Systems and methods for writing, reading, and controlling data stored in a polymer

Abstract

The disclosure provides a novel system of storing information using a charged polymer, e.g., DNA, the monomers of which correspond to a machine-readable code, e.g., a binary code, and which can be synthesized and/or read using a novel nanochip device comprising nanopores; novel methods and devices for synthesizing oligonucleotides in a nanochip format; novel methods for synthesizing DNA in the 3′ to 5′ direction using topoisomerase; novel methods and devices for reading the sequence of a charged polymer, e.g., DNA, by measuring capacitive or impedance variance, e.g., via a change in a resonant frequency response, as the polymer passes through the nanopore; and further provides compounds, compositions, methods and devices useful therein.

1 - 31 . (canceled) 
     
     
         32 . A method of synthesizing a DNA molecule using topoisomerase-mediated ligation, by adding single nucleotides or oligomers to a DNA strand in the 3′ to 5′ direction, comprising (i) reacting a DNA molecule with a topoisomerase charged with the desired nucleotide or oligomer, wherein the DNA molecule is on a substrate or magnetic bead, such that it can be selectively exposed to or removed from the reagents as required to provide the desired sequence. 
     
     
         33 . The method of  claim 32 , wherein the nucleotide or oligomer is blocked from further addition at the 5′ end and wherein the method further comprises (ii) deblocking the 5′ end of the DNA thus formed, and repeating steps (i) and (ii) until the desired nucleotide sequence is obtained. 
     
     
         34 . The method of  claim 33 , wherein single nucleotides are added. 
     
     
         35 . The method of  claim 33 , wherein oligomers are added. 
     
     
         36 . The method of  claim 33 , wherein the step of deblocking the 5′ end of the DNA is carried out using a phosphatase enzyme. 
     
     
         37 . The method of  claim 33 , wherein the DNA is double stranded, further comprising the step of repairing the DNA strand not joined by the topoisomerase using a ligase and ATP. 
     
     
         38 . The method of  claim 33 , wherein the topoisomerase-charged donor oligonucleotide comprises a 5′ overhang on the strand complementary to the strand bearing the topoisomerase, comprising a polyinosine sequence. 
     
     
         39 . The method of  claim 33 , wherein the topoisomerase is selected from vaccinia topoisomerase and SVF topoisomerase I. 
     
     
         40 . The method of  claim 33 , wherein a vaccinia topoisomerase which recognizes (C/T)CCTT is used to add deoxythymidine triphosphate (dTTP) nucleotides and a SVF topoisomerase I which recognizes CCCTG is used to add deoxyguanosine triphosphate (dGTP) nucleotides. 
     
     
         41 . The method of  claim 33 , wherein a nanopore separates a chamber comprising the topoisomerase from a chamber comprising a phosphatase, wherein the nanopore is large enough to allow movement of the DNA through the nanopore by electrical attraction but is not large enough to permit movement of the topoisomerase and the phosphatase through the nanopore. 
     
     
         42 . The method of  claim 32 , wherein oligomers are added. 
     
     
         43 . The method of  claim 42 , wherein the method further comprises (ii) removing all of the oligomer thus added with the exception of a single base, using a type IIS restriction enzyme; (iii) dephosphorylating the 5′end of the DNA thus formed using a phosphatase; and (iv) repeating steps (i), (ii) and (iii) until the desired nucleotide sequence is obtained. 
     
     
         44 . The method of  claim 43 , wherein the topoisomerase is selected from vaccinia topoisomerase and SVF topoisomerase I. 
     
     
         45 . The method of  claim 43 , wherein a vaccinia topoisomerase which recognizes (C/T)CCTT is used to add deoxythymidine triphosphate (dTTP) nucleotides and a SVF topoisomerase I which recognizes CCCTG is used to add deoxyguanosine triphosphate (dGTP) nucleotides. 
     
     
         46 . The method of  claim 43 , wherein a nanopore separates a chamber comprising the topoisomerase from a chamber comprising a phosphatase, wherein the DNA can pass through the nanopore by electrical attraction but the topoisomerase and the phosphatase through the nanopore cannot.