BACKGROUND

Nucleic acid digital data storage is a stable approach for encoding and storing information for long periods of time, with data stored at higher densities than magnetic tape or hard drive storage systems. Additionally, digital data stored in nucleic acid molecules that are stored in cold and dry conditions can be retrieved as long as 60,000 years later or longer.

Current methods rely on encoding the digital information (e.g., binary code) into base-by-base nucleic acids sequences, such that the base to base relationship in the sequence directly translates into the digital information (e.g., binary code). Sequencing of digital data stored in base-by-base sequences that can be read into bit-streams or bytes of digitally encoded information can be error prone and costly to encode since the cost of de novo base-by-base nucleic acid synthesis can be expensive. Opportunities for new methods of performing nucleic acid digital data storage may provide approaches for encoding and retrieving data that are less costly and easier to commercially implement.

SUMMARY

Provided herein are methods and systems for encoding digital information in nucleic acid (e.g., deoxyribonucleic acid, DNA) molecules without base-by-base synthesis, by encoding bit-value information in the presence or absence of unique nucleic acid sequences within a pool, comprising specifying each bit location in a bit-stream with a unique nucleic sequence and specifying the bit value at that location by the presence or absence of the corresponding unique nucleic acid sequence in the pool. These encoded nucleic acid molecules are particularly useful for encoding sensitive information or tagging artifacts with information in very small chemical quantities. By being associating an artifact with an amount of nucleic acid molecules encoding information, an artifact can be uniquely tagged in a way that is not readily apparent to outside users, such that the artifact can be used for secure authentication or tracking the origin of the artifact.

In an aspect, provided herein is a method for tagging a fluid for tracking or authentication. The method comprises obtaining a library of nucleic acid molecules representing digital information, and combining the fluid with a tag comprising the library of nucleic acid molecules to obtain a tagged fluid for tracking or authentication. Tagging fluids can be advantageous for certifying the authenticity of the fluid, like a valuable fuel or pharmaceutical, because the library can be designed to uniquely identify the fluid, its origin, its manufacture date, or any other characteristic of the fluid.

In some implementations, the method further comprises sampling the tagged fluid to obtain a sample containing at least a part of the library of nucleic acid molecules. Sampling may involve swabbing or drawing a volume from the tag or the tagged fluid. In some implementations, the method further involves sequencing nucleic acid molecules of the sample to obtain a sequencing readout. The sequencing readout may be compared to a reference sequence to determine a presence of a matching sequence. Thus, the information encoded by the library may be determined, and the fluid may be authenticated or identified.

The fluid may be any one of an oil, an ink, a compressed gas, or a drug. In some implementations, the method further comprises measuring a concentration of the tag in the tagged fluid to determine an amount of dilution. This step is useful for determining if the fluid was tampered with.

In some implementations, the tag comprises a molecular barcode specific to the tag. The information may comprise a message or a currency value. The information may comprise at least a kilobit of information. In some implementations, the method further comprises accessing the tagged fluid, thereby causing the tag in the tagged fluid to decay. In some implementations, the tag is part of a two-factor authentication system.

In some implementations, the library is randomly generated. In some implementations, the library is generated by selecting a subset of nucleic acid molecules from a pool of nucleic acid molecules. In some implementations, the information comprises a plurality of symbols, and each symbol is represented by a distinct sequence of a nucleic acid molecule of the library. In some implementations, the information is represented by the library of nucleic acid molecules via an encoding scheme wherein the information is mapped to a plurality of symbols having one of two possible symbol values, wherein a symbol of the plurality of symbols is represented by presence of a distinct nucleic acid molecule in the library if the symbol has a first symbol value of the two possible symbol values, and wherein the symbol is represented by absence of the distinct nucleic acid molecule if the symbol has a second symbol value of the two possible symbol values.

In another aspect, provided herein is a method for preparing a library of nucleic acid molecules for use in security and authentication. The method involves obtaining the library of nucleic acid molecules representing a security token, and applying a chemical operation to the library representing the security token to obtain a hashed library of nucleic acid molecules representing a hashed token. This method is advantageous over conventional methods by air-gapping the value of the security token by hashing the token prior to reading the library of nucleic acid molecules, such that the sequences of the pre-hashing library are never revealed.

In some implementations, the chemical operation effects one or more Boolean functions on the security token. For example, the one or more Boolean functions apply a hash function to the security token to obtain the hashed token represented by the hashed library. In some implementations, the hashed library is a subset of the library.

In some implementations, the method further comprises sequencing at least a portion of the nucleic acid molecules of the hashed library to obtain a sequencing readout. The sequencing readout may be compared to a database or look-up table to determine a presence or absence of a matching sequence. The method may further involve granting or denying access to a secured asset or location based on the determined presence or absence of the matching sequence, respectively. For example, sequencing comprises any one of high-throughput sequencing, shotgun sequencing, or nanopore sequencing.

In some implementations, the method further comprises applying an additional chemical operation to the hashed library to produce an output molecule if the hashed token matches a reference sequence, and determining a presence or absence of the output molecule via an assay. For example, the assay is one of polymerase chain reaction (PCR), real-time PCR, reverse transcription PCR (RT-PCR), fluorimetry, and gel electrophoresis. The output molecule may be a distinct nucleic acid molecule of the hashed library. In some implementations, the method further involves granting or denying access to a secured asset or location based on the presence of the output molecule. This implementation of validating the hashed token chemically to produce an output molecule is advantageous in that it obviates the need for sequencing of the hashed library; rather, the hashed library undergoes further chemical operations that may be cheaper or faster than sequencing in order to determine the authenticity of the security token.

In some implementations, the library comprises a unique molecular barcode. In some implementations, the security token comprises a randomly generated key. In some implementations, the security token is part of a two-factor authentication system. In some implementations, the library is collocated with an artifact, and wherein the security token is unique to the artifact. For example, the artifact is a fluid. The fluid may be any one of an oil, an ink, a compressed gas, or a drug. In some implementations, the method further involves measuring a concentration of the library in the fluid to determine an amount of dilution. As another example, the artifact is an organism or a document. In some implementations, the library is contained in any one of a well, a droplet, a spot, a sealed container, a gel, a suspension, or a solid matrix. In some implementations, the library is lyophilized.

In some implementations, the library is generated by selecting a subset of nucleic acid molecules from a pool of nucleic acid molecules. In some implementations, the security token comprises a plurality of symbols, and each symbol is represented by a distinct sequence of a nucleic acid molecule of the library. In some implementations, the library is randomly generated. In some implementations, the security token is represented by the library of nucleic acid molecules via an encoding scheme wherein the security token is mapped to a plurality of symbols having one of two possible symbol values, wherein a symbol of the plurality of symbols is represented by presence of a distinct nucleic acid molecule in the library if the symbol has a first symbol value of the two possible symbol values, and wherein the symbol is represented by absence of the distinct nucleic acid molecule if the symbol has a second symbol value of the two possible symbol values. In some implementations, the security token comprises at least a kilobit of information. In some implementations, the security token is unique to a user.

Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative implementations of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different implementations, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material.

