A molecular cryptography model based on structures of DNA self-assembly

A Deniable Encryption Method for Modulation-Based DNA Storage

Recent advancements in synthesis and sequencing techniques have made deoxyribonucleic acid (DNA) a promising alternative for next-generation digital storage. As it approaches practical application, ensuring the security of DNA-stored information has become a critical problem. Deniable encryption allows the decryption of different information from the same ciphertext, ensuring that the "plausible" fake information can be provided when users are coerced to reveal the real information. In this paper, we propose a deniable encryption method that uniquely leverages DNA noise channels. Specifically, true and fake messages are encrypted by two similar modulation carriers and subsequently obfuscated by inherent errors. Experiment results demonstrate that our method not only can conceal true information among fake ones indistinguishably, but also allow both the coercive adversary and the legitimate receiver to decrypt the intended information accurately. Further security analysis validates the resistance of our method against various typical attacks. Compared with conventional DNA cryptography methods based on complex biological operations, our method offers superior practicality and reliability, positioning it as an ideal solution for data encryption in future large-scale DNA storage applications.

Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption

Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A⁺/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A⁺/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pK_a, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.

An image cryptography method by highly error-prone DNA storage channel

Introduction: Rapid development in synthetic technologies has boosted DNA as a potential medium for large-scale data storage. Meanwhile, how to implement data security in the DNA storage system is still an unsolved problem. Methods: In this article, we propose an image encryption method based on the modulation-based storage architecture. The key idea is to take advantage of the unpredictable modulation signals to encrypt images in highly error-prone DNA storage channels. Results and Discussion: Numerical results have demonstrated that our image encryption method is feasible and effective with excellent security against various attacks (statistical, differential, noise, and data loss). When compared with other methods such as the hybridization reactions of DNA molecules, the proposed method is more reliable and feasible for large-scale applications.

A Novel Image Encryption Scheme for DNA Storage Systems Based on DNA Hybridization and Gene Mutation

With the rapid development of DNA (deoxyribonucleic acid) storage technologies, storing digital images in DNA is feasible. Meanwhile, the information security in DNA storage system is still a problem to solve. Therefore, in this paper, we propose a DNA storage-oriented image encryption algorithm utilizing the information processing mechanisms in molecule biology. The basic idea is to perform pixel replacement by gene hybridization, and implement dual diffusion by pixel diffusion and gene mutation. The ciphertext DNA image can be synthesized and stored in DNA storage system after encryption. Experimental results demonstrate it can resist common attacks, and shows a strong robustness against sequence loss and base substitution errors in the DNA storage channel. A DNA storage-oriented image encryption algorithm based on gene hybridization and gene mutation, First, we scramble rows and columns of the plaintext image by dynamic Josephus traversing. Second, we replace the pixels by gene hybridization. Finally, we diffuse the image matrix in binary domain and encode pixels into 8-base strands which are later further diffused by gene mutation. The ciphertext image can be synthesized according to the mutant gene codes and stored in any DNA storage system.

Dendritic Quaternary-Encoded Oligourethanes for Data Encryption

The use of sequence-defined digital polymers for data storage and encryption has received increasing attention due to their precision structures similar to natural biomacromolecules (e.g., DNA) but increased stability. However, the rapid development of sequencing techniques raises the concern of information leakage. Herein, dendritic quaternary-encoded oligourethanes bearing a photoresponsive trigger, self-immolative backbones, and a mass spectrometry tag of PEG dendron have been developed for data encryption. Although the sequence information in linear analogs can be readily deciphered by mass spectrometry, sequencing of dendritic oligourethanes cannot be achieved by either primary MS or tandem MS/MS owing to the unique spatial conformation. Intriguingly, the fragmentation pathways of a quaternary dendrimer under MS/MS conditions can be converted to 2772-bit 2D matrices with ≈1.98×10⁸⁷ permutations, serving as high-strength encryption keys for highly reliable data encryption.

An Operational DNA Strand Displacement Encryption Approach

DeoxyriboNucleic Acid (DNA) encryption is a new encryption method that appeared along with the research of DNA nanotechnology in recent years. Due to the complexity of biology in DNA nanotechnology, DNA encryption brings in an additional difficulty in deciphering and, thus, can enhance information security. As a new approach in DNA nanotechnology, DNA strand displacement has particular advantages such as being enzyme free and self-assembly. However, the existing research on DNA-strand-displacement-based encryption has mostly stayed at a theoretical or simulation stage. To this end, this paper proposes a new DNA-strand-displacement-based encryption framework. This encryption framework involves three main strategies. The first strategy was a tri-phase conversion from plaintext to DNA sequences according to a Huffman-coding-based transformation rule, which enhances the concealment of the information. The second strategy was the development of DNA strand displacement molecular modules, which produce the initial key for information encryption. The third strategy was a cyclic-shift-based operation to extend the initial key long enough, and thus increase the deciphering difficulty. The results of simulation and biological experiments demonstrated the feasibility of our scheme for encryption. The approach was further validated in terms of the key sensitivity, key space, and statistic characteristic. Our encryption framework provides a potential way to realize DNA-strand-displacement-based encryption via biological experiments and promotes the research on DNA-strand-displacement-based encryption.

One-time-pad cipher algorithm based on confusion mapping and DNA storage technology

In order to solve the problems of low computational security in the encoding mapping and difficulty in practical operation of biological experiments in DNA-based one-time-pad cryptography, we proposed a one-time-pad cipher algorithm based on confusion mapping and DNA storage technology. In our constructed algorithm, the confusion mapping methods such as chaos map, encoding mapping, confusion encoding table and simulating biological operation process are used to increase the key space. Among them, the encoding mapping and the confusion encoding table provide the realization conditions for the transition of data and biological information. By selecting security parameters and confounding parameters, the algorithm realizes a more random dynamic encryption and decryption process than similar algorithms. In addition, the use of DNA storage technologies including DNA synthesis and high-throughput sequencing ensures a viable biological encryption process. Theoretical analysis and simulation experiments show that the algorithm provides both mathematical and biological security, which not only has the difficult advantage of cracking DNA biological experiments, but also provides relatively high computational security.

One-time-pad cryptography scheme based on a three-dimensional DNA self-assembly pyramid structure

The security strength of the traditional one-time-pad encryption system depends on the randomness of the secret key. However, It can hardly to generatea truerandom key by using the existing technologies and methods, and it is also difficult to issue and store the random keywhich is at least as long as the plaintext. Therefore, we pay more attention to the logical operation used in the encryption and decryption but not to how to generate the random key. The calculator, a three-dimensional DNA self-assembly pyramid structure, is designed to construct four common logical operations (AND, OR, NOT, XOR) by programming DNA interactions. And two novel one-time-pad cryptography schemes, a single-bit one-time-pad algorithm and improved double-bit one-time-pad algorithm, are proposed based on the calculator. The security fragments, used to construct the three-dimensional DNA self-assembly pyramid structure, are intercepted from a reference chain which is selected from the DNA database. All of the interception parameters are transmitted to recipient by hiding in DNA sequences. Only the authorized user can get all secret parameters to reconstruct the structure. The secret random key sequences for the two one-time-pad cryptography algorithms are generated by using logistic map. It only needs to share two parameters and thresholding function in sender and recipient without code books. The simulation results and security analysis show that the encryption algorithms are effective and can provide higher computational complexity as well as a reduced cracking probability except for the difficult of biological experiments.

Multicomponent reactions provide key molecules for secret communication

A convenient and inherently more secure communication channel for encoding messages via specifically designed molecular keys is introduced by combining advanced encryption standard cryptography with molecular steganography. The necessary molecular keys require large structural diversity, thus suggesting the application of multicomponent reactions. Herein, the Ugi four-component reaction of perfluorinated acids is utilized to establish an exemplary database consisting of 130 commercially available components. Considering all permutations, this combinatorial approach can unambiguously provide 500,000 molecular keys in only one synthetic procedure per key. The molecular keys are transferred nondigitally and concealed by either adsorption onto paper, coffee, tea or sugar as well as by dissolution in a perfume or in blood. Re-isolation and purification from these disguises is simplified by the perfluorinated sidechains of the molecular keys. High resolution tandem mass spectrometry can unequivocally determine the molecular structure and thus the identity of the key for a subsequent decryption of an encoded message.