DNA-based watermarks using the DNA-Crypt algorithm

Abstract

Background: The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations in the genome can be corrected by the DNA-Crypt program leaving the encrypted information intact. Existing DNA cryptographic and steganographic algorithms use synthetic DNA sequences to store binary information however, although these sequences can be used for authentication, they may change the target DNA sequence when introduced into living organisms.

Results: The DNA-Crypt algorithm and image steganography are based on the same watermark-hiding principle, namely using the least significant base in case of DNA-Crypt and the least significant bit in case of the image steganography. It can be combined with binary encryption algorithms like AES, RSA or Blowfish. DNA-Crypt is able to correct mutations in the target DNA with several mutation correction codes such as the Hamming-code or the WDH-code. Mutations which can occur infrequently may destroy the encrypted information, however an integrated fuzzy controller decides on a set of heuristics based on three input dimensions, and recommends whether or not to use a correction code. These three input dimensions are the length of the sequence, the individual mutation rate and the stability over time, which is represented by the number of generations. In silico experiments using the Ypt7 in Saccharomyces cerevisiae shows that the DNA watermarks produced by DNA-Crypt do not alter the translation of mRNA into protein.

Conclusion: The program is able to store watermarks in living organisms and can maintain the original information by correcting mutations itself. Pairwise or multiple sequence alignments show that DNA-Crypt produces few mismatches between the sequences similar to all steganographic algorithms.

Figure 1

DNA One-Time pad. A_i: plain text, B_i: cipher text (and primer for the DNA polymerase), black box: stop Modified from Gehani et al. [2].

Figure 2

DNA binary strands. Short DNA strands represent the binary 1₂ (light blue), 0₂ (white), start and end marker (dark blue).These sequences can be ligated to long strands by using the sticky ends. Modified from Leier et al. [3].

Figure 3

steganographic algorithms. The function of steganographic algorithms.

Figure 4

The DNA-Crypt algorithm. The function of the DNA-Crypt algorithm.

Figure 5

The first input dimension. The first input dimension of the fuzzy controller is the mutation rate. The first input dimension is separated intro three triangular sets X_i = (a_m, a_λ, a_ρ). The first called "low" = (0, 0, 6) describes a low mutation rate. The second "middle" = (10, 4, 16) and the third "high" = (20, 14, 20) describe a middle and a high mutation rate.

Figure 6

The second input dimension. The second input dimension of the fuzzy controller is the length of the sequence containing the encrypted message. The triangular sets are "short" = (0, 0, 24), "middle" = (40, 16, 64) and "long" = (80, 56, 80).

Figure 7

The third input dimension. The third input dimension is the stability over time, which is represented by the number of generations. It is separated into "low" = (0, 0, 400), "middle" = (500, 100, 900) and "high" = (1000, 600, 1000).

Figure 8

The output dimension of the fuzzy controller. The triangular sets are "none" = (0, 0, 400), "Hamming – code" = (500, 100, 900) and "WDH – code" = (1000, 600, 1000). The maximum of a triangular set, calculated by the set of heuristics of the fuzzy controller, means a cut on the y axis. A cut at 0.28 for none correction code, at 0.67 for Hamming-code and at 0.45 for the WDH-code is shown. The first-of-maximum (fom) represents the recommended correction code, in this case the fuzzy controller recommends the Hamming-code.

Figure 9

Dotplot of Ypt7 and steganogram 1. Pairwise sequence alignment with Dotlet between the original sequence and the steganogram containing "this is a test" [26].

Figure 10

Dotplot of Ypt7 and steganogram 2. Pairwise sequence alignment with Dotlet between the original sequence and the steganogram containing "yet another test" [26].

Figure 11

Multiple sequence alignment. Multiple sequence alignment of the original sequence and two steganograms [27].