Vol.1, No.3, 181-184 (2009)
doi:10.4236/ns.2009.13023
SciRes Copyright © 2009 Openly accessible at http://www.scirp.org/journal/NS/
Natural Science
Hiding dat a in DNA of living organisms
Shu-Hong Jiao1, Robert Go utte 2
1Information and Telecom Department, Harbin Engineering University, Harbin, China
2Universite De Lyon , Lab Creatis Lrmn, INSA Lyon, France;
Received 12 June 2009; revised 16 July 2009; accepted 18 July 2009.
ABSTRACT
Recent research has considered DNA an inter-
esting medium for long-term and ultra compact
information storage and a stegomedium for hid-
den messages. Artificial components of DNA
with encoded information can be added to the
genome of living organisms, such as common
bacteria. With this approach, a medium for very
height densities information storage, water-
marks for protection patents of genetically mo-
dified organisms (GMOs) and secure public
keys for d ecryp ting hidd en infor mati on in stega-
nocryptography, can be obtained. In this paper,
we have selected a Bacillus subtilis gene (tatAD)
and use the specific properties of silent muta-
tions to obtain a biologically innocuous product.
An adapted code for the message insertion in
this gene is proposed.
Keywords: DNA; Genome; Coding; Steganography;
Living Organism
1. INTRODUCTION
There has been growing interest in using DNA to store
information, one the main reasons being the very high
storage densities that can be achieved. The durability
of DNA would make it particularly useful for preserving
archival material over extensive periods of time (long-
term storage). Message DNA has been used in computa-
tions in biologic mathematics, in
steganography and as a
mean of short-term trademarks. These different fields
use the specific properties of genetic code and the pos-
sibilities to encode artificial information.
However, the artificial introduction of a new gene or the
modification of an existing gene in the DNA of a living
organism, can involve prejudicial deterioration of the beha-
vior and the reproduction of this species. The solution sug-
gested must thus notably allow a great computer security,
but also the genetic consequences of their implementation.
2. THE GENETIC CODE
The genetic code is the biochemical basis of heredity and
nearly universal in all organisms (eukaryotes or pro-
karyotes): humans, animals, plants, bacteria and vi-
ruses.
DNA (deoxyribonucleic acid) is a long molecule,
with two strands rolled up in a double helix. Each strand
is formed by sugar phosphate backbone, connected with
single molecules called bases, which contain carbon, ni-
trogen and cyclical structures. The four bases are known
as adenine A, thymine T, guanine G and cytosine C.Any
strand of DNA adheres to its complementary strand, in
which T substitute for A, G for C, and vice versa. The
links between pairs of bases are responsible for binding
together two stands together to form the double helix.
The genetic information in DNA is found in the
ordered sequence of these four bases (the double helix
structure of DNA introduces redundant information,
resulting in complementary nitrogenous base links).
Unlike DNA, RNA (ribonucleic acid) is a single
stranded molecule and does not form of double helix.
The bases are the same that DNA, except U (uracil),
which replaces T. The complementarily becomes:
U ↔ A and G ↔ C
Messenger RNA (mRNA) carries all the genetic infor-
mation to ribosome for proteins synthesis by the cell.
A codon is a triplet of three bases (T,C,A and G). With
these four letters, 43═64 combinations are possible. With
three exceptions, each codon encode for one of the 20
amino acids, used in the proteins synthesis (the three ex-
ceptions are TAA, TAG and TGA: codons STOP).
ATG correspond at methionine within the gene; at the
beginning of the gene, ATG is also a signal START. Ribo-
some assembles individual amino acids into peptide chains.
Peptides are short chains of amino acids that are linked
together. If the number of amino acids in the chain reaches
around ten or more, such substances are called polypep-
tides and large polypeptides are called proteins.

S. H. Jiao et al. / Natural Science 1 (2009) 181-184
SciRes Copyright © 2009 Openly accessible at http://www.scirp.org/journal/NS/
182
Figure 1.1. The genetic code (DNA).
1) In yellow: The eight blocks with a single amino acid.
2) Blocks repaired with only two first bases.
Figure 1.2. Simplified code.
3. DEGENERACY OF GENETIC CODE
Many codons are degenerate, or redundant, meaning two
or more codons (synonymous codons) may code for the
same amino acid. See Figure 1.1. Degenerate codons
typically differ in their third position. (e.g.: GAA, GAC for
glutamine). See Fi gur e 1.2.
The degeneracy of the genetic code is what accounts for
the existence of “silent mutations”. A mutation occurs
when a DNA gene is damaged or changed. A silent muta-
tion is a mutation that does not alter the amino acid of a
gene, usually because of codon ambiguity.
4. STATE OF ART, PROPOSED CODE
AND SPECIFIC PROPERTIES
The first paper on hiding messages in DNA was published
by T. Clelland and al (ref 1) in 1999 and involved the in-
sertion of a brief message in a sample of human DNA. In
2001, these same authors published a paper showing of
possibilities of long-term storage of information in DNA
and used a classical codon encoding for the English al-
phabet. In 2003, C. Smith and al (ref 3) described a possi-
ble code for encrypting data.
In DNA and Boris Shimannovsky and al (ref 4) pro-
posed an interesting and original arithmetic code. Pak
Chung Wong and al (ref 5) presented new potential appli-
cations for DNA organic data memory.
The advantages of these approaches in production keys
were presented by Masanori Arita (ref 6) and Tanaka and
all, in 2005 (ref 7). Recently, Nozomu Yachie and al (ref 8)
presented a very complete methodology, simple, flexible
and robust of data storage based on sequence alignment of
genomic DNA of living organism. D. Heider and al publish,
in 2007, a program called DNA Crypt whose use is centred
on the patent protection of genetically modified organisms
(GMOs) (ref 9).
In this work we propose a method of coding that satis-
fies two conditions:
Limitation of changes in the gene marker
Possibility to transfer the encrypted message in a key,
made with a polypeptide chain.
5. CHOICE OF SITE
Bacillus subtilis is a non-pathogenic bacterium, which
form pores that can survive in extreme conditions. This
bacterium is a model which has already been chosen as
storage of information by several teams.
To illustrate our proposed code, we have selected a
component of this genome: the gene tatAD (alternate name
ycbz). See Figure 1.3. This gene is very short; its length is
210 base pairs, which correspond to 70 amino acids. It is a
protein classified stable.
Figure 1.3. Bacillus subtilis.

S. H. Jiao et al. / Natural Science 1 (2009) 181-184
SciRes Copyright © 2009 Openly accessible at http://www.scirp.org/journal/NS/
183
The following table lists the genetic code of these 70
amino acids
ATG TTT TCA AAC ATT GGA ATA CCG GGC
TTG ATT CTC ATC TTC GTC
ATC GCC ATT ATT ATT TTT GGC CCT TCC AAG
CTG CCG GAA ATC GGG
CGT GCC GCG AAA CGG ACA CTG CTG GAA TTT
AAC AGC GCC ACA AAC
TCA CTT GTG TCT GGT GAT GAA AAA GAA GAG
AAA TCA GCT GAG CTG
ACA GCG GTA AAG CAG GAC AAC AAC GCG GGC
A short list concern only the underlining codons: TCA
GGA CCG GGC CTC ……, codons-owned blocks of
the Table 2, in yellow mark.
6. IMPLEMENTATION
6.1. Encryption
By example, we consider the message “CODING”. After
translation with ASCII code (with 8 bits per character), this
message requires 48 bits.
● C 0 1 0 0 0 0 0 1
● O 0 1 0 0 1 1 1 1
● D 0 1 0 0 0 1 0 0
● I 0 1 0 0 1 0 0 1
● N 0 1 0 0 1 1 1 0
● G 0 1 0 0 1 1 1 1
With the rate of 2 bits per codon, this message requires
24 codons. For his implementation, only 35 codons are
selected (codons underlined).The beginning and the end of
this message necessarily belongs to these 35 codons, so
that only two 6 bits numbers (two times three codons) are
needed for their localization.
If we assume that the beginning is located at the 9th
codon, and is 48 bits long (24 codons), the end of the mes-
sage will be located at 32 th codon.
Beginning at 9→ 00 10 01
End at 32→ 01 00 00
Six codons are needed for their localization.
/1 2 3/-//4 5 6//7 8///9 10 11 12 13 14 15 16 17 18 19 20 21
22 23 24 25 26 27 28 29 30 31 32///33 34 35.
The coding consists in replacing the 3rd base of these
codons by A, C, G, T according this table:
A if 00 C if 01
G if 10 T if 11
Before coding we, in the first line have
ATG TTT TCA AAC ATT GGA ATA CCG GGC TTG
ATT CTC ATC TTC GTC
After coding we obtain:
ATG TTT TCA AAC ATT GGG ATA CCC GGG TTG
ATT CTA ATC TTC GTA
The first 24 codons selected on the short list are:
CCT TCC CTC CCG GGG CGT
GCC GCC CGG ACA CTG CTG
GCC ACA TCA CTT GTG TCT
GGT TCA GCT CTG ACA GCG
After coding, we obtain:
CCC TCA CTA CCT GGC CGA
GCT GCT CGC ACA CTC CTA
GCC ACA TCG CTC GTC TCA
GGT TCG GCC CTA ACC GCT
4 codons (underlined) are not modified by the coding.
Only 25 codons of the original gene’s 70 codons (tatAD)
are modified. All the mutations are particular missense
mutations: silent mutations; with its location, the encryp-
tion of this message requires 60 bits and 25 mutations.
Thus, on average, each silent mutation can insert slightly
more than 2 bits of hidden message.
6.2. Decryption
Decryption is particularly easy. After obtaining the begin-
ning and the end of the message from the first 6 codons of
the shortlist, it is sufficient to replace, in the sequence of
codons corresponding to the message, the last base of each
codon by its equivalent in bits:
(A→00, C→01, G→10, T→11)
In this example, a very short gene is used for demonstra-
tion purposes, but this method can be applied to longer
genes, that are more than 10000 base pairs long (such as
the gene srfAA de Bacillus subtilis) which then allows the
insertion of messages 50 that are time longer (~2400 bits
and therefore 300 ASCII characters).
7. MATERIALISAT ION OF THE KEY,
COMPLEMENTS
7.1. Producing the Key
It is possible to replace the list of 30 codon, which can be
synthesized and materialized in the form of a polypeptide,
as in the preceding example, with a new list of 60 amino
acids. Indeed, if we consider the beginning of the Short list
(after coding):
TCA GGG CCC ……..We have the possibility to intro-
duce a peptide chain:
Ser (TCA) Gly (GGG) Pro (CCC) ….
But it is not possible, with only this chain, to redis-
cover the different codons of the short list in reason of
the redundancy of the genetic code.
Ser correspond to TCT TCC TCA TCG
Gly to GGT GGG GGA CGG and
Pro to CCT CCC CCA CCG
For resolve this difficulty we propose the following
connections:
T C A G G G C C C
/\ /\ /\
T C X C A X’ G G X G G X’ C C X CCX’
If X =A and X’=C we obtain:

S. H. Jiao et al. / Natural Science 1 (2009) 181-184
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184
8. CONCLUSIONS
T C A C A C G G A G G C C C A C C C
Ser His Gly Gly Pro Pro
new peptidic chain. With the chain we can retrieve the
three codons of the short list
The use of the degeneracy of the genetic code and, in par-
ticular, the silent mutations, produces coding that does not
practically alter the properties of the inserted gene, nor the
characteristics of the host genome (very important condi-
tions when we working with the live organisms). Memori-
zation of the key information and the production of the
hidden message in the form of a physical polypeptide pro-
vide additional data transfer security, while the coding
protocol is being implemented).
For this, it is sufficient to conserve uniquely two
bases/in each codon.
T C C A G G G G C C C C and to regroup:
T C G G C C
C A G G C C
  
T C A G G G C C C
DNA is a storage medium extremely effective: it is com-
pact and his signature is innocuousness and secrecy. In the
spore form, Bacillus subtilis is resistant to extremes terres-
trial and extraterrestrial environment during the interstellar
travel, for example (ref 10). In the nearly future, this bio-
engineering method can be used in routine, for protection
of the gene patents, digital copyrights and tool for the
marking in biodiversity
for obtain the three original codons.
7.2. Comp lem ents
It is possible to associate this encryption method with
a binary encryption algorithm (AES, RSA, Blow-
fish). In this case, the inserted message is not the clear
version, but a secure version after using these specific al-
gorithms.
7.3. Simplified Version REFERENCES
If, in spite of the precaution to using silent mutations dur-
ing the identification of genetically modified organisms,
residual biological changes still exist in the host organism,
then a simplified version of the method discussed above
can be used.
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From the gene initially modified by the agrochemical
firm (if this gene is accessible to the user), we propose to
use this gene as stegomedium, to produce a custom key.
This key can allow access to the reference of manufacturer.
With this goal in mind, in the preceding example (with the
message “CODING” of 48bits), we select 24 codons of the
70 existing in the tatAD gene.
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total of 24x7=168 bits). These 168 bits are the customized
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marker gene is not altered by this operation. Information
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Openly accessible at