Digital to biological converter
The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information. The invention is useful, for example, for rapidly responding to viral and other biological threats that are specific to a particular locale.
1 . A method of synthesizing a double-stranded DNA (dsDNA) molecule according to provided biological sequence information comprising:
providing a system comprising an assembly unit that assembles the double-stranded DNA molecule according to the biological sequence information;
providing within or connected to the assembly unit vessels containing a plurality of oligonucleotide molecules and reagents for performing reactions to synthesize the dsDNA molecule;
and components that transport the reagents within the system and that execute steps in an automated method for synthesizing the dsDNA molecule; and wherein the method comprises the assembly of one or more dsDNA molecules by joining the plurality of oligonucleotides, and wherein no human intervention occurs after the method is initiated and until the dsDNA molecule is synthesized; and
wherein the system further comprises a non-transitory computer readable medium containing software programming instructions that direct steps in the assembly unit for the assembly of the plurality of oligonucleotide molecules into the dsDNA molecule in the automated method;
wherein the software programming instructions direct a step of PCR amplification in a first reaction zone of a reaction container, a step of error correction in a second reaction zone of a reaction container performed after the step of PCR amplification, a step of DNA assembly in a third reaction zone of a reaction container, and directs the transport of reagents from one reaction zone to the next, and wherein the reaction container is a reaction plate, and the reaction zones comprise one or more reaction wells on the reaction plate; and
wherein the system further comprises a robotic arm configured to transfer the oligonucleotide molecules from the first reaction zone to the second reaction zone, the oligonucleotide molecules successively accumulating in each reaction zone;
initiating the automated method; and
thereby synthesizing the dsDNA molecule in an automated method.
2 . The method of claim 1 wherein the system further comprises a transmitting unit and wherein the receiving unit are computers that are part of a computer network.
3 . The method of claim 1 wherein the oligonucleotides are provided to a sub-unit of the assembly unit for amplification of the oligonucleotides by the step of PCR.
4 . The method of claim 1 wherein the oligonucleotides are from 40-100 nucleotides in length.
5 . The method of claim 1 wherein the system further comprises software programming instructions and reagents directing steps for the transcription of the DNA molecule into an RNA molecule.
6 . The method of claim 5 wherein the system further comprises software programming instructions and reagents directing translation of the RNA molecule into a protein molecule.
7 . The method of claim 6 wherein the protein is further processed by the system to produce a virus particle or a portion of a virus particle.
8 . The method of claim 7 wherein the virus particle or portion of a virus particle comprises a protein antigen.
9 . The method of claim 1 wherein the assembly unit further comprises or is connected to a vessel comprising a host cell.
10 . The method of claim 1 wherein the system comprises a single reaction container.
11 . The method of claim 10 wherein the reaction container is a 96 well plate.
12 . The method of claim 1 wherein the reaction container is a 96 well plate having dimensions of about 127 mm×about 85 mm.
13 . The method of claim 1 wherein the double stranded DNA molecule is greater than 500 bp in size.
14 . The method of claim 1 wherein the assembly unit further comprises or is connected to vessels containing a nucleic acid molecule selected from the group consisting of: a plasmid, a vector, a regulatory sequence, a promoter sequence, a binding element for a trans-acting factor, and a signal sequence.
15 . The method of claim 1 wherein the plurality of oligonucleotide molecules are 30-110 nucleotides in length.
16 . The method of claim 1 further comprising assembling the oligonucleotides in an isothermal reaction.
17 . The method of claim 1 wherein the plurality of oligonucleotide molecules are assembled into the dsDNA molecule(s) in a simultaneous reaction.
18 . The method of claim 1 wherein the overlapping oligonucleotides are assembled in a reaction using an exonuclease and a DNA polymerase.
19 . The method of claim 1 further comprising synthesizing the dsDNA molecule into a plasmid or vector for further use.
20 . The method of claim 1 further comprising appending regulatory sequences or promoter sequence to the assembled dsDNA molecule.