A DNA information encryption and error correction method based on secondary structure fingerprint separation storage

Abstract

The application relates to the technical field of DNA data storage, in particular to a DNA information encryption error correction method based on secondary structure fingerprint separation storage, which comprises the following steps: an information DNA coding stage, a structure signature generation stage, a signature DNA coding stage, an information DNA and signature DNA synthesis stage and a decoding and error correction stage; the information DNA coding stage is used for coding original data into information DNA segments; the structure signature generation stage is used for calculating structure characteristic parameters, generating compact structure signatures, and associating segment IDs with the compact structure signatures to form a signature data set; the signature DNA coding stage is used for coding the signature data set into signature DNA segments; the information DNA and signature DNA synthesis stage is used for respectively synthesizing the information DNA segments and the signature DNA segments and physically storing the information DNA segments and the signature DNA segments separately; and the decoding and error correction stage is used for verifying and correcting a consensus sequence based on the signature data set to recover the original data. The application stores the structure signature in an independent DNA molecule, thereby realizing physical layer encryption protection.

Description

Technical Field

[0001] This application relates to the field of DNA data storage technology, and in particular to a method for encrypting and correcting DNA information based on secondary structure fingerprint separation storage. Background Technology

[0002] With the explosive growth of global data volume, traditional storage media (such as hard drives and magnetic tapes) are facing bottlenecks in storage density and energy consumption. DNA, as a carrier of biological information, possesses extremely high storage density (theoretically reaching 10^6 kilobytes per second). 9 With advantages such as GB / g, long storage time (thousands of years), and low maintenance cost, it has become a research hotspot for the next generation of storage technologies.

[0003] Existing DNA storage technologies mainly involve the following steps: encoding binary data into DNA base sequences, synthesizing and storing DNA molecules, and reading and decoding the sequences to recover the data. However, errors are inevitably introduced during DNA synthesis and sequencing, including base substitutions, insertions, and deletions, and chemical degradation may occur over time. To address these issues, existing technologies primarily employ the following error correction schemes:

[0004] (1) Mathematical redundancy error correction: When encoding, error correction codes such as Reed-Solomon codes, LDPC codes or fountain codes are introduced, and error detection and correction are achieved by adding check symbols.

[0005] (2) Sequence constraint coding: By designing coding tables that meet specific biochemical constraints (such as GC content balance and avoidance of homopolymers), the error rate in the synthesis and sequencing process can be reduced. For example, patent CN117542420A uses dual-rule coding to control GC content.

[0006] (3) Consensus on repeated sequencing: Consensus sequences are generated by majority voting on multiple reads of the same fragment through high-depth sequencing.

[0007] However, the above method has the following shortcomings:

[0008] (1) Mathematical redundancy correction requires adding a large number of check symbols inside the DNA sequence, which occupies valuable DNA storage space and reduces the effective information density.

[0009] (2) Existing methods lack the utilization of the physical properties of DNA molecules and fail to combine sequence information with structural information for cross-validation.

[0010] (3) Data security mainly relies on encryption through encoding algorithms and lacks physical protection mechanisms. Once the DNA molecule is obtained, the data may be read directly. Summary of the Invention

[0011] This application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation storage to solve the technical problems of error correction redundancy occupying DNA storage space and insufficient security in existing DNA storage technologies.

[0012] To address the aforementioned technical problems, this application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation and storage, comprising: an information DNA encoding stage, a structural signature generation stage, a signature DNA encoding stage, an information DNA and signature DNA synthesis stage, and a decoding and error correction stage. The information DNA encoding stage encodes the original data into information DNA fragments, each information DNA fragment containing a unique fragment ID and a data region sequence. The structural signature generation stage calculates structural feature parameters for the data region sequence of each information DNA fragment, generates a compact structural signature, and associates the fragment ID with the compact structural signature to form a signature dataset. The signature DNA encoding stage encodes the signature dataset into signature DNA fragments. The information DNA and signature DNA synthesis stage synthesizes the information DNA fragments and signature DNA fragments respectively, and stores them physically separately. The decoding and error correction stage reconstructs the signature dataset by sequencing the signature DNA library, obtains a consensus sequence by sequencing the information DNA library, verifies and corrects the consensus sequence based on the signature dataset, and reconstructs the original data.

[0013] In some exemplary embodiments, the information DNA encoding stage includes: Step A1: Globally encoding the raw data using fountain codes or Reed-Solomon codes to generate K data packets, each data packet containing a unique fragment ID and a cyclic redundancy check code; Step A2: Dividing each data packet into fixed-length information DNA fragments, each information DNA fragment including a pre-primer region, a data region, and a post-primer region; the data region is L nucleotides in length; Step A3: Recording the ID of each information DNA fragment and its data region sequence S. i Where i is the fragment index, i=1,2,…,N; N is the total number of information DNA fragments.

[0014] In some exemplary embodiments, the structural signature generation stage includes: Step B1: For each information DNA fragment, the data region sequence S i Step B2: Using bioinformatics algorithms to simulate its secondary structure and calculate structural feature parameters; Step B3: Generate a compact structural signature based on the structural feature parameters, wherein the compact structural signature is a fixed-length binary code; Step B4: Associate and store the ID of each information DNA fragment with its compact structural signature to form a signature dataset.

[0015] In some exemplary embodiments, the structural feature parameters in step B1 include: minimum free energy ΔG, structural entropy H, and base pairing probability distribution; the minimum free energy ΔG is calculated using a nearest neighbor model with a quantization accuracy of 0.1 kcal / mol; the structural entropy H is calculated using the following formula:

[0016]

[0017] Where, p j Let L be the probability that the j-th base participates in pairing, and L be the length of the data region.

[0018] In some exemplary embodiments, the compact structure signature described in step B2 is a 64-bit binary code, wherein the first 10 bits are the quantized value of the minimum free energy ΔG, and the last 54 bits are the hash values ​​of the structural entropy H and the base pairing probability distribution.

[0019] In some exemplary embodiments, the signature DNA encoding stage includes: step C1: applying error correction coding to the signature dataset to generate redundant signature data; step C2: dividing the redundant signature data into fixed-length signature DNA fragments, each signature DNA fragment including a signature fragment ID, a signature data area, and a fragment-level check code.

[0020] In some exemplary embodiments, applying error-correcting encoding to the signature dataset in step C1 includes: encoding the signature dataset using Reed-Solomon codes or fountain codes, adding 10% to 20% redundant data, allowing the complete signature dataset to be recovered even if signature DNA fragments are lost or erroneous.

[0021] In some exemplary embodiments, the information DNA and signature DNA synthesis stage includes: step D1: synthesizing all information DNA fragments and signature DNA fragments respectively; step D2: mixing and storing the information DNA fragments as an information DNA library, mixing and storing the signature DNA fragments as a signature DNA library, and storing the two separately.

[0022] In some exemplary embodiments, the decoding and error correction stage includes: Step E1: Sequencing the signature DNA library to obtain signature DNA reads; Step E2: Grouping the signature DNA reads according to the signature fragment ID and generating a consensus sequence, using fragment-level checksums and error correction codes to recover the complete signature dataset, and establishing a mapping table from information fragment IDs to compact structure signatures; Step E3: Sequencing the information DNA library to obtain information DNA reads; Step E4: Grouping the information DNA reads according to the information fragment ID, and generating a consensus sequence R for each group. iStep E5: For each information DNA fragment, check its cyclic redundancy check (CRC) code. If it passes and the base quality value is higher than a preset threshold, mark it as a candidate correct fragment. Step E6: For suspicious fragments other than those marked as candidate correct fragments, calculate their actual structural signature using the same method as in Step B1, and compare it with the expected structural signature obtained from the signature dataset. If they match, accept the consensus sequence. If they do not match, proceed to Step E7. Step E7: Locate low-confidence sites based on base quality values, enumerate possible base combinations for low-confidence sites, recalculate the structural signature for each combination, and select the sequence that matches the expected structural signature and passes the CRC code as the error correction result. Step E8: Assemble all information DNA fragments that have passed verification or error correction by ID, and decode and recover the original data using fountain codes or Reed-Solomon codes.

[0023] In some exemplary embodiments, the method for determining low-confidence sites in step E7 includes: selecting sites with base quality values ​​lower than a preset quality threshold, and the number of low-confidence sites not exceeding 3; if the number of low-confidence sites exceeds 3, the fragment is marked as unrecoverable and compensated by the global error correction capability of fountain codes or Reed-Solomon codes.

[0024] The technical solution provided in this application has at least the following advantages:

[0025] This application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation and storage, comprising: an information DNA encoding stage, a structural signature generation stage, a signature DNA encoding stage, an information DNA and signature DNA synthesis stage, and a decoding and error correction stage; the information DNA encoding stage encodes the original data into information DNA fragments, each information DNA fragment containing a unique fragment ID and a data region sequence; the structural signature generation stage calculates structural feature parameters for the data region sequence of each information DNA fragment, generates a compact structural signature, and associates the fragment ID with the compact structural signature to form a signature dataset; the signature DNA encoding stage encodes the signature dataset into signature DNA fragments; the information DNA and signature DNA synthesis stage synthesizes the information DNA fragments and signature DNA fragments respectively, and stores them physically separately; the decoding and error correction stage reconstructs the signature dataset by sequencing the signature DNA library, obtains a consensus sequence by sequencing the information DNA library, verifies and corrects the consensus sequence based on the signature dataset, and reconstructs the original data.

[0026] This application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation storage. By storing the structural signature in an independent DNA molecule, it achieves physical-layer encryption protection. Simultaneously, it utilizes secondary structure fingerprints to detect and correct errors without increasing the complexity of information DNA synthesis, thus improving the security and reliability of DNA storage. This method has the following advantages: First, it achieves dual encryption protection. By storing the structural signature in an independent DNA molecule, physically separated from the information DNA, both information DNA and signature DNA are required for correct data recovery during decoding, achieving physical-layer encryption protection. Even if an attacker obtains the information DNA, they cannot obtain complete and correct data without the signature DNA. Second, while achieving dual encryption protection, this method does not increase the complexity of information DNA synthesis. The information DNA sequence is entirely determined by data encoding, eliminating the need for special structural anchors or embedded redundant check symbols, reducing synthesis difficulty and cost. Furthermore, this method improves the effective density of DNA storage. By transferring error correction redundancy from information DNA to signature DNA, information DNA can store more original data, resulting in an overall system effective information density higher than traditional internal error correction schemes.

[0027] Moreover, this method utilizes biophysical error correction characteristics, for the first time using DNA secondary structure features as error-correcting fingerprints. It leverages the inherent correlation between sequence and structure to detect errors, complementing mathematical error-correcting codes to enhance error correction capabilities. Finally, this method not only has controllable computational overhead but also ensures high reliability of the signed DNA. By employing compact signatures (64 bits / fragment) and a hierarchical verification strategy, structural calculations are performed only on suspicious fragments, keeping the additional computational overhead of decoding within minutes. Furthermore, the signed DNA itself uses strong error-correcting coding, ensuring highly reliable recovery of structural signature data, thereby guaranteeing the reliability of the entire system. Attached Figure Description

[0028] One or more embodiments are illustrated by way of example with reference to the accompanying drawings. These illustrations do not constitute a limitation on the embodiments, and unless otherwise stated, the figures in the drawings are not to be limited by scale.

[0029] Figure 1 This is a flowchart illustrating a DNA information encryption and error correction method based on secondary structure fingerprint separation and storage, provided as an embodiment of this application.

[0030] Figure 2 This is a schematic diagram of the structure of an information DNA fragment provided in an embodiment of this application.

[0031] Figure 3 This is a schematic diagram of the structure of a signature DNA fragment provided in an embodiment of this application.

[0032] Figure 4A detailed flowchart of the decoding and error correction stages provided in one embodiment of this application. Detailed Implementation

[0033] As can be seen from the background technology, existing methods mainly suffer from technical problems such as low effective information density, lack of utilization of the physical properties of DNA molecules, and lack of physical protection mechanisms.

[0034] To address the aforementioned technical problems, this application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation and storage, comprising: an information DNA encoding stage, a structural signature generation stage, a signature DNA encoding stage, an information DNA and signature DNA synthesis stage, and a decoding and error correction stage. The information DNA encoding stage encodes the original data into information DNA fragments, each information DNA fragment containing a unique fragment ID and a data region sequence. The structural signature generation stage calculates structural feature parameters for the data region sequence of each information DNA fragment, generates a compact structural signature, and associates the fragment ID with the compact structural signature to form a signature dataset. The signature DNA encoding stage encodes the signature dataset into signature DNA fragments. The information DNA and signature DNA synthesis stage synthesizes the information DNA fragments and signature DNA fragments respectively, and stores them physically separately. The decoding and error correction stage reconstructs the signature dataset by sequencing the signature DNA library, obtains a consensus sequence by sequencing the information DNA library, verifies and corrects the consensus sequence based on the signature dataset, and reconstructs the original data. This application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation storage. The structural signature is stored in an independent DNA molecule to achieve physical layer encryption protection. At the same time, the secondary structure fingerprint is used to detect and correct errors without increasing the complexity of information DNA synthesis, thereby improving the security and reliability of DNA storage.

[0035] The embodiments of this application will now be described in detail with reference to the accompanying drawings. However, those skilled in the art will understand that many technical details have been provided in the embodiments of this application to facilitate a better understanding of the application. However, the technical solutions claimed in this application can be implemented even without these technical details and various variations and modifications based on the following embodiments.

[0036] refer to Figure 1This application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation and storage, including: an information DNA encoding stage, a structural signature generation stage, a signature DNA encoding stage, an information DNA and signature DNA synthesis stage, and a decoding and error correction stage. The information DNA encoding stage encodes the original data into information DNA fragments, each information DNA fragment containing a unique fragment ID and a data region sequence. The structural signature generation stage calculates structural feature parameters for the data region sequence of each information DNA fragment, generates a compact structural signature, and associates the fragment ID with the compact structural signature to form a signature dataset. The signature DNA encoding stage encodes the signature dataset into signature DNA fragments. The information DNA and signature DNA synthesis stage synthesizes the information DNA fragments and signature DNA fragments respectively, and stores them physically separately. The decoding and error correction stage uses sequencing of the signature DNA library to recover the signature dataset, sequencing of the information DNA library to obtain a consensus sequence, and verifying and correcting the consensus sequence based on the signature dataset to recover the original data.

[0037] In some embodiments, the information DNA encoding stage includes: Step A1: Globally encoding the raw data using fountain codes or Reed-Solomon codes to generate K data packets, each data packet containing a unique fragment ID and a cyclic redundancy check code; Step A2: Dividing each data packet into fixed-length information DNA fragments, each information DNA fragment including a pre-primer region, a data region, and a post-primer region; the data region is L nucleotides in length; Step A3: Recording the ID of each information DNA fragment and its data region sequence S. i Where i is the fragment index, i=1,2,…,N; N is the total number of information DNA fragments.

[0038] In some embodiments, the structural signature generation stage includes: Step B1: For each information DNA fragment, the data region sequence S i Step B2: Using bioinformatics algorithms to simulate its secondary structure and calculate structural feature parameters; Step B3: Generate a compact structural signature based on the structural feature parameters, wherein the compact structural signature is a fixed-length binary code; Step B4: Associate and store the ID of each information DNA fragment with its compact structural signature to form a signature dataset.

[0039] In some embodiments, the structural feature parameters in step B1 include: minimum free energy ΔG, structural entropy H, and base pairing probability distribution; the minimum free energy ΔG is calculated using a nearest neighbor model with a quantization accuracy of 0.1 kcal / mol; the structural entropy H is calculated using the following formula:

[0040]

[0041] Where, p jLet L be the probability that the j-th base participates in pairing, and L be the length of the data region.

[0042] In some embodiments, the compact structure signature in step B2 is a 64-bit binary code, where the first 10 bits are the quantized value of the minimum free energy ΔG, and the last 54 bits are the hash values ​​of the structural entropy H and the base pairing probability distribution.

[0043] In some embodiments, the signature DNA encoding stage includes: step C1: applying error correction coding to the signature dataset to generate redundant signature data; step C2: dividing the redundant signature data into fixed-length signature DNA fragments, each signature DNA fragment including a signature fragment ID, a signature data area, and a fragment-level check code.

[0044] In some embodiments, applying error-correcting encoding to the signature dataset in step C1 includes: encoding the signature dataset using Reed-Solomon codes or fountain codes, adding 10% to 20% redundant data, allowing the complete signature dataset to be recovered even if signature DNA fragments are lost or erroneous.

[0045] In some embodiments, the information DNA and signature DNA synthesis stage includes: step D1: synthesizing all information DNA fragments and signature DNA fragments respectively; step D2: mixing and storing the information DNA fragments as an information DNA library, mixing and storing the signature DNA fragments as a signature DNA library, and storing the two separately.

[0046] In some embodiments, the decoding and error correction stage includes: Step E1: Sequencing the signature DNA library to obtain signature DNA reads; Step E2: Grouping the signature DNA reads according to the signature fragment ID and generating a consensus sequence, using fragment-level checksums and error correction codes to recover the complete signature dataset, and establishing a mapping table from information fragment IDs to compact structure signatures; Step E3: Sequencing the information DNA library to obtain information DNA reads; Step E4: Grouping the information DNA reads according to the information fragment ID, and generating a consensus sequence R_i and base quality value for each group; Step E5: For each information DNA fragment, checking its cyclic redundancy checksum, if it passes and the base quality value is higher than a preset threshold, then marking it as a signature. The candidate correct fragment is marked as such; Step E6: For suspicious fragments other than those marked as candidate correct fragments, calculate their actual structural signature using the same method as in step B1, and compare it with the expected structural signature obtained from the signature dataset; if they match, accept the consensus sequence; if they do not match, proceed to step E7; Step E7: Locate low-confidence sites based on base quality values, enumerate possible base combinations for low-confidence sites, recalculate the structural signature for each combination, and select the sequence that matches the expected structural signature and passes the cyclic redundancy check code as the error correction result; Step E8: Assemble all the verified or corrected information DNA fragments by ID, and decode them using fountain codes or Reed-Solomon codes to recover the original data.

[0047] Specifically, in step E6, when calculating the measured structural signature, the same bioinformatics algorithm and the same simulation conditions as in step B1 are used. The simulation conditions include temperature and salt concentration parameters to ensure that the structural calculations during writing and reading are comparable.

[0048] In some embodiments, the method for determining low-confidence sites in step E7 includes: selecting sites with base quality values ​​lower than a preset quality threshold (e.g., Q < 20), and the number of low-confidence sites does not exceed 3; if the number of low-confidence sites exceeds 3, the fragment is marked as unrecoverable and compensated by the global error correction capability of fountain codes or Reed-Solomon codes.

[0049] As a preferred embodiment, the data region length L of the information DNA fragment is 120-150 nucleotides, and the signature data region length of the signature DNA fragment is 80-120 nucleotides.

[0050] This application also provides a DNA information encryption and error correction system based on secondary structure fingerprint separation and storage. This system is used to implement the DNA information encryption and error correction method based on secondary structure fingerprint separation and storage as described in the above embodiments. The system includes: an information DNA encoding module, a structural signature generation module, a signature DNA encoding module, a synthesis module, and a decoding module. The information DNA encoding module encodes the original data into information DNA fragments; the structural signature generation module calculates structural feature parameters for the data region sequence of each information DNA fragment to generate a compact structural signature; the signature DNA encoding module encodes the signature dataset into signature DNA fragments; the synthesis module synthesizes the information DNA fragments and signature DNA fragments respectively; and the decoding module sequences and decodes the signature DNA library and / or the information DNA library to recover the original data.

[0051] It should be noted that the method and system provided in this application can be widely applied to various DNA data storage systems, and are particularly suitable for scenarios requiring high security and reliability, such as long-term preservation of confidential documents and backup of important data. This method does not rely on a specific DNA synthesis or sequencing platform and has good versatility and scalability.

[0052] The following detailed description of the DNA information encryption and error correction method based on secondary structure fingerprint separation and storage provided in this application is illustrated through specific embodiments.

[0053] Example 1

[0054] This embodiment uses the storage of a 1GB text file as an example to illustrate the implementation process of the present invention in detail.

[0055] Step 1: Information DNA Encoding.

[0056] 1GB of raw data (approximately 8×10) 9 The bits are encoded using fountain code (LT code), generating K = 2.8 × 10^6. 7 Each data packet contains approximately 10% redundancy. Each data packet is accompanied by a 32-bit unique ID and a 16-bit CRC checksum.

[0057] Each data packet was segmented into informational DNA fragments, with a data region length L = 120 nt, and 15 nt universal primer sequences (for PCR amplification) were added to both ends. The total number of informational DNA fragments N = 2.8 × 10⁻⁶. 7 Information DNA fragment structure as follows Figure 2 As shown.

[0058] Step 2: Generate structural signature.

[0059] For each information DNA fragment, the data region sequence S iUsing the DNA folding module from the ViennaRNA software package, the temperature was set to 37°C and Na... + Calculate the secondary structure characteristics at a concentration of 1M.

[0060] Minimum free energy ΔG i The calculation uses the nearest neighbor model with an accuracy of 0.1 kcal / mol, and quantization occupies 10 bits.

[0061] Structural entropy H i Calculate the pairing probability of each base using the formula for calculating structural entropy H, combine the result with the pairing probability distribution, and then use SHA-256 hashing to extract the first 54 bits.

[0062] The 10-bit and 54-bit sequences are concatenated to generate a compact 64-bit signature. Each signature is associated with a corresponding 32-bit information fragment ID, forming a signature dataset with a total size of (32+64)×2.8×10. 7 ≈ 2.688 × 10 9 bit = 336 MB.

[0063] Step 3: Signature DNA Encoding.

[0064] Applying Reed-Solomon coding (RS(255,223)) to the 336MB signature dataset adds approximately 14% redundancy, resulting in 383MB of encoded signature data. The signature data is then segmented into signature DNA fragments, each 100 nt in length, containing: a 24-bit signature fragment ID, a 72-bit signature data area, and a 4-bit fragment-level CRC checksum. The total number of signature DNA fragments is approximately 383 × 10⁻⁶. 6 ×8 / 100 ≈ 3.06×10 7 One. The structure of the signature DNA fragment is as follows: Figure 3 As shown.

[0065] Step 4: DNA synthesis.

[0066] Information DNA library: Synthesized 2.8 × 10 7 Each informational DNA fragment is synthesized into 1000 copies and stored in test tube A.

[0067] Signature DNA library: Synthesized 3.06 × 10⁻⁶ 7 Each of the signed DNA fragments was synthesized into 5000 copies (higher redundancy), and the fragments were mixed and stored in test tube B. Test tube A and test tube B were physically separated and stored separately.

[0068] Step 5: Decoding and Error Correction. Figure 4 A detailed flowchart of decoding and error correction is shown.

[0069] (1) Sequencing and recovery of signature DNA.

[0070] The signature DNA in test tube B was subjected to high-throughput sequencing (Illumina NovaSeq), yielding reads with approximately 30× coverage. Reads were grouped according to signature fragment IDs, and consensus sequences were generated for each group. Fragment-level CRC checksums and RS code decoding were used to reconstruct the complete signature dataset, establishing a mapping table from information fragment IDs to 64-bit signatures.

[0071] (2) Information DNA sequencing and preliminary processing.

[0072] The informative DNA in test tube A was sequenced, yielding reads with approximately 20× coverage. These reads were grouped according to their information fragment IDs, and a consensus sequence R was generated for each group. i and base mass value Q i .

[0073] (3) Layered verification and error correction.

[0074] Quick screening: Check the CRC checksum of the consensus sequence. If it passes and the average Q > 30, mark it as a candidate correct segment (approximately 90%). The remaining approximately 10% (2.8 × 10⁻⁶) 6 (1) is marked as a suspicious fragment.

[0075] Signature verification: For suspicious fragments, calculate the experimental signature Sig' using the same ViennaRNA parameters as at the time of writing. i , and Sig in the mapping table i Compare. If they are equal, accept the sequence (approximately 80% of the suspicious segments).

[0076] Enumeration error correction: For suspicious segments with signature mismatches (approximately 5.6 × 10⁻⁶), 5 (Number of low-confidence loci), based on sequencing quality scores to locate low-confidence loci (Q<20). Assuming the average number of low-confidence loci k=2, enumerate all 4... 2 =16 combinations, recalculate the signature for each combination, and choose the one that matches Sig. i A sequence that matches and passes the CRC check. If none of the 16 combinations match, the segment is marked as unrecoverable (approximately 1%).

[0077] Ultimately, the unrecoverable fragments amounted to approximately 2.8 × 10⁻⁶. 4 One, compensated by the global error correction capability of the fountain code (the fountain code allows for the loss of about 5% of data packets).

[0078] (4) Data recovery.

[0079] All verified or corrected information DNA fragments were assembled by ID and fed into a fountain code decoder to recover the original 1GB text file. Verification showed that the file's MD5 value matched the original.

[0080] Step 6: Performance Evaluation.

[0081] This application mainly evaluates performance from three aspects: storage overhead, security, and error correction capability.

[0082] In terms of storage overhead, the total number of bases in the information DNA is 2.8 × 10⁻⁶. 7 ×120 = 3.36×10 9 nt; Total base count of signature DNA: 3.06 × 10⁻⁶ 7 × 100 = 3.06 × 10 9 The signature DNA accounts for 91% of the bases in the information DNA. However, the signature DNA stores error correction and encryption information. The information DNA itself has no redundancy, and its effective information density is higher than that of traditional internal redundancy schemes (traditional schemes usually require adding 20% ​​to 50% redundancy).

[0083] In terms of security, this method requires both test tube A and test tube B to recover data, achieving physical-level encryption.

[0084] In terms of error correction capability, the data was eventually fully recovered, proving the effectiveness of this method.

[0085] Example 2

[0086] This embodiment is basically the same as Embodiment 1, except that: in step B2, the compact structure signature uses 32 bits (reducing storage overhead), and in step E7, the error correction enumeration only tries four possibilities for one low-confidence site (reducing computational load). The results show that for sequencing data with a low error rate, this method can still effectively recover the data, but requires more fragments to rely on fountain code compensation.

[0087] Example 3

[0088] This embodiment is basically the same as Embodiment 1, except that the error correction encoding of the signature dataset in step C1 uses fountain codes (instead of RS codes), which allows for a higher proportion of lost signature DNA fragments. Experiments show that the signature dataset can still be completely recovered when the signature DNA sequencing coverage is reduced to 10× coverage.

[0089] Based on the above technical solutions, this application provides a DNA information encryption and error correction method based on secondary structure fingerprint separation and storage, including: an information DNA encoding stage, a structural signature generation stage, a signature DNA encoding stage, an information DNA and signature DNA synthesis stage, and a decoding and error correction stage; the information DNA encoding stage is used to encode the original data into information DNA fragments, each information DNA fragment containing a unique fragment ID and a data region sequence; the structural signature generation stage is used to calculate structural feature parameters for the data region sequence of each information DNA fragment, generate a compact structural signature, and associate the fragment ID with the compact structural signature to form a signature dataset; the signature DNA encoding stage is used to encode the signature dataset into signature DNA fragments; the information DNA and signature DNA synthesis stage is used to synthesize information DNA fragments and signature DNA fragments respectively, and physically separate and store them; the decoding and error correction stage is used to sequence the signature DNA library to recover the signature dataset, sequence the information DNA library to obtain a consensus sequence, verify and correct the consensus sequence based on the signature dataset, and recover the original data.

[0090] The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage provided in this application has the following advantages compared with the prior art:

[0091] (1) Double encryption protection: The structural signature is stored in an independent DNA molecule, physically separated from the information DNA. Decoding requires both the information DNA and the signature DNA to correctly recover the data, thus achieving physical-level encryption protection. Even if an attacker obtains the information DNA, they cannot obtain complete and correct data without the signature DNA.

[0092] (2) No increase in the complexity of information DNA synthesis: The information DNA sequence is completely determined by data encoding, without the need to design special structural anchors or embed redundant check symbols, thus reducing the difficulty and cost of synthesis.

[0093] (3) Improve the effective density of DNA storage: The error correction redundancy is transferred from information DNA to signature DNA. Information DNA can store more original data, and the overall system has a higher effective information density than traditional internal error correction schemes.

[0094] (4) Error correction using biophysical properties: For the first time, DNA secondary structure features are used as error correction fingerprints. Errors are detected by utilizing the intrinsic correlation between sequence and structure, which complements mathematical error correction codes and improves error correction capabilities.

[0095] (5) Controllable computational overhead: By adopting a compact signature (64 bits / fragment) and hierarchical verification strategy, structural calculations are only performed on suspicious fragments, and the additional computational overhead of decoding can be controlled within minutes.

[0096] (6) High reliability of signature DNA: The signature DNA itself adopts strong error correction coding, which can ensure the high reliability of structural signature data recovery, thereby ensuring the reliability of the entire system.

[0097] Those skilled in the art will understand that the above-described embodiments are specific examples of implementing this application, and in practical applications, various changes in form and detail may be made without departing from the spirit and scope of this application. Any person skilled in the art can make their own modifications and alterations without departing from the spirit and scope of this application; therefore, the scope of protection of this application should be determined by the scope defined in the claims.

Claims

1. A DNA information encryption and error correction method based on secondary structure fingerprint separation and storage, characterized in that, include: The process includes: information DNA encoding stage, structural signature generation stage, signature DNA encoding stage, information DNA and signature DNA synthesis stage, and decoding and error correction stage. The information DNA encoding stage is used to encode the raw data into information DNA fragments, each information DNA fragment containing a unique fragment ID and a data region sequence; The structural signature generation stage is used to calculate structural feature parameters for the data region sequence of each information DNA fragment, generate a compact structural signature, and associate the fragment ID with the compact structural signature to form a signature dataset. The signature DNA encoding stage is used to encode the signature dataset into signature DNA fragments; The information DNA and signature DNA synthesis stage is used to synthesize information DNA fragments and signature DNA fragments respectively, and then physically separate and store them. The decoding and error correction stage is used to sequence the signature DNA library to recover the signature dataset, sequence the information DNA library to obtain the consensus sequence, verify and correct the consensus sequence based on the signature dataset, and recover the original data.

2. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 1, characterized in that, The information DNA encoding stage includes: Step A1: Globally encode the original data using fountain code or Reed-Solomon code to generate K data packets, each containing a unique fragment ID and a cyclic redundancy check code; Step A2: Divide each data packet into fixed-length information DNA fragments. Each information DNA fragment includes a pre-primer region, a data region, and a post-primer region; the data region is L nucleotides in length. Step A3: Record the ID of each information DNA fragment and its data region sequence S. i Where i is the fragment index, i=1,2,…,N; N is the total number of information DNA fragments.

3. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 1, characterized in that, The structural signature generation stage includes: Step B1: Sequence S of the data region for each informational DNA fragment. i Bioinformatics algorithms were used to simulate its secondary structure and calculate structural characteristic parameters; Step B2: Generate a compact structure signature based on the structural feature parameters, wherein the compact structure signature is a fixed-length binary code; Step B3: Associate and store the ID of each information DNA fragment with its compact structure signature to form a signature dataset.

4. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 3, characterized in that, The structural feature parameters mentioned in step B1 include: minimum free energy ΔG, structural entropy H, and base pairing probability distribution; the minimum free energy ΔG is calculated using the nearest neighbor model with a quantization accuracy of 0.1 kcal / mol; the structural entropy H is calculated using the following formula: Where, p j Let L be the probability that the j-th base participates in pairing, and L be the length of the data region.

5. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 3, characterized in that, The compact structure signature described in step B2 is a 64-bit binary code, where the first 10 bits are the quantized value of the minimum free energy ΔG, and the last 54 bits are the hash values ​​of the structural entropy H and the base pairing probability distribution.

6. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 1, characterized in that, The signature DNA encoding stage includes: Step C1: Apply error-correcting coding to the signature dataset to generate signature data with redundancy; Step C2: Divide the redundant signature data into fixed-length signature DNA fragments. Each signature DNA fragment includes a signature fragment ID, a signature data area, and a fragment-level checksum.

7. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 6, characterized in that, Step C1 involves applying error-correcting coding to the signature dataset, including: The signature dataset is encoded using Reed-Solomon codes or fountain codes, with 10% to 20% redundant data added, allowing the complete signature dataset to be recovered even if signature DNA fragments are lost or erroneous.

8. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 1, characterized in that, The information DNA and signature DNA synthesis stage includes: Step D1: Synthesize all informational DNA fragments and the signature DNA fragment separately; Step D2: Mix and save the information DNA fragments as an information DNA library, mix and save the signature DNA fragments as a signature DNA library, and store the two separately by body.

9. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 3, characterized in that, The decoding and error correction stage includes: Step E1: Sequencing the signature DNA library to obtain signature DNA reads; Step E2: Group the signature DNA reads according to the signature fragment ID and generate consensus sequences. Use fragment-level check codes and error correction codes to recover the complete signature dataset and establish a mapping table from information fragment IDs to compact structure signatures. Step E3: Sequencing the information DNA library to obtain information DNA reads; Step E4: Group the information DNA reads according to the information fragment ID, and generate a consensus sequence R for each group. i and base mass value; Step E5: For each information DNA fragment, check its cyclic redundancy check code. If it passes and the base quality value is higher than the preset threshold, mark it as a candidate correct fragment. Step E6: For suspicious segments other than those marked as candidate correct segments, calculate their actual structural signatures using the same method as in Step B1, and compare them with the expected structural signatures obtained from the signature dataset: If the two are consistent, then the consensus sequence is accepted; If the two are inconsistent, proceed to step E7; Step E7: Locate low-confidence sites based on base quality values, enumerate possible base combinations for low-confidence sites, recalculate the structural signature for each combination, and select the sequence that matches the expected structural signature and passes the cyclic redundancy check code as the error correction result. Step E8: Assemble all verified or corrected DNA fragments by ID, and use fountain codes or Reed-Solomon codes to decode and recover the original data.

10. The DNA information encryption and error correction method based on secondary structure fingerprint separation and storage according to claim 9, characterized in that, The method for determining low-confidence sites in step E7 includes: Select sites with base quality values ​​lower than a preset quality threshold, and the number of low-confidence sites should not exceed 3; If the number of low-confidence sites exceeds 3, the segment is marked as unrecoverable, and the error correction capability of fountain codes or Reed-Solomon codes is used to compensate for it.

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