Methods, apparatus and systems for amplification-free dna data storage

Abstract

In various embodiments, amplification-free DNA information methods, apparatus and systems are disclosed. A method of amplification-free information storage and retrieval comprises encoding digital data such as binary into nucleotide sequence motifs using an encoding scheme, and synthesizing replicate DNA molecules using an amplification-free DNA writing process. The amplification-free process of decoding the information stored in the DNA comprises exposing at least one of the replicate DNA molecules to a molecular electronics sensor that generates distinguishable signals in a measured electrical parameter of the sensor, wherein the distinguishable signals correspond to the sequence motifs, providing decoding back to the digital data.

We claim: 
     
         1 . A method of archiving information, the method comprising:
 converting the information into one or more nucleotides using an encoding scheme, the nucleotides predetermined to generate distinguishable signals relating to the information in a measurable electrical parameter of a molecular electronics sensor;   assembling the one or more nucleotides into a nucleotide sequence; and   synthesizing a pool of replicate DNA molecules without amplification of the DNA molecules, wherein each replicate DNA molecule incorporates the nucleotide sequence.   
     
     
         2 . The method of  claim 1 , wherein the information comprises a string of binary data. 
     
     
         3 . The method of  claim 2 , wherein the encoding scheme converts one or more 0/1 bits of binary data within the string of binary data into a sequence motif comprising more than one nucleotide. 
     
     
         4 . The method of  claim 3 , wherein the step of converting the information comprises dividing the string of binary data into segments, wherein each segment encodes one sequence motif. 
     
     
         5 . The method of  claim 4 , wherein the binary data bit  0  encodes a homopolymer of A, and the binary data bit  1  encodes a homopolymer of C. 
     
     
         6 . The method of  claim 1 , wherein at least one of the one or more nucleotides comprises a modified nucleotide. 
     
     
         7 . The method of  claim 1 , wherein the one or more nucleotides comprise nucleotides that are resistant to secondary structure formation in the replicate DNA molecules compared to a variant of the same nucleotides. 
     
     
         8 . The method of  claim 1 , wherein the encoding scheme comprises any one or combination of BES 1 , BES 2 , BES 3 , BES 4 , BES 5  and BES 6 . 
     
     
         9 . The method of  claim 1 , further comprising:
 exposing at least one of the replicate DNA molecules to the molecular electronics sensor without prior amplification of the DNA molecules;   generating the distinguishable signals; and   converting the distinguishable signals into the information,   wherein the molecular electronics sensor comprises a pair of spaced-apart electrodes and a molecular sensor complex attached to each electrode to form a sensor circuit, wherein the molecular sensor complex comprises a bridge molecule electrically wired to each electrode in the pair of spaced-apart electrodes and a probe molecule conjugated to the bridge molecule.   
     
     
         10 . The method of  claim 9 , wherein the step of exposing at least one of the replicate DNA molecules to the molecular electronics sensor comprises suspending the pool of DNA molecules in a buffer, taking an aliquot of the buffer, and providing the aliquot to the sensor. 
     
     
         11 . The method of  claim 10 , wherein the buffer solution comprises modified dNTPs. 
     
     
         12 . The method of  claim 9 , wherein the measurable electrical parameter of the sensor comprises a source-drain current between the spaced-apart electrodes and through the molecular sensor complex. 
     
     
         13 . The method of  claim 9 , wherein the probe molecule comprises a polymerase and wherein the measurable electrical parameter of the sensor is modulated by enzymatic activity of the polymerase while processing any one of the replicate DNA molecules. 
     
     
         14 . The method of  claim 13 , wherein the polymerase comprises the Klenow Fragment of  E. coli  Polymerase I, and wherein the bridge molecule comprises a double-stranded DNA molecule. 
     
     
         15 . A method of archiving and retrieving a string of binary data in an amplification-free DNA information storage and retrieval system, the method comprising:
 dividing the string of binary data into segments of at least one binary bit;   assigning each segment to a sequence motif, each sequence motif comprising at least two nucleotides, the sequence motifs predetermined to generate distinguishable signals in a measurable electrical parameter of a molecular electronics sensor;   assembling the sequence motifs into a nucleotide sequence;   synthesizing a pool of replicate DNA molecules using an amplification-free DNA writing method on a solid support, each replicate DNA molecule incorporating the nucleotide sequence;   suspending the pool of DNA molecules in a buffer;   taking an aliquot of the buffer;   providing the aliquot to the sensor without prior amplification of the DNA molecules;   generating the distinguishable signals; and   converting the distinguishable signals into the string of binary data,   wherein the sensor comprises a pair of spaced apart electrodes and a molecular sensor complex attached to each electrode to form a molecular electronics circuit, wherein the molecular sensor complex comprises a bridge molecule electrically wired to each electrode in the pair of spaced-apart electrodes and a probe molecule conjugated to the bridge molecule.