Methods for arbitrary peptide synthesis
View Patent ↗Methods, apparatus, systems, computer programs and computing devices related to biologically assembling and/or synthesizing peptides and/or proteins are disclosed.
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;
at least partially based on the determined order, controlling the operation of the fluidic device with the one or more computing units so that at least one of the two or more types of charged tRNA or the one or more ribosome-based assemblers are flowed through one or more channels in the fluidic device to the reaction chamber; and
co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber.
2. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
synthesizing a target peptide by co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers.
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 co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing one or more first charged tRNA with the one or more ribosome-based assemblers;
co-localizing one or more second charged tRNA with the one or more ribosome-based assemblers; and
optionally repeating.
6. The method of claim 1 , wherein co-localizing sequentially the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing one or more first charged tRNA with the one or more ribosome-based assemblers, the one or more first charged tRNA charged with one or more first arbitrary amino acids;
removing 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 one or more second charged tRNA with the one or more ribosome-based assemblers, the one or more second charged tRNA charged with one or more second arbitrary amino acids;
removing 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.
7. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers at one or more first identifiable time intervals.
8. The method of claim 7 , 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.
9. 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.
10. The method of claim 9 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers 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.
11. The method of claim 9 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers 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.
12. 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.
13. The method of claim 12 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers 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.
14. The method of claim 12 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers 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.
15. The method of claim 12 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers 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.
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 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:
removing one or more of the two or more types of charged tRNA or one or more tRNA.
19. The method of claim 18 , wherein removing one or more of the two or more types of charged tRNA or one or more tRNA comprises:
removing sequentially one or more of the two or more types of charged tRNA or the one or more tRNA.
20. The method of claim 18 , wherein removing one or more of the two or more types of charged tRNA or one or more tRNA comprises:
removing sequentially one or more of the two or more types of charged tRNA or the one or more tRNA at one or more second identifiable time intervals.
21. The method of claim 18 , 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 the one or more tRNA.
22. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
injecting sequentially the two or more types of charged tRNA into one or more receptacles containing the one or more ribosome-based assemblers.
23. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially two or more charged anti-stop codon tRNA with the one or more ribosome-based assemblers.
24. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers, 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 acid.
25. The method of claim 1 , further comprising:
charging one or more tRNA with one or more natural amino acids, one or more arbitrary amino acid, or one or more unnatural amino acid.
26. The method of claim 1 , further comprising:
selecting the two or more types of charged tRNA.
27. The method of claim 26 , 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 target peptide sequence.
28. The method of claim 26 , 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.
29. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with one or more peptide assemblers.
30. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with one or more eukaryotic ribosome-based assemblers.
31. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with one or more mitochondrial ribosome-based assemblers.
32. The method of claim 1 , further comprising:
selecting the one or more ribosome-based assemblers.
33. The method of claim 1 , further comprising:
assembling one or more components of the one or more ribosome-based assemblers.
34. The method of claim 33 , 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.
35. The method of claim 33 , further comprising:
selecting the one or more components of the one or more ribosome-based assemblers.
36. The method of claim 1 , further comprising:
co-localizing the one or more ribosome-based assemblers at one or more identifiable locations.
37. The method of claim 36 , wherein co-localizing the one or more ribosome-based assemblers at one or more identifiable locations comprises:
co-localizing the one or more ribosome-based assemblers at the one or more identifiable locations at one or more fourth identifiable time intervals.
38. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers occurs at least partially following co-localizing the one or more ribosome-based assemblers at one or more identifiable locations.
39. The method of claim 1 , further comprising:
affixing the one or more ribosome-based assemblers at one or more identifiable locations.
40. The method of claim 1 , further comprising:
affixing the one or more ribosome-based assemblers to one or more devices.
41. The method of claim 40 , wherein affixing the one or more ribosome-based assemblers to one or more devices comprises:
affixing the one or more ribosome-based assemblers to one or more MEMS devices.
42. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers, wherein the one or more ribosome-based assemblers are co-localized with one or more nucleic acids.
43. The method of claim 42 , wherein co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers, wherein the one or more ribosome-based assemblers are co-localized with one or more nucleic acids comprises:
co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers, wherein the one or more ribosome-based assemblers are co-localized with the one or more nucleic acids having a selected protein coding sequence.
44. The method of claim 43 , further comprising:
synchronizing co-localizing sequentially the two or more charged types of tRNA with the one or more ribosome-based assemblers, with the selected protein coding sequence of the one or more nucleic acids.
45. The method of claim 1 , further comprising:
co-localizing one or more nucleic acids with the one or more ribosome-based assemblers.
46. The method of claim 45 , 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 fifth identifiable time intervals.
47. The method of claim 45 , wherein the co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers occurs at least partially following the co-localizing the one or more nucleic acids with the one or more ribosome-based assemblers.
48. The method of claim 45 , further comprising:
selecting the one or more nucleic acids.
49. The method of claim 48 , wherein selecting the one or more nucleic acids comprises:
selecting the one or more nucleic acids having a target protein coding sequence.
50. The method of claim 49 , further comprising:
synchronizing co-localizing sequentially the two or more types of charged tRNA with the one or more ribosome-based assemblers, with the target protein coding sequence of the one or more nucleic acids.
51. A method of extra-cellular peptide synthesis comprising:
determining, with one or more computing units, at an order that two or more charged tRNA are to be co-localized sequentially with one or more ribosome-based assemblers in a reaction chamber of a fluidic device;
at least partially based on the determined order, controlling the operation of the fluidic device with the one or more computing units so that at least one of the two or more charged tRNA or the one or more ribosome-based assemblers are flowed through one or more channels in the fluidic device to the reaction chamber; and
co-localizing the two or more charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber in vitro.
52. A method comprising:
determining an assembly order with one or more computing units; and
at least partially based on the determined assembly order, controlling the operation of a fluidic device with the one or more computing units so that at least one of the two or more types of charged tRNA or the one or more ribosome-based assemblers are flowed through one or more channels in the fluidic device to a reaction chamber of the fluidic device; and
co-localizing the two or more types of charged tRNA individually sequentially according to the determined assembly order with the one or more ribosome-based assemblers in the reaction chamber.
53. 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.
54. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber includes:
flowing the one or more ribosome-based assemblers from at least one biological assembler reservoir into the reaction chamber via one or more biological 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.
55. The method of claim 54 , wherein the reaction chamber is part of a microchip.
56. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber includes:
flowing a plurality of ribosome-based assemblers from corresponding biological assembler reservoirs, through corresponding biological 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.
57. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers 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.
58. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers 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.
59. The method of claim 58 , further comprising:
restricting the flow of the beads through the reaction chamber via a dam; and
allowing deacylated tRNA to flow past the dam.
60. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers 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.
61. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber includes:
selectively moving one or more magnetic beads having the one or more ribosome-based assemblers attached thereto through the one or more channels to two or more wells having the two or more types of charged tRNA therein.
62. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers 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.
63. The method of claim 1 , wherein co-localizing the two or more types of charged tRNA individually sequentially according to the determined order with the one or more ribosome-based assemblers in the reaction chamber includes:
flowing the one or more ribosome-based assemblers through a biological 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 biological assembler channel.
64. 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;
at least partially based on the determined timing, controlling the operation of the fluidic device with the one or more computing units so that at least one of the two or more types of charged tRNA or the one or more ribosome-based assemblers are flowed through one or more channels in the fluidic device to the reaction chamber; and
co-localizing the two or more types of charged tRNA individually sequentially according to the determined timing with the one or more ribosome-based assemblers in the reaction chamber.