CRISPR-Cipher: DNA-Based Data Storage and Hierarchical Encryption Using CRISPR-Cas9

We are living in the information age, a time during which massive amounts of digital data are generated every second. Never before has it been more important to save, encrypt, and transmit these data in a way that is secure and efficient. Biological systems, particularly DNA, have very large information densities, presenting unprecedented potential for data storage. Current storage methods that use computers inside of data centers consume enormous amounts of energy, so storing digital information as DNA offers a more sustainable alternative. However, given that DNA could potentially be used to store highly sensitive data, such as medical records or proprietary information, robust encryption methods must be put in place to protect against potential security breaches and ensure data privacy. This is where the CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats - CRISPR associated protein 9) system, renowned for its genetic engineering abilities, could be of use in an entirely new field. Using CRISPR-Cas9 to integrate DNA encryption directly into the storage medium represents a pivotal advancement in DNA-based data storage, guaranteeing the preservation of data integrity and confidentiality at a molecular level. Here, we introduce CRISPR-CIPHER (CRISPR Induced Partitioning for Hierarchical Encryption and Retrieval), a novel approach to encrypt DNA-based information. Our methodology leverages the precision and programmability inherent in the CRISPR-Cas9 system to partition DNA-encoded information into fragments. The resulting jumbled fragments effectively serve as encrypted messages that can only be correctly deciphered with the corresponding key composed of guide RNA sequences known only to the user. To achieve this, we coded an algorithm that takes alphanumeric data as input and transforms it into DNA format while generating a unique key. The encrypted message can be synthesized and partitioned using the Cas9 enzyme complexed with the RNA sequences outlined in the key. To decode the message, the fragments can be sequenced and decrypted by the same algorithm, when provided the key and sequence information. Our innovative approach merges the fields of synthetic biology and cryptography, forging a novel path towards secure, high-density data storage. Future applications of this work encompass a wide spectrum, ranging from secure transmission of sensitive information to the long-term archival of substantial data in a safe and confidential manner. CRISPR-CIPHER not only introduces a unique application of CRISPR-Cas systems but also pioneers a new genre of biological cryptography.