or more computing units, an order that two or more types of charged tRNA are to be sequentially flowed to one or more first identifiable locations in a reaction chamber of a fluidic deviceis based at least partially on the data.

39. The method of claim 33 , further comprising:

receiving data representative of at least one of a target peptide structure or charged tRNA sequences; and

wherein determining an assembly order with one or more computing units is based at least partially on the data.

40. A method comprising:

determining, with one or more computing units, a timing that two or more types of charged tRNA are to be sequentially flowed to one or more first identifiable locations in a reaction chamber of a fluidic device; and

controlling the operation of the fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed according to the determined timing through one or more channels in the fluidic device to the one or more identifiable locations at one or more first identifiable time intervals.