Apparatus 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 peptide synthesizer apparatus comprising:
two or more sources of charged tRNA, each source positioned to sequentially provide flow of one or more charged tRNA to one or more biological assemblers at one or more first locations; and
one or more computing units configured to control the two or more sources of charged tRNA, wherein the one or more computing units are further configured to,
receive information representative of one or more target peptide structures;
determine one or more temporal-spatial parameters for synthesizing the one or more target peptide structures based at least partially on the data, wherein the one or more temporal-spatial parameters are at least partially based on at least one of a target peptide sequence or a target nucleic acid sequence; and
direct each source to sequentially provide the one or more charged tRNA to the one or more first locations based at least partially on the temporal-spatial parameters one type of charged tRNA at a time sequentially.
2. The apparatus of claim 1 , wherein the one or more first locations is one or more temporal-spatial locations.
3. The apparatus of claim 2 , wherein the one or more temporal-spatial locations are moving along a predictable time or other sequential path.
4. The apparatus of claim 1 , wherein one or more first source of the two or more sources of charged tRNA includes a supply of one or more first type of charged tRNA, and one or more second source of the two or more sources of charged tRNA includes one or more second type of charged tRNA.
5. The apparatus of claim 4 , wherein the one or more first type of charged tRNA is different from the one or more second type of charged tRNA.
6. The apparatus of claim 4 , wherein one or more third source of the two or more sources of charged tRNA includes a supply of one or more third type of charged tRNA.
7. The apparatus of claim 6 , wherein the one or more third type of charged tRNA is different from the one or more first type of charged tRNA and the one or more second type of charged tRNA.
8. The apparatus of claim 1 , wherein each source includes one or more fluid flows that are positioned to sequentially provide the flow of the one or more charged tRNA to the one or more first locations at one or more first identifiable time intervals, 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 one or more biological assemblers, a predicted rate of translocation of one or more nucleic acids, or a predicted rate of release of tRNA.
9. The apparatus of claim 1 , wherein each source includes one or more fluid flows that are further positioned to sequentially remove one or more of the one or more charged tRNA or one or more tRNA from the one or more first locations.
10. The apparatus of claim 1 , wherein each source includes one or more fluid flows that are positioned to remove one or more of the one or more charged tRNA or one or more released tRNA from the one or more first locations.
11. The apparatus of claim 1 , wherein each source includes one or more fluid flows that are positioned to sequentially remove one or more of the one or more charged tRNA or one or more released tRNA from the one or more first locations.
12. The apparatus of claim 1 , further comprising:
one or more monitoring units.
13. The apparatus of claim 12 , wherein the one or more monitoring units are operable to measure one or more of amino acid incorporation into one or more peptides, biological assembler activity, nucleic acid translocation, or tRNA release.
14. The apparatus of claim 12 , wherein the one or more monitoring units are operable to measure one or more of presence or absence, concentration, or composition of one or more of the two or more charged tRNA or one or more tRNA.
15. The apparatus of claim 1 wherein the one or more computing units are operable to control one or more of an order or timing for one or more of providing the one or more charged tRNA to the one or more first locations or removing one or more of the one or more charged tRNA or one or more tRNA from the one or more first locations.
16. The apparatus of claim 15 , wherein the timing for one or more of providing the one or more charged tRNA to the one or more first locations or removing one or more of the one or more charged tRNA or the one or more tRNA from the one or more first locations is sequential timing.
17. The apparatus of claim 15 , wherein the timing for one or more of providing the one or more charged tRNA to the one or more first locations or removing one or more of the one or more charged tRNA or the one or more tRNA from the one or more first locations is one or more first identifiable time intervals.
18. The apparatus of claim 15 , wherein one or more of the order or the timing for one or more of providing the one or more charged tRNA to the one or more first locations or removing one or more of the one or more charged tRNA or the one or more tRNA from the one or more first locations is at least partially based on one or more of a target peptide sequence or a nucleic acid protein coding sequence.
19. The apparatus of claim 15 , wherein one or more of the order or the timing is 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 one or more biological assemblers, a predicted rate of translocation of one or more nucleic acids, or a predicted rate of release of tRNA.
20. The apparatus of claim 15 , wherein one or more of the order or the timing is at least partially based on monitoring of one or more of amino acid incorporation into one or more peptides, biological assembler activity, nucleic acid translocation, or tRNA release.
21. The apparatus of claim 15 , wherein one or more of the order or the timing is at least partially based on one or more of availability of one or more nucleic acid codons, concentrations of one or more of the two or more charged tRNA or the one or more tRNA, presence or absence of one or more of the two or more charged tRNA or the one or more tRNA, or presence or absence of one or more anti-codons on one or more of the two or more charged tRNA or the one or more tRNA.
22. A peptide synthesizer apparatus, comprising:
two or more sources of charged tRNA, each source positioned to sequentially provide flow of one or more charged tRNA to one or more biological assemblers at one or more first locations; and
one or more computing units configured to control the two or more sources of charged tRNA, wherein the one or more computing units are further configured to,
receive information representative of one or more target peptide structures;
synchronize a nucleic acid protein coding sequence and a target protein coding sequence for the target peptide structure that at least partially follows a genetic code that is different than that of the standard genetic code
determine one or more temporal-spatial parameters for synthesizing one or more peptides based at least partially on the data, wherein the one or more temporal-spatial parameters are at least partially based on at least one of a target peptide sequence or a target nucleic acid sequence; and
direct each source to sequentially provide the one or more charged tRNA to the one or more first locations based at least partially on the temporal-spatial parameters and the genetic code one type of charged tRNA at a time sequentially.
23. A peptide synthesizer apparatus, comprising:
two or more sources of charged tRNA, each source positioned to sequentially provide flow of one or more charged tRNA to one or more biological assemblers at one or more first locations; and
one or more computing units configured to control the two or more sources of charged tRNA, wherein the one or more computing units are further configured to,
receive information representative of a target peptide structure;
synchronize a nucleic acid protein coding sequence and a target protein coding sequence for the target peptide structure that at least partially follows a genetic code that is different than that of the standard genetic code;
determine one or more temporal-spatial parameters for synthesizing the target peptide structure based at least partially on the information, wherein the one or more temporal-spatial parameters are at least partially based on at least one of a target peptide sequence or a target nucleic acid sequence ; and
direct each source to sequentially provide the one or more charged tRNA to the one or more first locations based at least partially on the temporal-spatial parameters and at least partially on a genetic code that is different than that of the standard genetic code one type of charged tRNA at a time sequentially.