Data Encryption Based On Protein Synthesis - Nguyen Dang Binh

Data Encryption Based On Protein Synthesis
S. R. Alisobhani, F. Mehrabanpoor, Y. Nosrati and B. Sadeghi B.
Faculty of Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), Gavazang,
Abstract - Based on trial and error nature has arrived
to the best possible solutions, and throughout the history,
mankind has found solutions to his problems with an eye
on this source of valuable insights. One of these recent
insightful discoveries is the DNA in nuclei of living
organisms’ cells. DNA holds vast amounts of evolutional
information in the form of coded chemical components
.AS such, it could be used as a mechanism to encode and
transfer information. With respect to this aspect of DNA,
the methodology proposed in this article is on the grounds
of protein biosynthesis in living organs’ cells .In addition,
a combination of existing methodologies complementary
to our method is represented.
In this system, based on data encoding in the DNA,
initially, basic components of data are encoded and using
Huffman Code and exiting methods of fingerprinting,
encoded data are transferred to the destination.
Keywords: Cryptography, DNA, Huffman Code,
Protein Synthesis, fingerprint
1 Introduction
Generally speaking, Cryptography is the method
of protecting information by transforming the
messages into a form that an eavesdropper is
unable to understand it, for the purpose of secure
transmission [4, 7]. Only the ones who posses a
secret key can transform it back to the information
intended to be transmitted. On the other hand,
Encryption could be considered as a process of
scrambling the plain text (information intended to be
transmitted) by use of an algorithm and a secret key.
This results in the production of an encrypted
message, referred to as cipher text. The reverse
process, intended to make the encrypted information
readable again, is referred to as decryption
(i.e. deciphering). This is the goal of encryption to
make sure that adversaries are not capable of
decrypting the information without having the secret
key [4, 7].Concerning this objective, this article
proposes an encryption algorithm based on the
mechanism through which proteins are generated
within the cellular environment. Initially, the process
of protein biosynthesis, key players, and major steps
are briefly explained as a required concept. Then,
two coding schemes are introduced with binary and
alphabetic outputs. For alphabetic output, Huffman
coding as a method of data compression and
Zanjan, Iran.
encryption to binary digits is dealt with next [1].
Lastly, to enhance algorithm efficiency for a secure
transmission, fingerprinting is applied and explained.
2 Required Concepts of Protein
Biosynthesis
In terms of structure, proteins are of high
molecular weight and consist essentially of
combinations between carboxyl and amino groups of
amino acids forming a linear structure [3].
These polymers of amino acids are joined by
peptide bonds. Twenty different amino acids make
up essentially all proteins on earth. The fundamental
structure of each of these amino acids comprises of
a central carbon (Alpha carbon) bonded to
a hydrogen atom (H), carboxyl group (-COOH), an
Amino group (-NH2), and a unique side chain or
R-group. This is the side chain of the amino acid that
gives it a unique characteristic distinguishing it from
others. Besides, the side chain is the determinant of
the chemical characteristics of the amino acid. The
peptide bonds -responsible for joining the molecule
together- covalently bond the amino acids in the
chain. The carboxyl group of one amino acid with
amino group of the next amino acid forms the
peptide bond. This is a type of condensation reaction
resulting in the loss of a molecule of water [5].
The major regard of this article to propose
an encryption algorithm is aimed at protein
biosynthesis, a process through which proteins in
cellular environment are produced. However, central
to protein biosynthesis is the Central Dogma of
Molecular Biology [5] which explains the transcription
of DNA to RNA to Protein, three steps after having
DNA replicated:
1. The DNA codes for the production of
messenger RNA (mRNA) during transcription.
2. In eukaryotic cells, the mRNA is processed
(essentially by splicing) and migrates from the
nucleus to the cytoplasm.(We will not cover this step
in this article)
3. Messenger RNA carries coded information
to ribosome. The ribosome "reads" this information
and uses it for protein synthesis. This process is
called translation.

For For this this process process to to to begin, begin, begin, instructions instructions or
or
blueprints blueprints blueprints are are are required. required. These These instructions instructions instructions could could be
be
found on DNA. Deoxyribonucleic Deoxyribonucleic acid (DNA)
(DNA) is a
nucleic nucleic nucleic acid acid acid that that that contains contains the the genetic genetic genetic instructions
instructions
used used used in in in the the the development development development and and functioning functioning of of all
all
known known known living living living organisms. organisms. The The DNA DNA DNA is is situated situated situated in in in the
the
the
nucleus, nucleus, organized organized into into chromosomes.
chromosomes.
2.1 DNA
The The main main role role of of DNA DNA molecules molecules is the long long-term long
term
storage e of of information information needed needed to to construct other
other
components components components of of cells, cells, cells, such such as as as proteins proteins proteins and and and RNA
RNA
RNA
molecules. molecules. molecules. The The The DNA DNA DNA that that makes makes makes up up up the the the human
human
genome genome genome can can can be be be subdivided subdivided subdivided into into into information information bytes
bytes
bytes
called genes [5]; ; each each gene gene encodes encodes a unique
unique
protein protein that that performs a specialized special
special ized function in in the
the
cell. cell. cell. On On the the the other other other hand, hand, hand, other other DNA DNA DNA sequences sequences sequences have
have
have
structural structural structural purposes, purposes, or or or are are involved involved in in in regulating regulating regulating the
the
the
use use of of this this genetic genetic information.
information.
In In terms terms of of structure, DNA is a long polymer
polymer
made made made from from repeating repeating repeating units units units called called called nucleotides. nucleotides. nucleotides. In
In
living ving organisms, organisms, DNA DNA does does not not usually usually exist as a
single single single molecule, molecule, but but instead instead as as a a tightly-associated
tightly
tightly associated
pair of molecules. Two wo long strands of the DNA
entwine entwine entwine like like vines, vines, in in in the the shape shape shape of of of a a a double double double helix
helix
helix
[5, [5 8]. . The nucleotide nucleotide repeats, repeats
contain containing both the
segment segment segment of of of the the the backbone backbone backbone of of of the the the molecule, molecule, molecule, which
which
holds holds holds the the the chain chain together, together, together, and and a a a base, base, base, which which which interacts
interacts
interacts
with with with the the the other other other DNA DNA DNA strand strand in in the the the helix. helix. In In general, general, a
a
base base base linked linked linked to to to a a sugar sugar is is called called a a a nucleoside nucleoside nucleoside and and and a
a
a
base base base linked linked to to a a sugar sugar and and and one one or or more more phosphate
groups groups is is called called a a nucleotide.
nucleotide.
The The DNA DNA double double helix helix is is is stabilized stabilized by by hydrogen
bonds bonds bonds between between between the the bases bases attached attached attached to to the the the two
two
two
strands. strands. strands. The The The four four four bases bases found found found in in in DNA DNA DNA are are are adenine
adenine
(abbreviated (abbreviated (abbreviated A), A), A), cytosine cytosine cytosine (C), (C), guanine guanine (G) (G) (G) and
and
and
thymine th (T) ) [5, 8]. 8] Each ach type type of of base on one one strand
forms forms forms a a a bond bond bond with with with just just just one one type type of of of base base on on on the the the other
other
other
strand. strand. strand. This This is is called called complementary complementary complementary base base pairing
[5, 5, 8], 8] , , with with A A bonding bonding only only to to T, T, and and C C bonding bonding only
to to to G. G. This This arrangement arrangement arrangement of of two two two nucleotides nucleotides nucleotides binding
binding
together across the th
e double double helix helix is called a a base base pair
pair
[5, 8]. 8] Due to a weak bond between base pairs, DNA
strands strands strands could could could be be pulled pulled apart apart like like a a a zipper. zipper
zipper
2.2 CODONS
As As previously previously mentioned, mentioned, proteins proteins are are assembled
assembled
from from from amino amino acids acids acids using using using information information encoded encoded encoded in
in
in
genes. genes Each Each protein protein has has has its its its own unique amino acid
sequence sequence sequence that that that is is specified specified by by the the nucleotide
nucleotide
nucleotide
sequence sequence sequence of of of the the the gene gene gene encoding encoding encoding this this this protein. protein. protein. The
The
genetic genetic code code is is a a set set of of three-nucleotide three
three nucleotide sets sets called
called
CODONS and each three-nucleotide three
nucleotide combination
combination
stands for an amino acid, for example AUG AUG stands
for methionine [5, 8].
There are 4 4 bases bases in 3
3-letter combinations; there
are 64 64 possible codons codons ( (4 (
encode the twenty standard amino acids, giving
most amino acids more than one possible codon.
There are also three 'stop' or 'nonsense' codons
signifying the end of the the coding region
are the TAA, TGA and TAG codons.
Figure 2. 2
3 letter combinations; there
combinations). These
These
encode the the twenty twenty standard amino acids, giving
most amino acids more than one possible codon.
There are also three 'stop' or or 'nonsense' 'nonsense' codons
signifying the end of the coding region [5, 8]; ; these
are the TAA, TGA and TAG codons. This is shown in
Figure1 Figure1: : The chemical structure structure of DNA.
Hydrogen bonds bonds bonds are are shown shown as as as dotted dotted lines.
lines.
Figure 2: the combination of 4 base pairs in
codons
2.3 Transcription
DNA transcription transcription is is a a process process process that that involves involves the
the
transcribing of genetic information, information, i.e. i.e. the codons codons of
a gene from from DNA DNA to to RNA
RNA [5]. . Simply stated, in
transcription an an an mRNA mRNA mRNA template, template, template, encoding encoding encoding the
the
the
sequence of of of the the the protein protein protein in in in the the the form form form of of of a a trinucleotide
trinucleotide
code, is is transcribed transcribed from from from the the genome genome to to to provide provide provide a
a
a
template for for for translation. translation. Transcription Transcription Transcription copies copies the
the
template from from from one one one strand strand of of the the the DNA DNA DNA double double double helix,
helix,
helix,
called the template template strand
strand [5, 8].

Like DNA, RNA is composed of nucleotide bases.
RNA however, contains the nucleotides adenine,
guanine, cytosine and uricil (U) [5]. When RNA
polymerase transcribes the DNA, guanine joins with
cytosine and adenine joins with uricil. RNA
polymerase moves along the DNA until it reaches a
terminator sequence. At that point, RNA polymerase
releases the mRNA polymer and detaches from the
DNA [5, 8].
The outline of this stage involves following steps:
• DNA unwinds.
• RNA polymerase recognizes a specific
base sequence in the DNA called a promoter and
binds to it. The promoter identifies the start of a
gene, which strand is to be copied, and the direction
that it is to be copied.
• Complementary bases are assembled
(U instead of T).
• A termination code in the DNA indicates
where transcription will stop.
The mRNA produced is called an mRNA
transcript.
2.4 Translation
The next step is to produce a chain of amino
acids based on the sequence of nucleotides in the
mRNA. The nucleotide sequence of an mRNA
molecule is read from one end of mRNA to the other,
in groups of three successive bases previously
named codons. In the cytoplasm, mRNA combines
with one or more ribosomes. Ribosomes act as
catalysts to assemble individual amino acids into
polypeptide chains. Ribosomes contain a small and
a large subunit. Each subunit contains rRNA of
varying length and a set of proteins. One portion of
the mRNA molecule attaches to the smaller subunit
and a tRNA with its amino acid attaches to the other
subunit, thus the codon of the mRNA attracts a
complementary anticodon on the tRNA. This
codon-anticodon matching brings a specified amino
acid into position [5].
After pairing with mRNA, the tRNA amino-acid is
held in a vice-like grip on the ribosome’s larger
subunit. Then ribosome moves on to the new
location along the mRNA to repeat the same process
again. Second tRNA now approaches the ribosome
and pairs its anti codon with the second codon of
mRNA. Thus two tRNA molecules and their amino
acids stand next to one another on the mRNA. In a
fraction of a second these two amino acids are
joined together by a special enzyme to form a
dipeptide. Now the first tRNA is freed and moves
back to the cytoplasm leaving the amino acid
attached to the second amino acid. Ribosome, then,
proceeds by moving along the mRNA and doing the
same process again until it reaches the final one or
two codons of the mRNA which are chain
terminators or stop signals. The polypeptide bond is
formed by removal of water between amino acids.
Now the polypeptide is released from ribosome and
will coil to yield the functional protein [5].
3. Data Encryption
From the protein synthesis process, three factors
are taken for granted for proposed encryption
algorithm. Amino acids represent our basic units of
data, combinations of these basic units produce the
codes, which is codon in protein synthesis, and
codon tables serve the purpose of coding table (refer
to figure2).
These concepts are expanded in the following
lines.
3.1 Data Unit
Digital computers operate zeroes and ones,
meaning that entire data that computers are
processing to surprise human race, are enormous
amounts of information in the form of binary digits.
However, in order to construct coding tables, bits
cannot represent appropriate data units due to their
not having enough semantic weight. Instead, an
alternative is to consider an array of 8 bits, which is a
“Bite”. The advantage of this option is that we are
dealing with 256 different states rather than 2 states
of the former scheme. By encrypting these Bites
entire data will be encoded.
3.2. Coding Data Units and Table of Codes
With regard to figure 2, the combinations of four
elements (i.e. U, C, A, G) and 3 positions provides
4 3 =64 states from which almost twenty amino acids
are produced while more than one codon for some
unit (amino acid) is used. To enhance the coding
efficiency, appropriate number of elements should
be combined together in appropriate number of
positions to cater for n number of states. Two
methods are suggested differing in their output:
In the first method every two bits are
assumed one element. Because 2 bits account for 4
states (i.e. 00, 01, 10, 11) there are 4 different 2 bit
elements in one bite. So 4 4 =256 states. Figure 3
illustrates this coding scheme.
In the second method, similar to the
previous scheme, there are 4 elements in one bite;
the difference, however, is that in the second method
each of 00, 01, 10, 11 are assigned to an alphabetic
letter. Simply stated, the outcome is the
combinations of 4 letters. Again 4 4 =256.(we will refer
to this mechanism throughout the paper as second
method) Figure 4 illustrates this coding scheme.

Figure 3: Illustration of first method - One Bite of
data is translated to one Bite of code.
Figure 4: Illustration of second method - One Bite
of data is translated to a string.
In Figures 5-a, b, these two coding methods are
compared in term of their coding structure.
Figure 5-a: indicates the table of unique codes
based on first method.
Elements including: 00, 01, 10 and 11.
Figure 5-b: indicates the table of unique codes
based on second method.
Elements including: A, H, K and M
3.3 The transmission
Since data communication in digital systems is in
the form of 0 and 1, the first method well complies
with these communication channels. However,
because the second method produces the alphabetic
outputs rather than binary digits, additional encoding
is employed to transform alphabets to binary system
while improving security. This is carried out by
Huffman coding.
4 Required background of Huffman
Code
Huffman Coding is a lossless method of
compressing data and a form of entropy encoding
[1, 6]. Lossless data compression is an algorithm
where original data can be reconstructed from the
compressed data. Entropy encoding is lossless data
compression which assigns codes to symbols with
the length of each codeword proportional to the
frequency of that symbol [4, 7]. Specifically Huffman
codes are variable-length codes; shorter codeword
are assigned to symbols with the highest frequency.
This has an advantage over fixed-length codes as
the average overall bits produced after encoding the
data using variable-length codes, is fewer than
encoding the same data using fixed-length codes.
4.1 Encoding using Huffman Tree
The technique works by creating a binary tree of
nodes. This is done first by considering each symbol
to be encoded as a single tree, each consisting of
a single node. Each node is shown by the frequency
of its symbol. The trees which sum of their root
nodes is the least total frequency among other trees
are selected, “producing” the sub trees of a new root
which is the sum of the frequencies of the sub trees.
The sub trees are then removed from the forest.
This process is recursive and continues until only
one tree -The Huffman Encoding Tree- remains.
Each level is represented using one bit code, 0 or 1.
Classically a value of 0 is associated with an edge to
any left child and a value of 1 with an edge to any
right child .Thus the most frequent symbols’ codes
have fewer bits as they are nearer to the root [1].
There are two variations for constructing Huffman
codes: arbitrary and right-heavy Huffman coding. In
the former, after combining two least frequent
symbols as sub trees of the new root, the decision is
arbitrary as to assign which sub tree as the right or
left child of the root. However in the latter algorithm
this is always the sub tree having greater frequency
assigned as the right child. “By concatenating the
labels associated with the edges that make up the
path from the root to a leaf, we get a binary string.
Thus the mapping is defined [1].”

4.2 Decoding the Huffman code
In Huffman trees each symbol is a leaf which
results in that Huffman codes have prefix property.
In codes with prefix property, no codeword is the
prefix of any other codeword in the set. The
decoding is done by taking the root of the Huffman
tree and recording 0 if the left child is traversed and
1 if the right child is visited. By reaching a leaf that
symbol’s codeword is recovered.
5 Transmission encryption algorithms
In the section 3.3, we have stated that our second
encoding mechanism requires to be digitized. By
means of Huffman coding, the data could be
compressed and also encrypted for the second time.
With 4 alphabet letters, 256 states are arranged.
This results in the presence of maximum 256
different symbols and consequently the same
maximum number of leaves in each Huffman tree.
As all the possible states of arrangements of Amino
acids might not be used in the data being encrypted,
the number of leaves of each Huffman tree might be
fewer than 256.
Having constructed the Huffman tree, the output
of second method is used for the input of the tree
thus converting the arrays of alphabets into strings of
binary data. But the problem is, the Huffman
encoding tree should also be transmitted along with
the message, reducing the effectiveness of this
algorithm. One typical solution to the problem is to
encode symbols along with their frequencies using
RSA method and transmit them along with the
message. At the receiver’s end, Huffman tree could
be reconstructed from frequencies to decrypt the
message.
The alternative robust solution is to use the binary
image of the recipient’s fingerprint, or specifically the
binary image of his or her minutiae. In the process of
fingerprinting, minutiae are specific points in a finger
image which vary from person to person and also
from finger to finger. After fingerprinting, the number
and locations of minutiae for each finger is recorded
and a binary image is created from this information.
A binary image is defined as an image where each
pixel has 2 possible values, black or white. Therefore
each pixel can be stored in memory by one bit of
information which is 1 if it is black and 0 if it is white
[2].
When the Huffman tree is constructed for
a message, the symbols’ codeword are achieved
which are variable-length codes in a binary form.
Having the binary codeword of each symbol, in the
binary image of the recipient’s minutiae, the image
should be searched to find the adjacent pixels which
form each binary codeword. The addresses or
coordinates of the first set of pixels forming the
binary codeword of each symbol should be recorded
and transmitted along with the message [2, 1].
At the destination, for decrypting the message,
the intended recipient’s fingerprint should be used to
decode the message. The binary image of the
recipient’s minutiae is again used for achieving the
codeword of symbols. This is done by putting
together the information of pixels that their
addresses -or coordinates- are given for each
symbol’s codeword. As the minutiae of each finger of
each individual is likely to be unique, if adversaries
get access to the key, which is the symbols and their
codeword in terms of the recipient’s minutiae
information , it is nearly impossible for them to
decrypt the message as they do not have access to
the fingerprint of the recipient.
6 Conclusion and Future Works
In this paper, after a brief revision of protein
biosynthesis, we used it to introduce an encryption
mechanism with two coding schemes. We have also
taken the advantage of Huffman coding to further
strengthen our method and provide compatibility with
common communication medium. We are working
on other methods to generate keys rather than
minutiae of each finger. Besides, an extended
coding scheme supporting several data types is in
the center of attention.
Acknowledgments
We appreciate insightful instructions and
generous contributions of Dr.R.Gharib and
Mr.A.Abedini from whom we have learned a lot.
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