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 recording data using a nucleic acid memory strand, the method comprising the steps of:
creating an in silico sequence of bits that represents a dataset;
synthesizing a nucleic acid memory strand comprising a plurality of homopolymer tracts or heteropolymer tracts, the heteropolymer tracts comprising two or more different nucleotides or nucleotide analogs,
wherein each bit of the sequence of bits representing the dataset is encoded in a homopolymer or heteropolymer tract,
wherein homopolymer tracts are converted to bits by identifying transitions between homopolymer tracts, and
wherein heteropolymer tracts encode bits based on a ratio of the two or more different nucleotides or nucleotide analogs to each other within each heteropolymer tract.
2. The method of claim 1 , wherein the plurality of homopolymer tracts comprises between 2 and 10 repeated nucleotides.
3. The method of claim 1 , wherein each unit of said dataset is represented in base 2.
4. The method of claim 1 , wherein each unit of said dataset is represented in base 3 or higher.
5. The method of claim 1 , wherein the nucleic acid memory strand is from at least about 200 nucleotides in length to about 5,000 nucleotides in length.
6. The method of claim 1 , wherein said synthesizing step comprises controlling tract length by varying dNTP concentration.
7. The method of claim 1 , wherein said synthesizing step comprises controlling tract length by varying reaction time.
8. The method of claim 1 , wherein the plurality of tracts comprise two or more different nucleotides.
9. The method of claim 1 , wherein said synthesizing step comprises controlling tract composition by varying dNTP ratios.
10. The method of claim 1 , further comprising:
modifying a first end of the nucleic acid memory strand to prevent passage of the first end through a nanopore of a nanopore sequencing system;
passing a second end of the nucleic acid memory strand through the nanopore; and
modifying the second end of the nucleic acid memory strand to prevent passage of the second end through the nanopore, thereby capturing the nucleic acid memory strand in the nanopore.
11. The method of claim 1 , wherein the dataset is selected from the group consisting of a text file, an image file, and an audio file.
12. The method of claim 1 , wherein said synthesizing step comprises template-independent synthesis.
13. The method of claim 12 , wherein a nucleotidyl transferase enzyme is used to catalyze said template-independent synthesis.
14. The method of claim 12 , wherein polymerase theta is used to catalyze said template-independent synthesis.
15. The method of claim 1 , wherein the nucleic acid memory strand comprises covalently bound chemical protecting groups that prevent conversion of the nucleic acid memory strand into the dataset.