Synchronized DNA sources for unconditionally secure cryptography

Abstract

Secure communication is the cornerstone of modern infrastructures, yet achieving unconditional security -resistant to any computational attack- remains a fundamental challenge. The One-Time Pad (OTP), proven by Shannon to offer perfect secrecy, requires a shared random key as long as the message, used only once. However, distributing large keys over long distances has been impractical due to the lack of secure and scalable sharing options. Here, we introduce a DNA-based cryptographic primitive that leverages random pools of synthetic DNA to install a synchronized entropy source between distant parties. Our approach uses duplicated DNA molecules -comprising random index-payload pairs- as a shared secret. These molecules are locally sequenced and digitized to generate a common binary mask for OTP encryption, achieving unconditional security without relying on computational assumptions. We experimentally demonstrate this protocol between Tokyo and Paris, using in-house sequencing, generating a shared secret mask of $\sim$ 400 Mb with a residual error rate to achieve the usual overall decryption failure rate of $2^{-128}$. The min-entropy of the binary mask meets the most recent National Institute of Standards and Technology requirements (SP 800-90B), and is comparable to that of approved cryptographic random number generators. Critically, our system can resist two types of adversarial interference through molecular copy-number statistics, providing an additional layer of security reminiscent of Quantum Key Distribution, but without distance limitations. This work establishes DNA as a scalable entropy source for long-distance OTP, enabling high-throughput and secure communications in sensitive contexts. By bridging molecular biology and cryptography, DNA-based key distribution opens a promising new route toward unconditional security in global communication networks.

Figures (3)

• Figure 1: DNA-based One-Time-Pad cryptography. a In OTP cryptography, a message, mapped to binary (e.g. using ASCII-code) is encrypted with a random mask using a bit-by-bit XOR function ( b). The receiver decodes by applying a bit-by-bit XOR with the same random mask. c, Two independent pools containing random DNA strands, each of them being unique, playing the role of index and payload, associate at random ( d), and are extended over each other by a polymerase to form reverse-complemented duplexes ( e). f, The pool is optionally amplified and split into two pads: Alice keeps one and passes the other to Bob. Multiple pads can be duplicated and shared at once, providing synchronized random generation for many future exchanges. g Alice and Bob sequence their pad, and publicly share the indices to sift and assemble the corresponding secret payloads into a common binary mask, which they use to communicate via OTP ( h).
• Figure 2: Generating a shared binary mask using DNA pads. a Index-payload key architecture. b, Nucleobase distribution along the payload positions. c, Principle of block5 Purine Parity Digitization (5PPD). d, Probability of measuring a 1 (red) and 0 (blue) along the binary sequence obtained with a 5PPD of the sequences strands sequenced by Alice (circle) and Bob (square). e Pair distribution and correlation in DNA sequences before 5PPD. Pairs and triplets distribution after 5PPD. f, Estimated entropy of DNA binary masks according to the NIST standard 800-90B NIST80090B and comparison with a NIST-approved deterministic RNG NISTFIPS(see Supplementary Tables S4 and S5). The standard computes ten entropy estimates and retains the minimum value. The min-entropy is dictated by the compression entropy and all the other estimates are grouped in blue for Alice and Bob sequences. g Comparison with commercial RNGs Aslan2025. h DNA-OTP ciphering of 2704 $\times$ 2826 image, 130 Mb, of the Horsehead Nebula in the constellation of Orion. Credits: NASA, ESA, and the Hubble Heritage Team (AURA/STScI) ESA).
• Figure 3: Securization and simulation of attacks. a Installation of UMI tags to secure the channel. b Scenario 1: Eve steals a fraction of the DNA keys within Bob's pad, without replacement. c Scenario 2: Eve steals Bob's pad, amplifies the keys by PCR, splits the solution and replace Bob's pool. d Ensemble representation of the shared DNA keys for various fractions of theft in scenario 1, showing $\left\lbrace {\rm Alice } \cap {\rm Bob } \right\rbrace \cap \left\lbrace {\rm Eve} \right\rbrace = \O$ in all cases. The diagrams indicate the number of shared keys, in thousands. e Ensemble representation for various amplification factors by Eve, and normalized distribution of UMI multiplicity $mi$ in clusters in scenario 2. The four replicates for Alice are shown as a single chart with error bars. The safety probability $P=1-\alpha$ in inset is calculated from the type-I, critical $\alpha$ of $\chi^2$ test of the difference between native (Alices') and intercepted (Bobs') UMI multiplicity distributions. f Interference index defined as $(\sum_{i\geq 2} ( N(m_i)/N(m_1))_{\rm unshared \; keys})/(\sum_{i\geq 2} (N(m_i)/N(m_1))_{\rm shared \; keys})$