DNA Encryption Algorithms: Scope and Challenges in Symmetric Key Cryptography

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DNA Encryption Algorithms: Scope and Challenges in
Symmetric Key Cryptography
Anurag Roy Asoke Nath
Department of Computer Science Department of Computer Science
St Xavier’s College, Kolkata St Xavier’s College, Kolkata
Abstract - Data security is now a crucial issue now in our day to day life. The protection of personal identity,
personal finances depend on the protection of important and irreplaceable information. Cryptography is the science
of converting some readable information into something unreadable format, which are hard to decipher. In modern
times, cryptography has adopted a new medium: human DNA. At a time when conventional cryptography has been
losing strength to more advanced cryptanalysis, DNA cryptography has added more elements of confusion and
diffusion. The use of DNA sequences to encrypt data has strengthened the existing classical encryption algorithms.
Thus, DNA cryptography has added another dimension to conventional cryptography. In the present paper the
authors have made a systematics study on DNA encryption algorithms and how it can be used along with standard
classical encryption algorithms.
Keywords- DNA cryptography, substitution ciphers, block ciphers, symmetric key encryption, Playfair cipher,
decryption
I. INTRODUCTION
Cryptography is concerned with encryption, which is a process of converting ordinary, comprehensible messages
(plaintext) into unintelligible text (ciphertext). Decryption is the inverse of this process, as it converts the ciphertext back
to the original plaintext, given that the proper algorithm to invert the cipher is known to the party attempting the
decryption. Another concept in the subject of “Cryptography” is cryptanalysis. This essentially defines a study of the
encryption algorithm to find weaknesses or loopholes in the cipher, with an aim to extract the plaintext from the
ciphertext without necessarily knowing the 'key' or the decryption algorithm.
Some of the earliest ciphers are called substitution ciphers: letters in the plaintext were replaced by other letters after
undergoing a shift in the alphabet. These ciphers were easy to break, given the knowledge of the frequency of letters or
the combination of letters in a language. Eventually, stronger ciphers were created which worked on either the whole of
stream of plaintext at once or blocks of plaintext at a time.
Some of the modern cryptography encryption algorithms, such as the Feistel cipher, DES (influenced from the Feistel
cipher), MD5, etc, are already broken. Consequently, new directions of information security are being sought to protect
data. It was Adleman [1] who first demonstrated the use of DNA computing in solving real-world computation
problems. His main idea was to use actual chemistry to solve intractable problems, such as the seven-point Hamiltonian
path problem. This opened the door to the concept of using DNA in the field of cryptography to generate powerful, even
unbreakable ciphers.
Boneh, Dunworth and Lipton [2] have also claimed that by using DNA computing the Data Encryption Standard (DES)
can also be broken. This novel area in computing science has given rise to DNA steganography: the study of
camouflaging a DNA encoded message within the enormous complexity of human genomic DNA and then compressing
this information to a microdot [3].
Later advancements in DNA cryptography were made by Gehani, LaBean and Reif [4] with their formulation of a one-
time pad with DNA strands. Kang Ning [5] used another approach wherein he did not use real DNA computing; he
applied the principal ideas of molecular biology to develop an encryption method.

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The advantages of DNA cryptography are the following [6]:
1. A large degree of parallelism is supported in DNA computing, which helps in increasing computational speed.
2. The molecules of DNA are media with a large capacity of transmission.
3. Power consumption is low.
The remainder of the paper is arranged in the following sequence: background study of DNA cryptography and
cryptography, in general; a study of symmetric key cryptography or SKC (because the scope of this paper focuses
primarily on SKC) and a detailed literature review.
II. BACKGROUND
A. DNA (DE-OXYRIBO NUCLEIC ACID):
De-oxyribo Nucleic Acid or DNA is the genetic material in humans and almost every other organism. The same DNA is
contained in nearly every cell in a person's body. The information in DNA is stored in the form of four chemical bases:
adenine (A), guanine (G), cytosine (C) and thymine (T). Human DNA consists of about 3 billion bases. The order in
which these bases are arranged determine the information available to build and maintain an organism. This concept is
also used in many encryption algorithms which emulate the DNA structure. [7]
DNA bases pair up with each other. A is conjoined with T, and C with G. They form base pairs. Each base is also
attached to a sugar molecule and a phosphate molecule. Together, this combination is called a nucleotide. Nucleotides
are arranged in two long strands in a double helical structure. This construction is somewhat like a ladder, where the
base pairs for the ladder's rungs.
B. SYMMETRIC KEY CRYPTOGRAPHY:
Symmetric Key Cryptography (SKC) consists of algorithms for cryptography that use the same key for both the
encryption and decryption of data. The keys meant for the two functions can be identical or the key might go through a
simple transformation. Symmetric key algorithms require the sender and receiver to maintain absolute secrecy of the
key. Only those two parties are required to share the key with the help of a private link. This introduces drawbacks to
symmetric algorithms, when compared to public-key encryption (also known as asymmetric key encryption) [8].
Symmetric key ciphers can be of two types:
 Stream ciphers encrypt all the bytes of a plaintext message at a time.
 Block ciphers encrypt a number of bytes of the plaintext message at a time. Padding (increasing or decreasing
the number of redundant characters) is done to make the total length of the message a multiple of the length of
one block of messages.
C. DNA CRYPTOGRAPHY:
DNA cryptography can be thought of as hiding data in terms of DNA sequence. It is an emerging technology, which
works on concepts of DNA computing [9]. DNA can be used to store and transmit data. This new concept is a hope in
the direction of formulating new unbreakable algorithms.
DNA strands consist of millions of polymers of linked nucleotides. These nucleotides consist of one of four nitrogen
bases (Adenine, Guanine, Cytosine and Thymine), a pentose sugar and a phosphate. The growing popularity of DNA
cryptography can be attributed to the advantages of DNA computing over traditional computing:
 Speed: Conventional computers have been known to perform approximately 100 million instructions per
second (MIPS). Combining DNA strands has been predicted to make computations equivalent to 109
or better,
arguably 100 times faster than the fastest computer.
 Storage: DNA stores memory at the rate of 1 bit per cubic nanometre, whereas conventional storage media
requires 1012
cubic nanometre to store 1 bit.
 Power Requirements: DNA computing does not require power while computation is taking place. The chemical
reactions that create the building blocks of DNA take place without any external power source.
III. LITERATURE REVIEW AND DISCUSSION OF SOME RECENT DNA-BASED ENCRYPTION
ALGORITHMS
Research done on DNA cryptography is extensive, though the subject is novel and a lot of growth is predicted within the
scope of this emerging technology in the coming decades. As stated in an earlier section in this paper, substitution
ciphers brought about the beginning of cryptography. These were the first symmetric key ciphers. However, these
classical ciphers were broken over time. The advent of DNA cryptography has strengthened such obsolete encryption
techniques and paved the way for further innovation. In this section, I propose to review the literature which concerns
conventional techniques of encrypting data.

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Given below are examples of previous research done within this scope, with a detailed discussion of novel encryption
algorithms – inspired by DNA modelling - that have been introduced:
A. SECURE DATA TRANSFER THROUGH DNA CRYPTOGRAPHY USING SYMMETRIC ALGORITHM:
The paper with the above title [6] was written by Bonny B Raj, J Frank Vijay and T Mahalakshmi. The authors have
proposed a simple and basic substitution cipher which is inspired by the structure and sequence of DNA. To understand
this encryption technique, we have to first substitute the nucleotides for binary sequences. This paper has adopted the
following values:
A – 00, C – 01, G – 10, and T – 11
After the above information is available, the following steps are performed for encryption of data:
Step 1. The plaintext is first converted to their respective ASCII numbers (in decimal format).
Step 2. This stream of ASCII numbers are then grouped into blocks.
Step 3. The ASCII numbers are converted to binary numbers (0's and 1's).
Step 4. Encrypted sequences of binary numbers are broken into pairs. The possible pairs could be 00, 01, 10 and
11. The pairs are then substituted by the nucleotides, such as A for 00, T for 01, G for 10 and C for 11.
Step 5. This step involves the generation of a random key Pk. Now, Pk has to be a number between 1 and 256,
inclusive. This random key determines the permutation of the four characters A, T, G and C. For example,
when Pk is 1, the table given below is used for the conversion of ASCII code to nucleotide sequences:
Likewise, when Pk is 2, 'AAAA' maps to the ASCII code 2, and indicates the ASCII code 3 when Pk is 3 and so on.
Step 6. An index table is generated corresponding to the value of Pk.
Step 7. The final ciphertext is obtained from the table after converting the ASCII, using the rule in Step 4.
Decryption is just the reversal of the encryption process. Discussed below is an example of encryption.
Step 8. Let us take a simple plaintext, say the word CAT.

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Step 1. ASCII of the characters are C = 67, A = 65 and T = 84.
C (67) → 01000011 → GAAG
A (65) → 01000001 → GAAA
T (84) → 01010100 → GCAT
Step 2. After the combination of DNA substitution, the message is GAAG – GAAA – GCAT.
Step 3. From the random key generation, the DNA encrypted message becomes 57, 55, 74.
Step 4. Hence, the final ciphertext for this particular random key is 57, 55, 74.
B. A DNA AND AMINO ACIDS-BASED IMPLEMENTATION OF PLAYFAIR CIPHER
This paper [10] was the result of collaboration between Mona Sabry, Mohamed Hashem, Taymoor Nazmy and
Mohamed Essam Khalifa from the Ain Shams University, Cairo, Egypt. It discusses the traditional Playfair Cipher and
also introduces an innovative method to implement this algorithm using principles of genetics. A drawback of the
Playfair Cipher is that it can only encrypt English alphabets. It cannot encrypt numerals or special characters. This novel
algorithm, however, eliminates the problem.
Firstly, it is important to understand the Playfair algorithm, which can be found here [11]. The algorithm makes use of
the concept of translating DNA codes to Amino Acids to increase the confusion. Sequences of nucleotides are generated
as sequences of messenger RNA (mRNA). The relationship between the nucleotide sequences and amino acid sequences
are determined by a genetic code, known as codons (they are three letter words, e.g. ACT, UAG, GUU). Just like in the
paper discussed previously, DNA nucleotides indicate pairs of bits; A for 00, C for 01, G for 10 and T for 11. Given
below are the steps of encryption using this modified algorithm:
Step 1. The plaintext is converted to bits, which is then converted to sequences of nucleotides (A, C, G and T). The
DNA form is then converted to the standard amino acid form using the table given below:
Ala/A GCU, GCC, GCA, GCG Leu/L UUA, UUG, CUU, CUC, CUA, CUG
Arg/R CGU, CGC, CGA, CGG, AGA, AGG Lys/K AAA, AAG
Asn/N AAU, AAC Met/M AUG
Asp/D GAU, GAC Phe/F UUU, UUC
Cys/C UGU, UGC Pro/P CCU, CCC, CCA, CCG
Gln/Q CAA, CAG Ser/S UCU, UCC, UCA, UCG, AGU, AGC
Glu/E GAA, GAG Thr/T ACU, ACC, ACA, ACG
Gly/G GGU, GGC, GGA, GGG Trp/W UGG
His/H CAU, CAC Tyr/Y UAU, UAC
Ile/I AUU, AUC, AUA Val/V GUU, GUC, GUA, GUG
START AUG STOP UAA, UGA, UAG
Step 2. In the table above, we only have 20 amino acids (i.e. 20 letters), in addition to 1 START and 1 STOP codon.
The Playfair Cipher would require 25 characters (since I & J are considered to be one character). B, O, U, X
and Z are letters that still need to be filled. The START codon is repeated with M. Hence, that will not be used.
B is assigned the 3 STOP codons. Here, we notice that 3 amino acids (L. R and S) have 6 codons each.
Studying the sequence of DNA in each of them, we notice that they each have 4 codons of the same type and 2
of another type. Those 2 codons from L, R and S are shifted to the letters O, U and X respectively. Letter Z
takes the codon UAC from Y.
Another aspect of this step is to determine which codon to choose to indicate each letter in the alphabet. Since
each letter has codons varying from 1 to 4, a number is added which indicates the DNA sequence that would
substitute the character. This number is called the “Ambiguity' of the particular character [AMBIG].
Step 3. Now that the secret key and the plaintext message is converted in the form of Amino Acids, the traditional
Playfair Cipher matrix can be built using the secret key. The plaintext is then passed through this matrix to
obtain the ciphertext.
Hence, if the plain text is of length L, the ciphertext would be of length 3L, because each character is converted
to a 3 character-long sequence of DNA.

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The Ambiguity key is helpful in increasing the “confusion” aspect of the cipher. For example, with an AMBIG
value of 3, P will be converted to CCA. Hence, one character can be mapped to different sequences of DNA,
which makes cryptanalysis substantially harder.
C. A METHOD TO ENCRYPT INFORMATION WITH DNA-BASED CRYPTOGRAPHY
This paper was jointly authored by Mohammadreza Najaftorkaman (Griffith University Gold Coast, Australia) and
Nazanin Sadat Kazazi (UTM, Malaysia) [12]. This paper, like the other two discussed previously, introduces the idea of
using DNA based cryptosystem on the traditional Vigenere cipher. The discussion of the classical Vigenere Cipher can
be found here [13]. The proposed algorithm follows the steps discussed below:
Step 1. Data Preprocessing. This is the first step. The data in binary numbers is converted yet again to a DNA string.
This paper, however, proposes a unique technique to convert binary data to DNA strings. The rule is tabulated
below:
Binary Data DNA
00 AA
01 T
10 C
11 GG
0 A
1 G
Step 2. Generation of a Key. This process involves the generation of a key for the Vigenere substitution. In this step,
the NCBI (National Center for Biotechnology Information), which is the master bank of the human genome, is
used. A MATLAB software generates a very large, random stream of DNA from the NCBI database from
which the key is extracted. The key (in red) can start from any position in the string and be of any length,
depending on the sender's choice:
AGGTCACCGTACAGATCAGTCGTAACCAGTGACAGCATGACACGTCAGTCCAGTCGATCACGGTG
CCAAACGTGGAGACAGTCAC.....
Step 3. Encryption Process. In this step, an algorithm was developed to substitute the plaintext using the secret key.
The Vigenere Cipher, which is a polyalphabetic cipher, follows the substitution rules of the table given below:
A T C G
A A T C G
T T C G A
C C G A T
G G A T C
Decryption can be done simply with the knowledge of the secret key. Referring to this Vigenere-DNA table, the
plaintext can be obtained from the ciphertext.
IV. CONCLUSION
Data security is a major concern in the world today. With the enormous price attached to data, enterprises all over the
world are putting much more effort and cost than ever to protect data. Theoretical analysis has shown that the inclusion
of the biological element in computing has not only enhanced computing power, but also improved cryptosystems that
were previously obsolete. Symmetric key cryptography methods which have adopted DNA technology is more powerful
against attacks.

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The primary inferences from this study are:
 Binary information can be converted to DNA codes. Furthermore, binary cryptography methods can be
reapplied using DNA coding technology.
 Preprocessing is imperative when any DNA cryptosystem is applied.
 DNA cryptography is stronger against attacks as it has a greater degree of intractability.
V. REFERENCES
[1] Adleman L M, Molecular Computation of Solutions to Combinatorial Problems, Science, Vol 266, pp 1021-1024,
November 1994.
[2] Dan Boneh, Cristopher Dunworth, and Richard Lipton. "Breaking DES Using a Molecular Computer". Technical
Report CS-TR-489-95, Department of Computer Science, Princeton University, USA, 1995.
[3] TAYLOR Clelland Catherine, Viviana Risca, Carter Bancroft, 1999, "Hiding Messages in DNA Microdots".
Nature Magazine Vol.. 399, June 10, 1999.
[4] Gehani, T. LaBean, and J. Reif, DNA-Based Cryptography, Lecture Notes in Computer Science, Springer, Vol
2950, pp 167-188 2004.
[5] KANG Ning, "A Pseudo DNA Cryptography Method", Independent Research Study Project for CS5231, October
2004.
[6] Bonny B Raj, J Frank Vijay, and T Mahalakshmi, “Secure Data Transfer through DNA Cryptography using
Symmetric Algorithm”, International Journal of Computer Applications, Volume 133- No. 2, January 2016.
[7] Watson, J. D., & Crick, F. H. C. A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953).
[8] SFWR 4C03: Computer Networks and Computer Security, Lecturer: Kartik Krishnan, March 8-11 2004, North
Carolina State University.
[9] S. T. Amin, M. Saeb, S. El-Gindi, A DNA-based Implementation of YAEA Encryption Algorithm, IASTED
International Conference on Computational Intelligence,San Francisco, pp 120-125, 2006.
[10] Mona Sabry, Mohamed Hashem, Taymoor Nazmy, “A DNA and Amino Acids-Based Implementation of Playfair
Cipher”, International Journal of Computer Science and Information Security, Vol. 8, No. 3, 2010.
[11] Practical Cryptography, http://practicalcryptography.com/ciphers/playfair-cipher/
[12] Mohammadreza Najaftorkaman, Nazanin Sadat Kazazi, “A Method to Encrypt Information with DNA-Based
Cryptography”, International Journal of Cyber-Security and Digital Forensics (IJCSDF), The Society of Digital
Information and Wireless Communications, 2015.
[13] Computer Science, Michigan Technological University: http:// www.cs.mtu.edu /~shene/NSF-4/Tutorial/VIG/Vig-
Base.html

DNA Encryption Algorithms: Scope and Challenges in Symmetric Key Cryptography

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DNA Encryption Algorithms: Scope and Challenges in Symmetric Key Cryptography