Med Biol Eng Comput (2014) 52:741–747
DOI 10.1007/s11517-014-1177-3
Original Article
Hiding message into DNA sequence through DNA coding
and chaotic maps
Guoyan Liu · Hongjun Liu · Abdurahman Kadir 
Received: 14 April 2013 / Accepted: 27 June 2014 / Published online: 15 July 2014
© International Federation for Medical and Biological Engineering 2014
Abstract The paper proposes an improved reversible
substitution method to hide data into deoxyribonucleic
acid (DNA) sequence, and four measures have been taken
to enhance the robustness and enlarge the hiding capacity,
such as encode the secret message by DNA coding, encrypt
it by pseudo-random sequence, generate the relative hiding
locations by piecewise linear chaotic map, and embed the
encoded and encrypted message into a randomly selected
DNA sequence using the complementary rule. The key
space and the hiding capacity are analyzed. Experimen-
tal results indicate that the proposed method has a better
performance compared with the competing methods with
respect to robustness and capacity.
Keywords  Data hiding · DNA sequence · DNA coding ·
Chebyshev · PWLCM
G. Liu  data in DNA sequence by substituting three consecutive bases
Department of Dermatology, Affiliated Hospital of Weifang
Medical University, Weifang 261031, China
H. Liu (*)  data in mRNA. Chang et al. [2] proposed two schemes to
School of Information Engineering, Weifang Vocational College,
Weifang 261041, China
e-mail: smithliu@126.com
A. Kadir  between a real DNA sequence and a faked one. Secondly,
School of Computer Science and Engineering, Xinjiang
University of Finance and Economics, Ürümqi 830012, China
A. Kadir 
Postdoctoral Research Workstation of Computer Application
Technology, Xinjiang University, Ürümqi 830046, China
1 Introduction
In the past few years, plenty of data hiding schemes have
been proposed to embed the secret message into images
[5, 9, 11, 16]. A successful scheme is that the data in host
image cannot be easily detected or attacked by the intrud-
ers, but the aim is difficult to achieve.
In recent years, biotechnology has been applied in many
aspects of human’s life, and using biological information
as a carrier instead of image to hide message has become
an interesting and more secure option, for the host image
may be distorted to some degree and can be easily detected.
DNA sequences have some inherent properties that can be
employed to hide all kinds of message, especially for the
short text or digital information.
Some researchers have turned to research how to hide data
into DNA sequences. Clelland et al. [3] firstly proposed the
data hiding method in DNA microdots. Leier et al. [6] pro-
posed a robust scheme using a special key sequence called a
primer to decode an encrypted DNA sequence. A robustness
analysis was provided by the authors, but a capacity analysis
was not provided. Peterson [10] proposed a method to hide
as a character. Shimanovsky et al. [12] proposed an unrecov-
erable scheme, i.e., exploited the codon redundancy to hide
hide data in DNA sequence based upon software views.
Two facts make the DNA sequence suitable for data hid-
ing. Firstly, it is almost impossible to find the difference
there are a large number of DNA sequences publicly avail-
able on various Web sites, such as the EBI database [14]; a
rough estimation puts the number of DNA sequences pub-
licly available to be about 163 million (EMBL nucleotide
sequences database release 101) [15].
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The principle of hiding data into DNA sequence is as
follows: a reference sequence S is randomly selected from
some publicly available DNA sequence databases, only the
sender and the receiver are aware of the reference sequence.
The sender transforms S into a new sequence S ′ by embed-
ding the secret message M into it. After the sequence S ′ is
sent to the receiver with other real sequences, the receiver
examines the received sequences to identify S ′, recovers the
secret message M, and converts S ′ back to S.
Shiu et al. [13] proposed three data hiding methods to
embed the secret message into a reference DNA sequence.
Method 1, 2, and 3 are insertion method, complementary
pair method, and substitution method, respectively. The
results show that Method 2 offers the worst capacity, while
Method 3 shows the best capacity. Method 1 is the most
robust, and Method 3 is the least. Of the three methods,
only Method 3 remains zero payload, which indicates that
encrypted reference sequence can confuse the attacker, and
difficult to be exactly identified.
Guo et al. [4] proposed a new DNA sequence-based
data hiding scheme. They establish an injective mapping
between one complementary rule and two secret bits in a
message. Based on this mapping mechanism, the proposed
scheme can effectively hide two secret bits in a message by
replacing one character. This approach can greatly improve
the embedding capacity in data hiding. Robustness and
security analyses show that the probability of an attacker’s
making a successful recovery of the hidden data is negli-
gible. According to the experimental results, the proposed
scheme has a stable and efficient embedding capacity with a
low modification rate, and the fake DNA sequence does not
need to expand the length of the reference DNA sequence.
In this paper, we propose an improved data hiding
method based on the substitution method in Ref. [13] and
take four measures to enhance the robustness and enlarge
the hiding capacity. ➀ Encoding the secret message by DNA
coding to reduce the size; ➁ Encrypting the secret message
by Chebyshev chaotic maps to enhance the robustness; ➂
Generating the hiding locations randomly by the PWLCM
system to resist attacking; ➃ Using the complementary rule
to hide 2-bit in one nucleotide to enlarge the hiding capac-
ity. Experimental results demonstrate the effectiveness.
Table 1  Translation table from A = CGA H = CGC
alphabets to DNA nucleotides
B = CCA I = ATG
C = GTT J = AGT
D = TTG K = AAG
E = GGT L = TGC
F = ACT M = TCC
G = TTT N = TCT
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Med Biol Eng Comput (2014) 52:741–747
2 Encode and encrypt secret message
2.1 Encode secret message using DNA coding
Each DNA sequence contains four nucleic acid bases,
which are A (adenine), C (cytosine), G (guanine), and
T (thymine), where A and T, C and G are complemen-
tary pairs. In the binary code, 0 and 1 are complemen-
tary, so 0 (00) and 3 (11) are complementary pair, 1 (01)
and 2 (10) are complementary pair too. So in the 4! = 24
kinds of coding, there are only 8 of them to meet the
complementary rule, for example, 0123 can be encoded
to CTAG, CATG, GTAC, GATC, TCGA, TGCA, ACGT,
and AGCT. Here, we select one of them to encode the
secret message.
DNA coding proposes a novel encoding method as
an alternative to traditional ASCII coding. Nucleotides
are used as a quaternary coding, and each letter can be
denoted by three nucleotides. The length of DNA coding
is only 6-bit, which is shorter than the 8-bit ASCII cod-
ing. In Ref. [6], Clelland et al. proposed the translation
table from alphabets to DNA nucleotides, as shown in
Table 1.
If we use C, T, A, G to denote 0 (00), 1 (01), 2 (10),
3 (11), then use CGA (001110) to denote the letter A, and
use CCA (000010) to denote the letter B, etc., then, the
secret message to be hidden can be encoded to a DNA
sequence, for example, “AB” can be encoded to CGACCA
(001110000010). Respectively, to decode the sequence, we
can get the secret message.
Although the DNA coding in Table 1 can only be
expressed as capital letters, numbers, and several punctua-
tion marks, it is still sufficient to encode the secret message
M; suppose the length of M is L, the length of the encoded
message M ′ is 3L.
2.2 Encrypt the DNA sequence by Chebyshev maps
After encoding the secret message M by DNA coding to get
M ′, we can further generate a DNA sequence by Cheby-
shev maps to encrypt it.
The Chebyshev maps can be described as follows:
O = GGC V = CCT 2 = TAG 9 = GCG
P = GGA W = CCG 3 = GCA =ATA
Q = AAC X = CTA 4 = GAG , = TCG
R = TCA Y = AAA 5 = AGA . = GAT
S = ACG Z = AAT 6 = GGG : = GCT
T = TTC 0 = TTA 7 = ACA ; = ATT
U = CTG 1 = ACC 8 = AGG – = ATC
Med Biol Eng Comput (2014) 52:741–747 743

zi+1 = cos(w cos−1 zi ), −1 ≤ zi ≤ 1, (1) mi′ = xi′ ⊕ xi , i = 1, 2, . . . 3L. (5)

where w is the degree of Chebyshev maps, its correspond-

ing invariant density is as follows: 3 Generate the relative hiding locations by PWLCM
system
√

ρ(z) = 1 (π 1 − z2 ). (2)
When we hide the secret message into a reference DNA
Chebyshev maps have important properties of excel- sequence, it is necessary to identify the embedding loca-
lent cryptosystem [8]. If w ∈ [2, 6], its Lyapunov exponent tion. In our previous work, the second author and collab-
is positive, which indicates that the Chebyshev maps are orators designed an algorithm to embed the signal, which
chaotic. can ensure the message not to be easily cracked [7]. Here,
We use Eqs. (1) and (3) to generate a pseudo-random we employ the PWLCM system to generate the random
sequence X = {x1 , x2 , . . . , x3L }, which is applied to encrypt embedding locations.
the encoded message M ′ by bitwise exclusive or (XOR) The equation of PWLCM system is shown in Eq. (6).
operation to eliminate the statistic significance.  �
  yi qi , �
 0 ≤ yi < qi
 00, zi ∈ (−1, −0.5] yi+1 = Fqi (yi ) = (yi − qi ) (0.5 − qi ) , qi ≤ yi < 0.5 ,


 01, z ∈ (−0.5, 0] 
yi ≥ 0.5
i 
F (1 − y ),
xi = . (3) qi i

 10, z i ∈ (0, 0.5] (6)


11, zi ∈ (0.5, 1]
where yi ∊ [0, 1). When the control parameter qi ∊ (0, 0.5),
Suppose M = {m1 , m2 , . . . , mi , . . . mL }, each let- Eq. (6) evolves into chaotic state.
ter mi  ∊  M can be expressed as three nucleic acid bases PWLCM system has uniform invariant distribution and
′
m(i−1)×3+1 ′
, m(i−1)×3+2 ′
, m(i−1)×3+3 ∈ {C, T , A, G} by DNA very good ergodicity, confusion, and determinacy, so it
coding, then M can be expressed as M ′ = {m1′ , m2′ , . . . , can provide an excellent random sequence, which is suit-
′
m(i−1)×3+1 ′
, m(i−1)×3+2 ′
, m(i−1)×3+3 ′ }
, . . . , m3L . After the able for the cryptosystem [1]. The plot and distribution of
PWLCM system is shown in Fig. 1.
bitwise XOR operation by Eq. (4), we can get the result
Here, we generate the relative embedding loca-
XM ′ = {x1′ , x2′ , . . . , m(i−1)×3+1
′ ′
, m(i−1)×3+2 ′
, m(i−1)×3+3 ,...,
tions sequence P = {p1 , p2 , . . . , p3L } by PWLCM sys-
′ } , i.e., XM ′ = X ⊕ M ′.
x3L tem. After iterating Eq. (6) for finite times to elimi-
xi′ = mi′ ⊕ xi , nate the transient process, continue to iterate it for 3L
i = 1, 2, . . . 3L. (4)
times to get Y = {y1 , y2 , . . . , y3L }, and then convert Y to
M′ can also be recovered by Eq. (5), i.e., M′ = XM ′ ⊕ X. sequence P = {p1 , p2 , . . . , p3L } to serve as the relative

Fig. 1  Plot and distribution of PWLCM system. a The plot of PWLCM system. b The distribution of x and q with 1,000 iterations

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hiding locations. If the randomly selected reference DNA
sequence is long enough, the value of pi is determined
by the length of secret message L. If pi ∈ {1, 2, 3, 4},
the values can be generated by Eq. (7). If pi ∈ {1, 2} or
pi ∈ {1, 2, 3}, their values can be generated by the similar
equations.
 Step 3. Concatenate all mk’s, 1 ≤ k ≤ j − 1, to be M. M
 1, yi ∈ (−1, −0.5]


 2, y ∈ (−0.5, 0]
i
pi = . (7)

 3, yi ∈ (0, 0.5]


4, yi ∈ (0.5, 1]
4 Message hiding and recovery
4.1 The substitution method in Ref. [13]
The substitution method proposed by Ref. [13] uses a refer-
ence DNA sequence S. It assumed that S  =  ACGGAATT-
GCTTCAG and the secret message M = m1, m2, …, mp is
0111010. The length of S is 15, which is longer than the
length of M, p, which is 7 in this case. It is stipulated that
the complementary rule used in this method must sat-
isfy that for each letter x of a DNA sequence, all x, C(x),
C(C(x)) and C(C(C(x))) are not equal, where C(x) is the
complement of x. This property is to guarantee the comple-
mentary rule to be an injective mapping. For instance, the
following complementary rule may apply:
(AT )(CA)(GC)(TG)
Let the reference DNA sequence S = s1, s2, …, sm and
the secret message M = m1, m2, …, mp. The method works
as follows:
Step 1. Suppose the length of the reference sequence
S is 15. Select p distinct numbers randomly from 1 to
15. Assume that p  = 7 and these selected p numbers
are 2, 3, 5, 10, 12, 13 and 15, then let A  = {A1, A2, …,
Ap} = {2, 3, 5, 10, 12, 13, 15}
Step 2. Transform S into S ′ by the following rule:
For each integer i from 1–15:
if i is equal to some Aj and mj is 1, 1 ≤ j ≤ p, set si to be
C(si);
else if i is equal to some Aj and mj is 0, do not change si;
else if i is not equal to any Aj, set si to be C(C(si));
Thus S ′ = GCCATGCCAACTAGG.
Step 3. Send S ′ to the receiver.
The receiver knows the reference sequence S and the
complementary rule. Let the ith character of S ′ and S be
denoted as si′ and si, respectively. The recovery process is
as follows:
Step 1. Initialize i and j to be 1.
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Med Biol Eng Comput (2014) 52:741–747
Step 2. For i from 1 to 15:
if si′ is the same with and si, then set mj = 0 and j = j + 1;
else if si′ is the same with C(si), then set mj  = 1 and
j = j + 1;
is the secret message. Set all si′’s to be si′’s to recover S ′ back
to the reference sequence S.
4.2 Improved message hiding method
The improved substitution method also uses a reference
DNA sequence S, and set the secret message “OK” as M,
then M ′  =  GGCAAG. Suppose the length of S is LS, only
when
3L

LS ≥ 1 + pi ,
i=1
S can be long enough to hide M ′. The complementary rule
must satisfy that for each nucleotide x in DNA sequence,
all of the x, C(x), C(C(x)) and C(C(C(x))) are not equal,
C(C(C(C(x))))  =  x, where C(x) is the complement of x,
which can guarantee the complementary rule of injective
mapping.
For this method, first of all, complementary pairs should
be defined. That is, a unique counterpart is assigned for
each base pair. For instance, the following complementary
rule may be applied:
(AT )(CA)(GC)(TG).
By this rule, if x = A, we can get
C(A) = T ,
C(C(A)) = C(T ) = G,
C(C(C(A))) = C(C(T )) = C(G) = C,
C(C(C(C(A)))) = C(C(C(T ))) = C(C(G)) = C(C) = A.
Let the reference DNA sequence S = s1 , s2 , . . . , sLS,
and the secret message M ′ = m1 , m2 , . . . , m3L, the hiding
steps are as follows:
Input: The reference sequence S, secret message M, and
a complementary rule, the keys to generate sequence X.
Output: A faked DNA sequence S ′ with the secret mes-
sage M hidden inside.
Step 1. Encode M to M ′ by DNA coding, and encrypt it
by Eq. (4) to get the sequence XM ′ = {m1′ , m2′ , . . . , m3L
′ }.
Step 2. Generate the hiding relative locations sequence
P = {p1 , p2 , . . . , p3L }.
Step 3. Initialize i to 1.
Step 4. For each element si ∊ S, we use the complemen-
tary rule to do the following operations:
Med Biol Eng Comput (2014) 52:741–747 745

j = i;
i
pk, do not change si;

if j � = 1 +
k=1
i
if j =1+ pk , then
k=1
do case
case mi′ = 00, set sj′ = sj;
case mi′ = 01, set sj′ = C(sj); Fig. 2  Process of message hiding
case mi′ = 10, set sj′ = C(C(sj));
case mi′ = 11, set sj′ = C(C(C(sj))); set w = 4.2926871 and z0 = 0.2182135678932276 in Eq.
end case. (1) to get X = GTCAAG, then XM ′ = X ⊕  M ′ = CACGCT.
We use Eq. (7) to generate the relative hiding locations
Step 5. After the above steps, sequence S is changed into P = {2, 1, 4, 3, 2, 3}. The process of transforming S to S ′
sequence S ′, then send S ′ to receiver. is shown in Fig. 2, and S ′ can be transformed into S by the
inverse transformation while extracting the secret message.
4.3 Improved message recovery method
5.2 Analysis of key space
The receiver can use the following algorithm to recover the
hidden message. For an intruder to discover the secret message, the fol-
Input: A faked DNA sequence S ′ = s1′ , s2′ , . . . , sL′ S, a lowing information is necessary: ➀ the reference DNA
reference DNA sequence S = s1 , s2 , . . . , sLS, the comple- sequence, ➁ the complementary rule, ➂ the sequence X,
mentary rule, the keys to generate sequence X. and ➃ the sequence P.
Output: The hidden secret message M. For ➀, there are roughly 163 million DNA sequences
Step 1. Generate the hiding relative locations available publicly. Thus, the probability for an attacker to
P = {p1 , p2 , . . . , p3L } with the same key. make a successful guess is
Step 2. Initialize i to 1.
Step 3. For each element si′  ∊  S ′, do the following 1
,
operation: 1.63 × 108
so the key space SDNA = 1.63 × 108.
j = i; i For ➁, the number of legal complementary rules should
if j = 1 + pk then

be considered. There are six legal complementary rules as
do case k=1 follows:
case sj′ = sj, mi′ = 00;
case C(sj′) = sj, mi′ = 11;
(AT )(TC)(CG)(GA), (AT )(TG)(GC)(CA), (AC)(CT )(TG)(GA),

case C(C(sj′)) = sj, mi′ = 10; (AC)(CG)(GT )(TA), (AG)(GT )(TC)(CA), and (AG)(GC)(CT )(TA).
case C(C(C(sj′))) = sj, mi′ = 01; The probability to make correct guess is 1/16.6, so the
end case. key space is 6.
For ➂, the variation of z0 ∊ [0, 1] is with a precision of
Step 4. After the Step 3, we can get −16
10 , so the key space for initial condition z0 is Sz0 = 1016.
′ }, then decrypt it by Eq. (5) to get
XM ′ = {m1′ , m2′ , . . . , m3L To ensure a large divergence of a chaotic trajectory
M and decode it by DNA coding to get the secret message
′
from the initial condition, the iteration times n should
M. be relatively large but not too much; it is usually set
n ∊ [100, 1,000]. We provide an increase of the key space
dimension in Eqs. (1) and (6) by 9 × 102, so the total key
5 Experiments and comparisons space Sn = 8.1 × 105.
The variation of the parameter w in the chaotic region is
5.1 Simulation results between 2 and 6 with a step of 10−7, so Sw = 4 × 107.
For ➃, the variation of y0 ∊ [0, 1] is with a precision of
Here, we set the plain text “OK” as secret mes- 10−16, so the key space for initial condition y0 is Sy0 = 1016.
sage M, according to Table 1, the result of DNA cod- Because of qi ≈ yi/2, and yi ∊ [0, 1], then Sqi = Sy0 = 1016.
ing is M ′  =  GGCAAG. Assume that S  =  ACGGAATT- Finally, the algorithm has S = 6SDNA Sz0 Sn Sw Sy0
GCTTCAGT. We use C, T, A, G to denote 00, 01, 10, 11, Sqi = 3.5575 × 1070 combinations of the secret keys.
the complementary rule (AT)(CA)(GC)(TG) is applied. We Even though the fake DNA sequence is identified, it is still

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Table 2  Comparison of cracking probability

Method Substitution methods in Ref. [13] Methods in Ref. [4] Proposed method

Cracking probability 1
× 1 1
× 1
× 1 1
× 1
× 1
× 1
× 1
× 1
1.63×108 6 1.63×108 6 24 1.63×108 6 1016 1.8×105 4×107 1032

Table 3  Comparison of hiding capacity

Sequence Number of Payload Hiding capacity
nucleotides
Substitution method in Method in Ref. Proposed method
Ref. [13] [4]
pi ∈ {1, 2, 3, 4} pi ∈ {1, 2, 3} pi ∈ {1, 2}

AC153526 200,117 0 25,015 114,898 66,706 100,059 133,411

AC166252 149,884 0 18,736 86,562 49,961 74,942 99,923
AC167221 204,841 0 25,605 115,214 68,280 102,421 136,561
AC168874 206,488 0 25,811 123,846 68,829 103,244 137,659
AC168897 191,456 0 23,932 122,708 63,819 95,728 127,637
AC168901 200,203 0 25,025 111,642 66,734 100,102 133,469
AC168907 194,226 0 24,278 115,786 64,742 97,113 129,484
AC168908 218,028 0 27,254 129,204 72,676 109,014 145,352

virtually impossible for the sequence to be correctly recov-
ered without the correct keys.
5.3 Security comparison
We compare the methods in Refs. [4, 13] with our method,
and the results are shown in Table 2. We can find that by
these measures, the cracking probability of the proposed
method apparently much lower than the three methods.
5.4 Hiding capacity
message is encoded by DNA coding, encrypted by pseudo-
random sequence and generated by Chebyshev chaotic
maps. The random hiding locations are generated by the
PWLCM system to resist attacks. The complementary
rule is applied to hide 2-bit in one nucleotide to enlarge
the hiding capacity. Experimental results indicate that the
hiding capacity of the proposed method is greater than the
competing method, and it also has a better performance in
robustness and capacity. In contrast with some traditional
data hiding schemes those using image as carrier, the pro-
posed method is easy to implement and hard to detect.

By the substitution method in Ref. [13], each nucleotide
can only be embedded into one bit. In order to enlarge the
hiding capacity, we encode the secret message by 6-bit
DNA coding, instead of 8-bit ASCII coding, and each
nucleotide can be embedded into 2-bit by the complemen-
tary rule. We use the same eight DNA sequences in Refs.
[4, 13] as the test sample from Web site [14]; the compar-
ison of the maximal hiding capacity is shown in Table 3,
from which we can find that the hiding capacity of the
improved substitution method is greater than the substitu-
tion method in Ref. [13]. If we set pi to different values,
their corresponding results are shown in Table 3.
6 Conclusion
An improved data hiding method into DNA sequence
is designed. Four measures have been taken to enhance
the robustness and enlarge the hiding capacity. The plain
Acknowledgments The research is supported by the National
Natural Science Foundation of China (No. 61363082) and the Minor-
ity Nationality Technology Talent Cultivation Plan of Xinjiang (No.
201123116).
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