Attaining the 2nd Chargaff Rule by Tandem Duplications

Erwin Chargaff in 1950 made an experimental observation that the count of A is equal to the count of T and the count of C is equal to the count of G in DNA. This observation played a crucial rule in the discovery of the double stranded helix structure by Watson and Crick. However, this symmetry was also observed in single stranded DNA. This phenomenon was termed as 2nd Chargaff Rule. This symmetry has been verified experimentally in genomes of several different species not only for mononucleotides but also for reverse complement pairs of larger lengths up to a small error. While the symmetry in double stranded DNA is related to base pairing, and replication mechanisms, the symmetry in a single stranded DNA is still a mystery in its function and source. In this work, we define a sequence generation model based on reverse complement tandem duplications. We show that this model generates sequences that satisfy the 2nd Chargaff Rule even when the duplication lengths are very small when compared to the length of sequences. We also provide estimates on the number of generations that are needed by this model to generate sequences that satisfy 2nd Chargaff Rule. We provide theoretical bounds on the disruption in symmetry for different values of duplication lengths under this model. Moreover, we experimentally compare the disruption in the symmetry incurred by our model with what is observed in human genome data

Attaining the 2nd Chargaff Rule by Tandem Duplications

Erwin Chargaff in 1950 made an experimental observation that the count of A is equal to the count of T and the count of C is equal to the count of G in DNA. This observation played a crucial rule in the discovery of the double stranded helix structure by Watson and Crick. However, this symmetry was also observed in single stranded DNA. This phenomenon was termed as 2nd Chargaff Rule. This symmetry has been verified experimentally in genomes of several different species not only for mononucleotides but also for reverse complement pairs of larger lengths up to a small error. While the symmetry in double stranded DNA is related to base pairing, and replication mechanisms, the symmetry in a single stranded DNA is still a mystery in its function and source. In this work, we define a sequence generation model based on reverse complement tandem duplications. We show that this model generates sequences that satisfy the 2nd Chargaff Rule even when the duplication lengths are very small when compared to the length of sequences. We also provide estimates on the number of generations that are needed by this model to generate sequences that satisfy 2nd Chargaff Rule. We provide theoretical bounds on the disruption in symmetry for different values of duplication lengths under this model. Moreover, we experimentally compare the disruption in the symmetry incurred by our model with what is observed in human genome data

Steganographic Model for encrypted messages based on DNA Encoding

Information has become an inseparable part of human life. Some information that is considered important, such as state or company documents, require more security to ensure its confidentiality. One way of securing information is by hiding the information in certain media using steganography techniques. Steganography is a method of hiding information into other files to make it invisible. One of the most frequently used steganographic methods is Least Significant Bit (LSB).In this study, the LSB method will be modified using DNA Encoding and Chargaff's Rule. Chargaff's Rule or complementary base pairing rule is used to construct a complementary strand. The modification of the LSB method using DNA encoding and Chargaff's Rule is expected to increase the security of the information.The MSE test results show the average value of the LSB method is 0.000236368, while the average value for the DNA Encoding-based Steganography method is 0.000770917. The average PSNR value for the LSB method was 76.82 dB while the DNA Encoding-based Steganography method had an average value of 70.88 dB. The time of inserting and extracting messages using the Steganography method based on DNA Encoding is relatively longer than the LSB method because of its higher algorithmic complexity. The message security of the DNA Encoding-based Steganography method is better because there is encryption in the algorithm compared to the LSB method which does not have encryption

Attaining the 2nd Chargaff Rule by Tandem Duplications

Erwin Chargaff in 1950 made an experimental observation that the count of A is equal to the count of T and the count of C is equal to the count of G in DNA. This observation played a crucial role in the discovery of the double stranded helix structure by Watson and Crick. However, this symmetry was also observed in single stranded DNA. This phenomenon was termed as the 2nd Chargaff Rule. This symmetry has been verified experimentally in genomes of several different species not only for mononucleotides but also for reverse complement pairs of larger lengths upto a small error. While the symmetry in double stranded DNA is related to base pairing and replication mechanisms, the symmetry in a single stranded DNA is still a mystery in its function and source. In this work, we define a sequence generation model based on reverse complement tandem duplications. We show that this model generates sequences that satisfy the 2nd Chargaff Rule even when the duplication lengths are very small when compared to the length of sequences. We also provide estimates on the number of generations that are needed by this model to generate sequences that satisfy the 2nd Chargaff Rule. We provide theoretical bounds on the disruption in symmetry for different values of duplication lengths under this model. Moreover, we experimentally compare the disruption in the symmetry incurred by our model with what is observed in human genome data