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 co-localized sequentially with one or more ribosome-based assemblers in a reaction chamber of a fluidic device;

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 through one or more channels in the fluidic device to the reaction chamber according to the determined order; and

assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber.

2. 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.

3. 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.

4. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

assembling the target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA at one or more first identifiable time intervals.

5. The method of claim 4 , wherein the one or more first identifiable time intervals are at least partially based on one or more of a predicted rate of incorporation of two or more amino acids into one or more peptides, a predicted rate of activity of the one or more ribosome-based assemblers, a predicted rate of translocation of one or more nucleic acids, or a predicted rate of release of tRNA.

6. 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.

7. The method of claim 6 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

assembling the target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA at one or more first identifiable time intervals, and

wherein the one or more first identifiable time intervals are at least partially 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.

8. The method of claim 6 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

assembling the target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA at one or more first identifiable time intervals, and

wherein the one or more first identifiable time intervals are at least partially based on availability of one or more nucleic acid codons.

9. 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.

10. The method of claim 9 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

assembling the target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA at one or more first identifiable time intervals, and

wherein the one or more first identifiable time intervals are at least partially based on the concentrations of one or more of the two or more types of charged tRNA or the one or more tRNA.

11. The method of claim 9 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

assembling the target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA at one or more first identifiable time intervals, and

wherein the one or more first identifiable time intervals are at least partially 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.

12. The method of claim 9 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

assembling the target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA at one or more first identifiable time intervals, and

wherein the one or more first identifiable time intervals are at least partially 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.

13. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

co-localizing the one or more ribosome-based assemblers and one or more first charged tRNA;

co-localizing the one or more ribosome-based assemblers and one or more second charged tRNA; and

optionally repeating.

14. The method of claim 13 , further comprising:

co-localizing the one or more ribosome-based assemblers and one or more third charged tRNA.

15. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

co-localizing the one or more ribosome-based assemblers and one or more first charged tRNA, the one or more first charged tRNA charged with one or more first arbitrary amino acids;

separating the one or more ribosome-based assemblers from one or more of the one or more first charged tRNA or one or more first tRNA, the one or more first tRNA released during peptide synthesis;

co-localizing the one or more ribosome-based assemblers and one or more second charged tRNA, the one or more second charged tRNA charged with one or more second arbitrary amino acids;

separating the one or more ribosome-based assemblers from one or more of the one or more second charged tRNA or one or more second tRNA, the one or more second tRNA released during peptide synthesis and optionally repeating.

16. The method of claim 1 , further comprising:

consuming sequentially the two or more types of charged tRNA.

17. The method of claim 1 , further comprising:

eliminating sequentially one or more of the two or more types of charged tRNA or one or more tRNA.

18. The method of claim 1 , further comprising:

separating sequentially one or more of the two or more types of charged tRNA or one or more tRNA from the one or more ribosome-based assemblers.

19. The method of claim 18 , wherein separating sequentially one or more of the two or more types of charged tRNA or one or more tRNA from the one or more ribosome-based assemblers comprises:

separating sequentially one or more of the two or more types of charged tRNA or the one or more tRNA from the one or more ribosome-based assemblers at one or more second identifiable time intervals.

20. The method of claim 1 , wherein co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in a reaction chamber comprises:

co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in a defined sequence.

21. The method of claim 20 , further comprising:

determining the defined sequence for co-localizing the one or more ribosome-based assemblers and the two or more types of charged tRNA.

22. The method of claim 21 , wherein determining the defined sequence for co-localizing the one or more ribosome-based assemblers and the two or more types of charged tRNA comprises:

determining the defined sequence for co-localizing the one or more ribosome-based assemblers and the two or more types of charged tRNA based at least partially on a target peptide sequence.

23. The method of claim 21 , wherein determining the defined sequence for co-localizing the one or more ribosome-based assemblers and the two or more types of charged tRNA comprises:

determining the defined sequence for co-localizing the one or more ribosome-based assemblers and the two or more types of charged tRNA based at least partially on a nucleic acid protein coding sequence.

24. The method of claim 23 , wherein a protein coding region of the nucleic acid sequence includes two or more stop codons.

25. The method of claim 24 , wherein the protein coding region includes at least three stop codons.

26. The method of claim 24 , wherein the protein coding region includes two or more alternating stop codons.

27. The method of claim 24 , wherein the protein coding region includes one or more of one or more singlet codons, one or more doublet codons, one or more triplet codons, one or more quadruplet codons or one or more quintuplet codons.

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

29. The method of claim 28 , further comprising:

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

30. The method of claim 1 , wherein the two or more types of charged tRNA are one or more charged anti-stop codon tRNA.

31. The method of claim 1 , further comprising:

selecting the two or more types of charged tRNA.

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

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

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

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

34. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

co-localizing sequentially one or more peptide assemblers and the two or more types of charged tRNA.

35. The method of claim 1 , wherein co-localizing sequentially one or more ribosome-based assemblers and the two or more types of charged tRNA comprises:

co-localizing sequentially one or more prokaryotic ribosome-based assemblers and the two or more types of charged tRNA.

36. The method of claim 1 , wherein co-localizing sequentially one or more ribosome-based assemblers and the two or more types of charged tRNA comprises:

co-localizing sequentially one or more eukaryotic ribosome-based assemblers and the two or more types of charged tRNA.

37. The method of claim 1 , wherein co-localizing sequentially one or more ribosome-based assemblers and the two or more types of charged tRNA comprises:

co-localizing sequentially one or more mitochondrial ribosome-based assemblers and the two or more types of charged tRNA.

38. The method of claim 1 , further comprising:

selecting the one or more ribosome-based assemblers.

39. The method of claim 1 , further comprising:

assembling one or more components of the one or more ribosome-based assemblers.

40. The method of claim 39 , wherein assembling one or more components of the one or more ribosome-based assemblers comprises:

assembling the one or more components of the one or more ribosome-based assemblers at one or more third identifiable time intervals.

41. The method of claim 39 , further comprising:

selecting the one or more components of the one or more ribosome-based assemblers.

42. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber comprises:

co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA, wherein the one or more ribosome-based assemblers are co-localized with one or more nucleic acids.

43. The method of claim 42 , further comprising:

synchronizing the co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA, with a protein coding sequence of the one or more nucleic acids.

44. The method of claim 1 , further comprising:

co-localizing one or more nucleic acids with the one or more ribosome-based assemblers.

45. The method of claim 44 , wherein co-localizing one or more nucleic acids with the one or more ribosome-based assemblers comprises:

co-localizing the one or more nucleic acids with the one or more ribosome-based assemblers at one or more fourth identifiable time intervals.

46. The method of claim 44 , wherein assembling the target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA occurs at least partially following co-localizing the one or more nucleic acids with the one or more ribosome-based assemblers.

47. The method of claim 44 , further comprising:

selecting the one or more nucleic acids.

48. 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 co-localized sequentially with one or more ribosome-based assemblers in a reaction chamber of a fluidic device;

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 through one or more channels in the fluidic device to the reaction chamber according to the determined order; and

assembling a target peptide in vitro by co-localizing sequentially the one or more ribosome-based assemblers, and the two or more types of charged tRNA.

49. A method comprising:

determining an assembly order with one or more computing units;

controlling the operation of a fluidic device with the one or more computing units so that the two or more types of charged tRNA are individually sequentially flowed through one or more channels in the fluidic device to a reaction chamber of the fluidic device according to the determined assembly order; and

assembling a target peptide by co-localizing the one or more ribosome-based assemblers, and the two or more types of charged tRNA in the reaction chamber.

50. 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 co-localized sequentially with one or more ribosome-based assemblers in a reaction chamber of a fluidic device is based at least partially on the data.

51. 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 through one or more channels in the fluidic device to the reaction chamber according to the determined order includes:

flowing the one or more ribosome-based assemblers from at least one ribosome-based assembler reservoir into the reaction chamber via one or more ribosome-based assembler channels; and

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.

52. The method of claim 51 , wherein the reaction chamber is part of a microchip.

53. 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 through one or more channels in the fluidic device to the reaction chamber according to the determined order includes:

flowing a plurality of ribosome-based assemblers from corresponding ribosome-based assembler reservoirs, through corresponding ribosome-based assembler channels, through a common input channel, and into the reaction chamber; and

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

54. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber includes:

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

55. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber includes:

flowing the two or more types of charged tRNA through the reaction chamber; and

flowing beads having the one or more ribosome-based assemblers attached thereto through the reaction chamber.

56. The method of claim 55 , further comprising:

restricting the flow of the beads through the reaction chamber via a dam; and

allowing deacylated tRNA to flow past the dam.

57. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber includes:

flowing the one or more ribosome-based assemblers through the reaction chamber having the two or more types of charged tRNA fixed therein in a selected spatial order related to a target peptide synthesis sequence.

58. The method of claim 1 , wherein assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber includes:

flowing the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber.

59. 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 through one or more channels in the fluidic device to the reaction chamber according to the determined order includes:

flowing the one or more ribosome-based assemblers through a ribosome-based assembler channel; and

sequentially flowing each of the two or more types of charged tRNA through corresponding tRNA channels as the one or more ribosome-based assemblers flow through the ribosome-based assembler channel.

60. A method comprising:

determining, with one or more computing units, a timing that two or more types of charged tRNA are to be co-localized sequentially with one or more ribosome-based assemblers in a reaction chamber of a fluidic device;

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 through one or more channels in the fluidic device to the reaction chamber according to the determined timing; and

assembling a target peptide by co-localizing sequentially the one or more ribosome-based assemblers and the two or more types of charged tRNA in the reaction chamber.