Assembly of nucleic acid sequences in emulsions
Methods and compositions for synthesizing nucleic acid sequences in an emulsion are provided.
1. A method of synthesizing a target nucleic acid sequence comprising the steps of:
localizing a plurality of oligonucleotide subsequences defining an oligonucleotide set corresponding to a particular target nucleic acid sequence by hybridization to a predesigned sequence attached to a bead that is unique to each oligonucleotide set;
placing the bead within an emulsion droplet;
separating the plurality of oligonucleotide subsequences from the bead such that the plurality of oligonucleotide subsequences remain within the emulsion droplet; and
assembling within the emulsion droplet the plurality of oligonucleotide subsequences to form the target nucleic acid sequence.
2. The method of claim 1 wherein the target nucleic acid sequence includes at least 300 nucleotides.
3. The method of claim 1 wherein the target nucleic acid sequence includes at least 1,000 nucleotides.
4. The method of claim 1 , wherein the target nucleic acid sequence includes at least 2,500 nucleotides.
5. The method of claim 1 , wherein the target nucleic acid sequence includes at least 5,000 nucleotides.
6. The method of claim 1 , wherein the target nucleic acid sequence is a DNA sequence.
7. The method of claim 6 , wherein the DNA sequence is a regulatory element, a gene, a pathway or a genome.
8. The method of claim 1 further comprising obtaining the target nucleic acid.
9. A method of synthesizing a plurality of target nucleic acid sequences comprising the steps of:
for each target nucleic acid sequence within the plurality, localizing a plurality of oligonucleotide subsequences defining an oligonucleotide set corresponding to a particular target nucleic acid sequence by hybridization to a predesigned sequence attached to a bead that is unique to the oligonucleotide set so as to create a plurality of beads with a plurality of oligonucleotide sets corresponding to the plurality of target nucleic acid sequences;
placing the plurality of beads within a plurality of emulsion droplets;
separating the plurality of oligonucleotide subsequences from a bead within an emulsion droplet;
assembling within the emulsion droplet the plurality of oligonucleotide subsequences to form one of the plurality of target nucleic acid sequences.
10. The method of claim 9 , wherein the plurality of oligonucleotide sets includes at least 50 oligonucleotide sets.
11. The method of claim 9 , wherein the plurality of oligonucleotide sets includes at least 100 oligonucleotide sets.
12. The method of claim 9 , wherein the plurality of oligonucleotide sets includes at least 500 oligonucleotide sets.
13. The method of claim 9 , wherein the plurality of oligonucleotide sets includes at least 750 oligonucleotide sets.
14. The method of claim 9 , wherein the plurality of oligonucleotide sets includes at least 1000 oligonucleotide sets.
15. The method of claim 9 wherein members of the plurality of target nucleic acid sequences include at least 500 nucleotides.
16. The method of claim 9 wherein members of the plurality of target nucleic acid sequences include at least 1,000 nucleotides.
17. The method of claim 9 , wherein members of the plurality of the target nucleic acid sequences include at least 2,500 nucleotides.
18. The method of claim 9 , wherein members of the plurality of the target nucleic acid sequences include at least 5,000 nucleotides.
19. The method of claim 9 , wherein members of the plurality of the target nucleic acid sequences include DNA sequences.
20. The method of claim 19 , wherein the DNA sequences are a regulatory element, a gene, a pathway or a genome.
21. The method of claim 9 further comprising obtaining the plurality of target nucleic acids.
22. A method of synthesizing a target nucleic acid sequence comprising the steps of:
amplifying a plurality of oligonucleotide subsequences defining an oligonucleotide set corresponding to a particular target nucleic acid sequence by using orthogonal primers that hybridize to a pair of orthogonal primer binding sites that are unique to the oligonucleotide set;
removing the orthogonal primer binding sites from the amplified plurality of oligonucleotide subsequences;
attaching the amplified plurality of oligonucleotide subsequences to a bead;
synthesizing a complementary strand to each of the amplified plurality of oligonucleotide subsequences to produce a plurality of double stranded nucleic acids;
placing the bead within an emulsion droplet;
separating the plurality of double stranded nucleic acids from the bead such that the plurality of double stranded nucleic acids remain within the emulsion droplet; and
assembling within the emulsion droplet the plurality of double stranded nucleic acids to form the target nucleic acid sequence.
23. The method of claim 22 wherein the target nucleic acid sequence includes at least 500 nucleotides.
24. The method of claim 22 wherein the target nucleic acid sequence includes at least 1,000 nucleotides.
25. The method of claim 22 , wherein the target nucleic acid sequence includes at least 2,500 nucleotides.
26. The method of claim 22 , wherein the target nucleic acid sequence includes at least 5,000 nucleotides.
27. The method of claim 22 , wherein the target nucleic acid sequence is a DNA sequence.
28. The method of claim 27 , wherein the DNA sequence is a regulatory element, a gene, a pathway or a genome.
29. The method of claim 22 further comprising obtaining the target nucleic acid.
30. A method of synthesizing a plurality of target nucleic acid sequences comprising the steps of:
amplifying a plurality of oligonucleotide subsequences defining a plurality of oligonucleotide sets with each oligonucleotide set corresponding to a particular target nucleic acid sequence by using orthogonal primers that hybridize to a pair of orthogonal primer binding site sequences that are unique to each oligonucleotide set;
removing the orthogonal primer binding sites from the amplified plurality of oligonucleotide subsequences;
for each oligonucleotide set, attaching corresponding amplified oligonucleotide subsequences defining the set to a bead;
synthesizing a complementary strand to each of the amplified oligonucleotide subsequences to produce a plurality of double stranded nucleic acids;
placing the bead within an emulsion droplet;
separating the plurality of double stranded nucleic acids from the bead such that the plurality of double stranded nucleic acids remain within the emulsion droplet;
assembling within the emulsion droplet the plurality of double stranded nucleic acids to form one of the plurality of target nucleic acid sequences.
31. The method of claim 30 , wherein the plurality of oligonucleotide sets includes at least 50 oligonucleotide sets.
32. The method of claim 30 , wherein the plurality of oligonucleotide sets includes at least 100 oligonucleotide sets.
33. The method of claim 30 , wherein the plurality of oligonucleotide sets includes at least 500 oligonucleotide sets.
34. The method of claim 30 , wherein the plurality of oligonucleotide sets includes at least 750 oligonucleotide sets.
35. The method of claim 30 , wherein the plurality of oligonucleotide sets includes at least 1000 oligonucleotide sets.
36. The method of claim 30 wherein members of the plurality of target nucleic acid sequences include at least 500 nucleotides.
37. The method of claim 30 wherein members of the plurality of target nucleic acid sequences include at least 1,000 nucleotides.
38. The method of claim 30 , wherein members of the plurality of the target nucleic acid sequences include at least 2,500 nucleotides.
39. The method of claim 30 , wherein members of the plurality of the target nucleic acid sequences include at least 5,000 nucleotides.
40. The method of claim 30 , wherein members of the plurality of the target nucleic acid sequences include DNA sequences.
41. The method of claim 40 , wherein the DNA sequences are a regulatory element, a gene, a pathway or a genome.
42. The method of claim 30 further comprising obtaining the plurality of target nucleic acids.