DNA molecular coding method based on dual-ternary charge conservation

Abstract

The invention discloses a DNA molecular coding method based on dual-ternary charge conservation, which comprises the following steps: S1, dual-ternary coding mapping, including the steps of data preprocessing, base mapping screening and sequence generation; s2, charge optimization, including steps of initial charge calculation, charge deviation detection and dynamic replacement; s3, codon allocation, which comprises the steps of data area coding, rare codon screening and dynamic allocation; and S4, physical isolation, including isolator design and functional region design steps. According to the method, high-density and low-error information storage is realized through a base double-coding bit mapping rule, a chain charge constraint algorithm and a biological codon dynamic allocation mechanism.

Description

Technical Field

[0001] The present invention relates to the technical field of DNA storage coding, and in particular to a DNA molecular coding method based on dual-ternary charge conservation. Background Art

[0002] DNA has an extremely high density, with a storage potential per unit mass 420 billion times greater than that of a magnetic disk. Its storage potential per unit volume is one million times greater than that of a hard drive and one thousand times greater than that of flash memory. DNA also has an extremely long storage lifespan, maintaining readability for thousands or even tens of thousands of years.

[0003] The building blocks of DNA molecules are deoxyribonucleotides. Based on their nitrogenous bases, deoxyribonucleotides can be divided into adenine deoxyribonucleotide (AMP), guanine deoxyribonucleotide (GMP), cytosine deoxyribonucleotide (CMP), and thymine deoxyribonucleotide (TMP). These four nitrogenous bases are referred to as A, G, C, and T. Deoxyribonucleotides containing different bases polymerize to form the chain-like helical DNA molecule. The four bases A, T, C, and G, arranged in different sequences, can store the genetic information of organisms. Therefore, DNA molecules can be considered a natural four-base information storage medium.

[0004] Currently, DNA storage encoding technology has the following technical problems: 1. Coding efficiency bottleneck. Traditional DNA storage uses single-base fixed binary mapping (such as A=00, T=01, C=10, G=11), and the upper limit of single-base information density is 2 bits.

[0005] 2. Charge imbalance problem: the net charge deviation of the DNA chain leads to a decrease in the polymerase binding efficiency, and the homopolymer sequence causes an increase in the synthesis error rate.

[0006] 3. Biological function conflicts. The existing coding scheme cannot circumvent the function of standard genetic codons. Summary of the Invention

[0007] The purpose of the present invention is to provide a DNA molecular encoding method based on dual ternary charge conservation, so as to achieve high-density, low-error information storage through base dual encoding bit mapping rules, chain charge constraint algorithm and biological codon dynamic allocation mechanism.

[0008] The present invention is implemented by adopting the following technical solution: a DNA molecular encoding method based on double ternary charge conservation, comprising the following steps: S1: Dual ternary encoding mapping, including data preprocessing, base mapping screening, and sequence generation steps; S2: charge optimization, including initial charge calculation, charge deviation detection, and dynamic replacement steps; S3: codon assignment, including data region encoding, rare codon screening, and dynamic assignment steps; S4: Physical isolation, including isolator design and functional area design steps.

[0009] Furthermore, step S1 includes the following sub-steps: S11: Input data and split it into dual ternary coding units in groups of 6 bits; S12: Screening a unique base combination that meets the conditions according to a preset double ternary encoding table; S13: Arrange the screened bases in order to generate an initial DNA chain.

[0010] Furthermore, the conditions are A(+1, +1), corresponding to a charge of +2; T / U(-1, -1), corresponding to a charge of -2; C(-1, +1), corresponding to a charge of 0; and G(+1, -1), corresponding to a charge of 0.

[0011] Furthermore, step S2 includes the following sub-steps: S21: Traverse the DNA chain and calculate the charge value of each base. The charge value is calculated by summing the double ternary digits of the base, where A=+2, T / U=-2, C=0, and G=0; add them together to get the total charge: ; S22: Compare the absolute value of the total charge with 2. If it is less than or equal to 2, terminate; if it is greater than 2, perform a dynamic replacement step.

[0012] Furthermore, the dynamic replacement step is specifically as follows: preferentially replacing the base with the largest absolute value of the charge deviation; after the replacement is completed, updating the total charge, and looping step S2 until the absolute value of the total charge is less than 2, or the maximum number of iterations is reached.

[0013] Furthermore, step S3 includes the following sub-steps: S31: Encode the DNA chain into groups of 3 bases; S32: Use the NCBI codon frequency tool to filter codons with a usage frequency of <5%; S33: Input the ternary encoding stream of the target data and output a DNA sequence that complies with the charge constraint and avoids functional codons.

[0014] Furthermore, step S4 includes the following sub-steps: S41: Isolation area design, inserting a C / G alternating sequence between the data area and the functional area; S42: Functional region design, the functional region uses standard genetic codons and retains the start codon and stop codon.

[0015] Furthermore, the method further comprises the steps of: S5: Convert the optimized DNA sequence into an instruction format compatible with the solid phase synthesizer.

[0016] The beneficial effect of the present invention is that the present invention realizes high-density, low-error information storage through base dual-coding bit mapping rules, chain charge constraint algorithm and biological codon dynamic allocation mechanism. BRIEF DESCRIPTION OF THE DRAWINGS

[0017] In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the following briefly introduces the drawings required for use in the embodiments or the description of the prior art. Obviously, the drawings described below are only some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on the structures shown in these drawings without paying any creative work.

[0018] Figure 1 It is a dual ternary encoding and charge mapping model; Figure 2 Flowchart of charge conservation optimization algorithm; Figure 3 This is a diagram of the data-functional area physical isolation architecture. DETAILED DESCRIPTION

[0019] To make the objectives, technical solutions, and advantages of the embodiments of the present invention more clear, the technical solutions of the embodiments of the present invention will be clearly and completely described below in conjunction with the accompanying drawings of the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Generally, the components of the embodiments of the present invention described and shown in the drawings herein can be arranged and designed in various different configurations.

[0020] It should be noted that similar reference numerals and letters denote similar items in the following drawings, and therefore, once an item is defined in one drawing, it does not need to be further defined or explained in subsequent drawings.

[0021] The following embodiments of the present invention are described in detail with reference to the accompanying drawings. In the absence of conflict, the following embodiments and features in the embodiments may be combined with each other.

[0022] See also Figures 1 to 3 , a DNA molecular encoding method based on double ternary charge conservation, which achieves high-density, low-error information storage through base double encoding bit mapping rules, chain charge constraint algorithm and biological codon dynamic allocation mechanism.

[0023] The present invention is implemented by adopting the following technical solution: a DNA molecular encoding method based on double ternary charge conservation, comprising the following steps: S1: Dual ternary encoding mapping, including data preprocessing, base mapping screening, and sequence generation steps; S2: charge optimization, including initial charge calculation, charge deviation detection, and dynamic replacement steps; S3: codon assignment, including data region encoding, rare codon screening, and dynamic assignment steps; S4: Physical isolation, including isolator design and functional area design steps.

[0024] In this embodiment, step S1 includes the following sub-steps: S11: Data preprocessing: input data (such as binary files) and split it into double ternary coding units in groups of 6 bits; Example: Binary `01000010` (ASCII character "B") is split into `01 00 00 10`, and each group is converted to ternary: `01` → ternary `(+1, 0)`, `00` → ternary `(0, 0)`, `10` → ternary `(+1, -1)`.

[0025] S12: Based on the preset dual ternary encoding table, unique base combinations that meet the conditions are selected: A(+1, +1), corresponding to a charge of +2; T / U(-1, -1), corresponding to a charge of -2; C(-1, +1), corresponding to a charge of 0; and G(+1, -1), corresponding to a charge of 0. The selection logic is: If a ternary digit combination has no direct corresponding base, the alternative with the smallest absolute charge value is prioritized. In other words, each base is represented by two ternary digits (-1, 0, +1): A(+1, +1), T / U(-1, -1), C(-1, +1), and G(+1, -1).

[0026] S13: Arrange the selected bases in order to generate the initial DNA chain. For example: `(+1,0) → C`, `(0,0) → C`, `(+1,-1) → G`. The final sequence is `ACCG` (needs to be filled).

[0027] In this embodiment, step S2 includes the following sub-steps: S21: Initial charge calculation, traverse the DNA chain, calculate the charge value of each base (such as A=+2, T / U=-2, C / G=0), and add them up to get the total charge: ; S22: Charge deviation detection, compare the absolute value of the total charge with 2. If it is less than or equal to 2, terminate; if it is greater than 2, perform dynamic replacement step.

[0028] The dynamic replacement step is specifically as follows: bases with the largest absolute value of charge deviation (such as A or T) are replaced first. After the replacement is completed, the total charge is updated, and step S2 is repeated until the absolute value of the total charge is less than 2 or the maximum number of iterations (such as 1000) is reached.

[0029] Example of dynamic replacement operation: Initial sequence: `AAAA` (total charge = +8); Select the 3rd A (charge +2) for replacement; Candidate replacement bases: C or G (charge 0); Replaced sequence: `AACA` (total charge = +6), repeat until the absolute value of Q is less than 2.

[0030] In this embodiment, step S3 includes the following sub-steps: S31: Data region encoding rules, encode the DNA chain into groups of 3 bases (such as `CGA`); among them, the disabled codon table: load the NCBI standard genetic code table (ID: 1), excluding the start codon (ATG) and stop codons (TAA / TAG / TGA).

[0031] S32: Rare codon screening: Use the NCBI codon frequency tool to screen codons with a usage frequency of <5% (such as arginine AGA and serine TCT). For example: if the data needs to encode the amino acid "serine", TCT (frequency 3.1%) is preferred over TCG (frequency 0.8%).

[0032] S33: Input the ternary encoding stream of the target data and output a DNA sequence that complies with the charge constraint and avoids functional codons.

[0033] In this embodiment, step S4 includes the following sub-steps: S41: Isolation area design, inserting a C / G alternating sequence (such as `CGCG`) between the data area and the functional area; charge verification: C (-1+1=0), G (+1-1=0), the total charge sum is always 0 after alternating arrangement.

[0034] S42: Functional region design. The functional region uses standard genetic codons, retaining the start codon (ATG) and stop codon (TAA). The example sequence is: `ATG GCT GAA TGG...TCA GTA TAA`.

[0035] Finally, the optimized DNA sequence is converted into an instruction format compatible with the solid-phase synthesizer (such as a FASTA file) and synthesis adaptation is performed. The synthesis control protocol of Chinese patent CN110628882A can be called to drive the synthesis reaction according to the base sequence, and the parameters are modified: synthesis temperature (50°C±5°C), reaction time (30 seconds / base), and cleaning step (acetonitrile rinse).

[0036] Verification and testing process Charge compliance testing uses ion mobility spectrometry to measure the net charge of the synthesized DNA strands and verify that the total charge is less than 2.

[0037] For biological function testing, the DNA sequence was introduced into the E. coli expression system to detect whether non-target proteins were produced (expected probability <0.1%).

[0038] Data recovery was tested by PCR amplification and high-throughput sequencing (Illumina platform), and the synthesis error rate was calculated (target value ≤ 0.38 errors / kb).

[0039] For the sake of simplicity, the aforementioned embodiments are described as a series of actions. However, those skilled in the art should be aware that this application is not limited by the order of the actions described, because according to this application, some steps can be performed in other orders or simultaneously. Secondly, those skilled in the art should also be aware that the embodiments described in this specification are preferred embodiments, and the actions involved are not necessarily required by this application.

[0040] The above embodiments describe the basic principles, main features, and advantages of the present invention. Those skilled in the art should understand that the present invention is not limited to the above embodiments. The above embodiments and descriptions are merely illustrative of the principles of the present invention. Without departing from the spirit and scope of the present invention, modifications and variations made by those skilled in the art without departing from the spirit and scope of the present invention should be within the scope of protection of the appended claims.

Claims

1. A DNA molecular encoding method based on dual ternary charge conservation, characterized in that: The steps include: S1: Dual ternary encoding mapping, including data preprocessing, base mapping screening, and sequence generation steps; S2: charge optimization, including initial charge calculation, charge deviation detection, and dynamic replacement steps; S3: codon assignment, including data region encoding, rare codon screening, and dynamic assignment steps; S4: Physical isolation, including isolator design and functional area design steps.

2. A DNA molecular encoding method based on dual ternary charge conservation as claimed in claim 1, characterized in that: Step S1 includes the following sub-steps: S11: Input data and split it into dual ternary coding units in groups of 6 bits; S12: Screening a unique base combination that meets the conditions according to a preset double ternary encoding table; S13: Arrange the screened bases in order to generate an initial DNA chain.

3. A DNA molecular encoding method based on dual ternary charge conservation as claimed in claim 2, characterized in that: The conditions are A(+1, +1), corresponding to a charge of +2; T / U(-1, -1), corresponding to a charge of -2; C(-1, +1), corresponding to a charge of 0; and G(+1, -1), corresponding to a charge of 0.

4. A DNA molecular encoding method based on dual ternary charge conservation as claimed in claim 1, characterized in that: Step S2 includes the following sub-steps: S21: Traverse the DNA chain and calculate the charge value of each base. The charge value is calculated by summing the double ternary digits of the base, where A=+2, T / U=-2, C=0, and G=0; add them together to get the total charge: ； S22: Compare the absolute value of the total charge with 2. If it is less than or equal to 2, terminate; if it is greater than 2, perform a dynamic replacement step.

5. A DNA molecular encoding method based on dual ternary charge conservation as claimed in claim 4, characterized in that: The dynamic replacement step is specifically as follows: preferentially replacing the base with the largest absolute value of charge deviation; after the replacement is completed, updating the total charge; and looping through step S2 until the absolute value of the total charge is less than 2 or the maximum number of iterations is reached.

6. A DNA molecular encoding method based on dual ternary charge conservation as claimed in claim 1, characterized in that: Step S3 includes the following sub-steps: S31: Encode the DNA chain into groups of 3 bases; S32: Use the NCBI codon frequency tool to filter codons with a usage frequency of <5%; S33: Input the ternary encoding stream of the target data and output a DNA sequence that complies with the charge constraint and avoids functional codons.

7. A DNA molecular encoding method based on dual ternary charge conservation as claimed in claim 1, characterized in that: Step S4 includes the following sub-steps: S41: Isolation area design, inserting a C / G alternating sequence between the data area and the functional area; S42: Functional region design, the functional region uses standard genetic codons and retains the start codon and stop codon.

8. The DNA molecular encoding method based on dual ternary charge conservation according to claim 1, characterized in that: Also includes the steps: S5: Convert the optimized DNA sequence into an instruction format compatible with the solid phase synthesizer.

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