Methods and systems for DNA data storage

Patent metadata

Field	Value
Publication number	US-10902939-B2
Application number	US-201816477106-A
Country	US
Kind code	B2
Filing date	Jan 10, 2018
Priority date	Jan 10, 2017
Publication date	Jan 26, 2021
Grant date	Jan 26, 2021

Abstract

In various embodiments, an information storage system comprises: a writing device for synthesizing a nucleotide sequence that encodes a set of information; and a reading device for interpreting the nucleotide sequence by decoding the interpreted nucleotide sequence into the set of information, wherein the reading device comprises a molecular electronics sensor, the sensor comprising a pair of spaced apart electrodes and a molecular complex attached to each electrode to form a molecular electronics circuit, wherein the molecular complex comprises a bridge molecule and a probe molecule, and wherein the molecular electronics sensor produces distinguishable signals in a measurable electrical parameter of the molecular electronics sensor, when interpreting the nucleotide sequence.

First claim

We claim:

1. An information storage system comprising:
a writing device that synthesizes a nucleotide sequence that encodes a set of information; and
a reading device that interprets the nucleotide sequence by decoding the interpreted nucleotide sequence into the set of information,
wherein the reading device comprises a molecular electronics sensor, the sensor comprising a pair of spaced apart electrodes and a molecular complex attached to each electrode to form a molecular electronics circuit, wherein the molecular complex comprises a bridge molecule and a probe molecule, and
wherein the molecular electronics sensor produces distinguishable signals in a measurable electrical parameter of the molecular electronics sensor, when interpreting the nucleotide sequence.

2. The system of claim 1 , wherein the set of information is binary.

3. The system of claim 1 , wherein the nucleotide sequence comprises a DNA sequence.

4. The system of claim 3 , further comprising at least one of error detecting schemes or error correction schemes for minimizing errors within the DNA sequence.

5. The system of claim 4 , wherein the error detecting schemes are selected from repetition code, parity bits, checksums, cyclic redundancy checks, cryptographic hash functions and hamming codes, and the error correction schemes are selected from automatic repeat request, convolutional codes, block codes, hybrid automatic repeat request and Reed-Solomon codes.

6. The system of claim 1 , wherein the writing device comprises a CMOS chip based array of actuator pixels for DNA synthesis, the actuator pixels directing voltage/current or light-mediated deprotection within a DNA synthesis reaction comprising a phosphoramidite or ligation chemistries.

7. The system of claim 1 , wherein the probe molecule comprises a polymerase enzyme, and wherein the measurable electrical parameter of the sensor is modulated by enzymatic activity of the polymerase enzyme.

8. The system of claim 7 , wherein the polymerase enzyme comprises a native polymerase enzyme or a genetically engineered polymerase enzyme selected from Klenow, Phi29, TAQ, BST, T7, or a reverse transcriptase.

9. The system of claim 7 , wherein the reading device further comprises a buffer solution, operating parameters for measuring the measurable electrical parameter, and two or more sequence segments of a DNA template molecule, that, when processed by the polymerase, produce the distinguishable signals in the measurable electrical parameter when performed in the conditions provided by the buffer solution and the operating parameters.

10. The system of claim 9 , wherein the buffer solution comprises modified dNTPs.

11. The system of claim 9 , wherein the sequence segments of the DNA template molecule that produce the distinguishable signals comprise any one or combination of different DNA bases, modified DNA bases, DNA base analogues, multi-base sequences or motifs, or homopolymer runs of DNA bases.

12. The system of claim 1 , wherein the measurable electrical parameter of the sensor comprises a source-drain current between the spaced apart electrodes and through the molecular complex.

13. The system of claim 1 , wherein the molecular electronics sensor is part of a CMOS sensor array chip further comprising a plurality of molecular electronics sensors and supporting pixel circuitry that performs measurement of the measurable electrical parameter.

14. The system of claim 1 , wherein the molecular electronics sensor further comprises a gate electrode adjacent the spaced apart electrodes.

15. The system of claim 1 , wherein the bridge molecule comprises a double stranded DNA oligomer, a protein alpha helix, a graphene nanoribbon, a carbon nanotube, an antibody, or a Fab arm of an antibody.

16. A method of interpreting a set of information encoded in a nucleotide sequence of a polynucleotide molecule, the method comprising:
supplying the polynucleotide molecule to a molecular electronics sensor capable of producing distinguishable signals in a measurable electrical parameter of the molecular electronics sensor, relating to the set of information;
generating the distinguishable signals; and
converting the distinguishable signals into the set of information,
wherein the molecular electronics sensor comprises a pair of spaced apart electrodes and a molecular complex attached to each electrode to form a molecular electronics circuit, wherein the molecular complex comprises a bridge molecule and a probe molecule.

17. The method of claim 16 , wherein the set of information is binary.

18. The method of claim 16 , wherein the nucleotide sequence comprises a DNA sequence.

Assignees

• Roswell Biotechnologies Inc

Inventors

• Merriman Barry L
• Geiser Tim
• Mola Paul

Classifications

• C12Q1/6869 Primary

  Methods for sequencing · CPC title

• G01N33/48721

  Investigating individual macromolecules, e.g. by translocation through nanopores (Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68) · CPC title

• G01N27/4145 Primary

  specially adapted for biomolecules, e.g. gate electrode with immobilised receptors · CPC title

• G01N27/3276

  being a hybridisation with immobilised receptors (using a FET type sensor G01N27/4145; concerning the hybridisation C12Q1/68) · CPC title

• C12Q2565/607

  being a sensor, e.g. electrode · CPC title