Homopolymer encoded nucleic acid memory
Nucleic acid memory strands encoding digital data using a sequence of homopolymer tracts of repeated nucleotides provides a cheaper and faster alternative to conventional digital DNA storage techniques. The use of homopolymer tracts allows for lower fidelity, high throughput sequencing techniques such as nanopore sequencing to read data encoded in the memory strands. Specialized synthesis techniques allow for synthesis of long memory strands capable of encoding large volumes of data despite the reduced data density afforded by homopolymer tracts as compared to conventional single nucleotide sequences.
1. A method of synthesizing a plurality of nucleic acid memory strands, the method comprising:
providing an array of two or more substrate-linked nucleic acids with addressable delivery of activation energy to each of the substrate-linked nucleic acids;
extending one or more of the substrate-linked nucleic acids with a homopolymer tract of two or more repeating nucleotides by delivering addressable activation energy to one or more of the substrate-linked nucleic acids in the presence of a plurality of blocked nucleotide analogs and a template-independent polymerase, wherein the template-independent polymerase incorporates unblocked nucleotide analogs and not blocked nucleotide analogs and wherein the addressable activation energy converts the blocked nucleotide analogs into unblocked nucleotide analogs,
wherein the addressable activation energy comprises light, pH change, or heat.
2. The method of claim 1 , wherein the blocked nucleotide analog is converted to an unblocked nucleotide analog by removal of a blocking group.
3. The method of claim 1 , wherein the addressable activation energy comprises light or heat.
4. The method of claim 2 , wherein the removable blocking group is at the 3′-OH of the blocked nucleotide analog.
5. The method of claim 2 , wherein the removable blocking group is on the purine or pyrimidine base of the nucleotide analog.
6. The method of claim 1 , wherein the blocked nucleotide analog comprises a removable blocking group on a 3′-OH of the deoxyribose or ribose of a nucleotide triphosphate and a non-removable modification on a purine or pyrimidine base of the nucleotide analog.
7. The method of claim 1 , wherein the plurality of blocked nucleotide analogs are modified nucleotides of a same nucleobase comprising removable 3′-O-blocking groups and two or more non-removable molecular modifications that allow differentiation between the modified nucleotide analogs of the same nucleobase.
8. The method of claim 1 further comprising:
stopping the extension;
extending the homopolymer tract with an additional homopolymer tract of two or more repeating nucleotides by delivering addressable activation energy to the homopolymer tract in the presence of another plurality of blocked nucleotide analogs and the template-independent polymerase.
9. The method of claim 8 , wherein the extension is stopped after a predetermined length of time in order to obtain a desired length for the homopolymer tract.
10. The method of claim 1 , wherein rate of extension is modulated by modifications to the blocked nucleotide analogs.
11. The method of claim 10 , wherein the rate modulating modifications are removed from the homopolymer tract after extension.
12. The method of claim 1 , wherein the rate modulating modifications are removed during extension.
13. The method of claim 1 , wherein the repeating nucleotides of the homopolymer tract are between 2 and about 10.
14. The method of claim 8 , further comprising repeating the stopping and extending steps to synthesize a nucleic acid memory strand.
15. The method of claim 14 , wherein the nucleic acid memory strand is from about 200 nucleotides in length to about 5,000 nucleotides in length.
16. The method of claim 1 , wherein a predetermined concentration of the blocked nucleotide analogs is provided in the extending step to obtain a desired length for the homopolymer tract.
17. The method of claim 8 , wherein the homopolymer tract and additional homopolymer tract comprise different nucleobases.
18. The method of claim 14 wherein the nucleic acid memory strand encodes a dataset selected from the group consisting of a text file, an image file, and an audio file.
19. The method of claim 18 , further comprising displaying a readable format of the dataset.
20. The method of claim 14 , wherein a unit of data is represented in base 2.
21. The method of claim 14 , wherein a unit of data is represented in base 3.
22. The method of claim 14 , wherein a unit of data is represented in base 4.
23. The method of claim 14 , wherein a unit of data is represented in greater than base 4.
24. The method of claim 14 , wherein data is represented by the extent of decaging or resultant tract length at individual steps of memory strand synthesis.
25. The method of claim 14 , wherein data encoded in the nucleic acid memory strand is retrieved by DNA sequencing.
26. The method of claim 14 , wherein data encoded in the nucleic acid memory strand is retrieved by passage of the nucleic acid memory strand through a nanopore.