Methods of gene assembly using DNAzymes and use in DNA data storage
Building DNA strands at a high rate that are suitable for data storage. Methods include using DNAzyme and utilizing libraries of pre-prepared oligos. A system for the DNA strand synthesis includes: a DNA symbol library comprising a number of single strand oligo symbols; a DNA linker library comprising a first set of single strand oligo linkers and a second set of single strand oligo linkers; and a DNAzyme library comprising a number of DNAzymes. An S1 end of a first DNAzyme is adapted to join the S1 end of a symbol and an S2 end of the first DNAzyme is adapted to join an S2 end of a first linker, and an S1 end of a second DNAzyme is adapted to join an S1 end of a second linker and an S2 end of the second DNAzyme is adapted to join an S2 end of the symbol.
1 . A system for DNA synthesis, comprising:
a DNA symbol library comprising a number of single strand oligo symbols, each symbol having an activated 3′-phosphorimidazolide S1 end and a 5′-hydroxyl S2 end;
a DNA linker library comprising a first set of single strand oligo linkers each having a 3′-phosphorimidazolide S1 end and a 5′-hydroxyl S2 end, and a second set of single strand oligo linkers each having an activated 3′-phosphorimidazolide S1 end and a 5′-hydroxyl S2 end; and
a DNAzyme library comprising a number of DNA ligating DNAzymes, each DNA ligating DNAzyme having a 3′-phosphorimidazolide complementary S1 end and a 5′-hydroxyl complementary S2 end;
wherein each of the linkers has a sequence specificity for the DNA ligating DNAzymes, and one or both of the S1 end and the S2 end of each of the linkers hybridizes to a complementary one of the DNA ligating DNAzymes;
and wherein:
the S1 end of a first DNA ligating DNAzyme joins the S1 end of a symbol and the S2 end of the first DNA ligating DNAzyme joins the S2 end of a first linker, and
the S1 end of a second DNA ligating DNAzyme joins the S1 end of a second linker and the S2 end of the second DNA ligating DNAzyme joins the S2 end of the symbol.
2 . The system of claim 1 , wherein the symbols comprise a base section having four to eight nucleotides, and a 3′-phosphorimidazolide S1 end section and a 5′-hydroxyl S2 end section each having six to ten nucleotides, independently.
3 . The system of claim 2 , wherein the symbols comprise two joined nibbles, each nibble having a base sub-section and an end section.
4 . The system of claim 1 , wherein the linkers comprise six to twenty nucleotides.
5 . The system of claim 1 , wherein the DNA ligating DNAzymes are E47 DNAzymes.
6 . A system for DNA synthesis, comprising:
a first DNA symbol library comprising a number of single strand oligo first nibble symbols, each first nibble symbol having a base section and a 3′-phosphorimidazolide S1 end;
a second DNA symbol library comprising a number of single strand oligo second nibble symbols, each second nibble symbol having a base section and a 5′-hydroxyl S2 end;
a DNA linker library comprising a first set of single strand oligo linkers each having a 3′-phosphorimidazolide S1 end and a 5′-hydroxyl S2 end, and a second set of single strand oligo linkers each having a 3′-phosphorimidazolide S1 end and a 5′-hydroxyl S2 end; and
a DNAzyme library comprising a number of DNA ligating DNAzymes, each DNA ligating DNAzyme having a 3′-phosphorimidazolide complementary S1 end and a 5′-hydroxyl complementary S2 end;
wherein:
wherein each of the linkers has a sequence specificity for the DNA ligating DNAzymes, and one or both of the S1 end and the S2 end of each of the linkers hybridizes to a complementary one of the DNA ligating DNAzymes;
the base section of a first nibble symbol joins the base section of a second nibble symbol;
the S1 end of a first DNA ligating DNAzyme joins the S1 end of one of the first nibble symbols and the S2 end of the first DNA ligating DNAzyme joins the S2 end of a first linker, and
the S1 end of a second DNA ligating DNAzyme joins the S1 end of a second linker and the S2 end of the second DNA ligating DNAzyme joins the S2 end of one of the second nibble symbols.
7 . The system of claim 6 , wherein the first nibble symbols and the second nibble symbols have combined base sections having four to eight nucleotides, the first nibble symbol has a 3′-phosphorimidazolide S1 end section having six to ten nucleotides, and the second nibble symbol has a 5′-hydroxyl S2 end section each having six to ten nucleotides.
8 . The system of claim 6 , wherein the linkers comprise six to twenty nucleotides.
9 . The system of claim 6 , wherein, combined, the first DNA symbol library and the second DNA symbol library has 256 nibbles.
10 . A method of making a DNA strand, comprising:
providing a DNA symbol library comprising a number of single strand DNA oligo symbols, each symbol having a 3′-phosphorimidazolide S1 end and a 5′-hydroxyl S2 end;
providing a DNA linker library comprising a first set of single strand DNA oligo linkers having a 3′-phosphorimidazolide S1 end and a second set of single strand DNA oligo linkers having a 5′-hydroxyl S2 end, wherein each of the linkers has a sequence specificity for the DNA ligating DNAzymes, and one or both of the S1 end and the S2 end of each of the linkers hybridizes to a complementary one of the DNA ligating DNAzymes;
providing a DNAzyme comprising a number of DNA ligating DNAzymes having a 3′-phosphorimidazolide complementary S1 end and a 5′-hydroxyl complementary S2 end;
joining the S1 end of a first DNA ligating DNAzyme to the S1 end of a symbol and the S2 end of the first DNA ligating DNAzyme to the S2 end of a first linker; and
joining the S1 end of a second DNA ligating DNAzyme to the S1 end of a second linker and the S2 end of the second DNA ligating DNAzyme to the S2 end of the symbol.
11 . The method of claim 10 , wherein:
joining the S1 end of a first DNA ligating DNAzyme to the S1 end of a symbol and the S2 end of the first DNA ligating DNAzyme to the S2 end of a first linker; and
joining the S1 end of a second DNA ligating DNAzyme to the S1 end of a second linker and the S2 end of the second DNA ligating DNAzyme to the S2 end of the symbol, are done simultaneously.
12 . The method of claim 10 , further comprising joining the DNA strand made in claim 10 with a second DNA strand.
13 . The method of claim 12 , wherein joining the DNA strand made in claim 10 with the second DNA strand is via an enzyme assembly.
14 . The method of claim 12 , wherein joining the DNA strand made in claim 10 with the second DNA strand is via another DNA ligating DNAzyme.
15 . The method of claim 1 , wherein the DNA ligating DNAzymes are E47 DNAzymes.
16 . The system of claim 1 , wherein the DNA ligating DNAzymes are E47 DNAzymes.