IEEE PHOTONICS TECHNOLOGY LETTERS, VOL. 30, NO.
12, JUNE 15, 2018
Silicon Nanowire Optical Rectangular Waveguide
Biosensor for DNA Hybridization
Ritu Raj Singh , Student Member, IEEE, and Vishnu Priye, Senior Member, IEEE
Abstract— Silicon nanowire optical rectangular waveguide
(SNORW)-based biosensor is proposed for the first time to detect
deoxyribonucleic acid (DNA) hybridization. It works on the
principle of detecting the change in refractive index during the
hybridization process when double strand DNA splits into single
strands of DNA or two single strands renaturate into a double
strand DNA. Considering the fabrication on 220- and 330-nm
silicon technology, first a typical configuration of SNORW is
optimized to provide physical compactness and high-power con-
finement. Next, parameters characterizing link layer and DNA
are added, and change in power confinement is ascertained
when double strand DNA (dsDNA) splits into two single strand
DNA (ssDNA) or two ssDNA renaturate to form a dsDNA.
A mean to enhance the difference in power confinement in the
presence of 100% ssDNA and 100% dsDNA is also proposed.
As the splitting/renaturation of DNAs is a slow process, power
confinement when different percentages of dsDNA and ssDNA
coexist is also evaluated.
Index Terms— Biosensors, optical sensing, SNORW, silicon
photonics, DNA hybridization, silicon nanowire.
I. I NTRODUCTION
D UE to recent technological advancement in photonic inte-
grated circuits, silicon waveguides have been used in dif-
ferent biosensing applications. Recently, label-free biosensing
has gained considerable attention by researchers to overcome
the difficulties associated with labeled biosensing [1], [2].
In biosensing, the development of an effective DNA-sensing
system is extremely important, in which technologies for
DNA hybridization are currently under intense investigation
by researchers worldwide. The complicated functionalization
process involved in DNA hybridization can be overcome by
using label free detection involving linker layer rather than
conventional targeted DNA sequence [3]. In DNA hybridiza-
tion process, breaking of hydrogen bonds between comple-
mentary base pairs of dsDNA results in ssDNA; whereas
ssDNA of two species when allowed to renaturate to yield
hybrid DNA. Similar strands join together and form comple-
mentary base pairs by reforming hydrogen bonds. The degree
of similarity between two species can be estimated by DNA
hybridization percentage.
In recent years, optical biosensors based on dielectric
and plasmonic waveguides [4]–[6] are atracting attention of
many researchers worldwide. Research has shown that opti-
cal sensors with gold layer in plasmonic waveguide are
Manuscript received April 22, 2018; accepted May 3, 2018. Date of publi-
cation May 10, 2018; date of current version May 23, 2018. (Corresponding
author: Ritu Raj Singh.)
The authors are with the Electronics Engineering Department, IIT
(Indian School of Mines) Dhanbad, Dhanbad 826004, India (e-mail:
riturajsingh64@gmail.com; vish.ism99@gmail.com).
Color versions of one or more of the figures in this letter are available
online at http://ieeexplore.ieee.org.
Digital Object Identifier 10.1109/LPT.2018.2835152
1041-1135 © 2018 IEEE. Personal use is permitted, but republication/redistribution requires IEEE permission.
See http://www.ieee.org/publications_standards/publications/rights/index.html for more information.
1123
much more effective to detect analytes as compared to
other plasmonic biosensors [7]. However, optical plasmonic
waveguide or hybrid plasmonic waveguide have high loss and
low propagation length as compared to dielectric waveguide.
DNA hybridization can be realized by using both plasmonic as
well as dielectric waveguide [8]–[10]. Silicon waveguide with
its inherent advantage of low material cost can be applied to
DNA hybridization sensing using horizontal [8] and vertical
slot waveguides [9], fabricated on Silicon-on-Insulator (SOI)
substrate. In slot waveguides confinement of power is in low
index region with high sensitivity have been reported for DNA
hybridization [8], [9]. Horizontal slot waveguides [8] have
high surface to volume ratio than vertical slot waveguides [9],
hence horizontal slot waveguide is better DNA hybridization
sensing device as compared to vertical slot waveguide.
Current literatures have acknowledged that an arrangement
of silicon nanowires array on silicon oxide substrate can work
as an opical waveguide, and follow the same principle of guid-
ance as of slot waveguide. In such silicon nanowire optical rec-
tangular waveguide, the light is highly confined in low refrac-
tive indexed nano-slots between silicon wires, resulting strong
intraction between light and sensing material. Moreover, sil-
icon nanowire based waveguides have very high surface to
volume ratio. Thus, the power confining ability and field
distribution are highly sensitive [10], [11] to the slight change
in refractive index of measurand. Silicon nanowire optical
rectangular waveguide shows advantage of high confinement
factor, high sensitivity, small size, easily integrable, fast
response and highly selective with low power consumption.
In this letter, a detailed investigation for optical sensing of
DNA hybridization is proposed using Silicon Nanowire Opti-
cal Rectangular Waveguide (SNORW). Characteristic proper-
ties like power confinement, mode field intensity, normalized
power and waveguide sensitivity are successfully studied for
optimized dimensions. The change in refractive index during
the hybridization process is identified for the different SOI
fabrication technologies. Renaturation and separation through
power confinement when different percentages of dsDNA and
ssDNA coexist are evaluated.
II. G EOMETRY OF SNORW
In Silicon Nanowire Optical Rectangular Waveguide
(SNORW), silicon wires are mainly processed by diffusion
process on Au nano-particles, in which spherical Au particle
yield cylindrical shaped silicon nanowires. Accordingly, ver-
tically grown cylindrical 2-dimensional periodic array pattern
having circular cross-section is shown in Fig. 1(a). SNORW
is developed in accordance to Silicon On Insulator (SOI)
technology, in which fused silica (SiO2 ) as a substrate is
used. The silicon wires have cross sectional dimension of
few nanometers, and are named as nanowires or nanorods.
These nanorods collectively form a waveguide and support
1124 IEEE PHOTONICS TECHNOLOGY LETTERS, VOL. 30, NO. 12, JUNE 15, 2018

Fig. 1. Schematic of SNORW for detection of DNA hybridization.

(a) SNORW structure; (b) cross sectional view (x-y plane) with linker and
DNA layer; and (c) top view (x-z plane) of single silicon nanowire.

optical wave propagation with dominant Quasi-TE mode.

Gaps between these nanowires holds field intensity and mode
distribution inside lower refractive index material.
Here, SNORW is utilized to detect DNA hybridization, for
which silicon nanowires are coated with Silanes which acts
as a linker/glue [9], [12] between silicon and DNA. Linker
of 1nm [9] width and DNA layer is glued over linker layer
with fixed width of 8nm as shown in Fig. 1(b) and Fig. 1(c),
where ‘h’, ‘g’ and ‘d’ represents height, gap and diameter
of silicon rods respectively with “k” number of wires in one
row of SNORW structure. The entire arrangement of SNORW
with linker and DNA is kept inside water (H2 O) as shown
in Fig. 1(b). The top view of one silicon nanorod is shown
in Fig. 1(c).
III. P OWER C ONFINEMENT OF SNORW
To increase the robustness of the proposed SNORW struc-
ture, it is essential to calibrate all the parameters at a specific
value to obtain maximum efficiency and compactness in the
structure. By Finite Element Method (FEM) based optical
modal analysis the field intensity mode pattern is obtained.
Dominant Quasi-TE optical mode is found to be propagated
inside the gap regions between nanorods. The proportion of
power inside the gap regions to the entire cross-sectional area
is termed as power confinement. The power confinement (g )
can be expressed by the mathematically simplified equation as:

Gappings | E(x, y) | d x d y
2
g =  (1)
Total | E(x, y) | d x d y
2 ness consequently. So, the better option would be to compro-
The optimization of structure is carried out by taking
cladding as H2 O without linker and DNA. The refractive index
of Si, SiO2 and H2 O are 3.476, 1.444 and 1.31 individually.
For illustrative purpose, the height of silicon rods are fixed
to 220nm SOI technology. Certain parameters such as ‘k’,
‘g’ and ‘d’ are thoroughly examined to provide maximum
throughput power. The power confinement is calculated by
varying the diameter of silicon nanorods from 10nm to 40nm
in steps of 10nm and varying gap between adjacent nanorods
from 10nm to 20nm in steps of 5nm. SNORW with ‘k’
Fig. 2. Power confinement of water filled SNORW cladding with
(a) g = 10nm; (b) g = 15nm; and (c) g = 20nm.
nanowires on SiO2 substrate in arrayed forest pattern and the
‘k’ ranges from 5 to 40 is investigated. Power confinement
at operating wavelength of 1550nm for various SNORW
parameters combinations are shown in Fig. 2. By analysing
Fig. 2(a), 2(b) and 2(c), it can be clearly observed that after
k = 15 the power confinement gets saturated. Thus, k = 15 is
most suitable for proposed structure. Again by considering ‘g’
parameter estimation of 10nm, 15nm and 20nm as exhibited
in Fig. 2(a), 2(b) and 2(c) respectively, it can be determined
that g = 10nm have maximum power confinement inside gap
region of SNORW. To satisfy the need of proposed structure
to be compact, the diameter of each nanowire is calibrated
to 30nm. As it can be seen in Fig. 2(a) that maximum power
confinement is provided at d = 40nm, however by increasing
the diameter to 40nm the structure compromises the compact-
mise with the diameter = 30nm rather then the compactness of
the sensor. Hence, the optimization of the proposed SNORW
structure for peerless performance, the parameters ‘k’, ‘g’ and
‘d’ are calibrated at 15, 10nm and 30nm respectively.
IV. R ESULT AND D ISCUSSION
The optimized structure of SNORW with water as cladding
material is now implemented for DNA hybridization sensing.
Firstly, deposit of linker layer of 1nm thickness on the
silicon wire surface is considered. Consequently, 8nm thick
SINGH AND PRIYE: SNORW BIOSENSOR FOR DNA HYBRIDIZATION
Fig. 3. (a) Field Distribution, and (b) x-cut field profile of optimized SNORW
for 100% ssDNA and dsDNA with h = 220nm, d = 30nm, g = 10nm
and k = 15.
DNA layer is applied over the linker surface. The whole
arrangement of SNORW with linker and DNA is submerged
into water. The refractive index of linker, ssDNA and dsDNA
are 1.42, 1.456 and 1.53 respectively [13], [14]. The optical
waveguide properties due to change in refractive index during
the hybridization process when double strand DNA splits into
single strands of DNA, or two single strands renaturate into
a double strand DNA is thoroughly explored at communica-
tion wavelength of 1550nm, where sources and detectors are
readily available.
A. Mode Field Distribution
The optimized SNORW structure with k = 15, g = 10nm
and d = 30nm, along with 220nm standard height of
silicon-wire in SOI fabrication technology is utilized to get
mode field distribution. Field intensity pattern for SNORW
is calculated for the dominant fundamental quasi-TE mode
and shown in Fig. 3(a). Impact on the variation of mode
field profile for 100% ssDNA and 100% dsDNA as sensing
measurand layer is shown in Fig. 3(b). Optical waveguide to
act as an optical bio-sensing device should requisite to vary
its mode field intensity pattern by changing the refractive
index of measurand layer.
Field intensity inside linker region is higher than that of
DNA region due to comparatively low refractive index of
linker than ssDNA and dsDNA, so the spikes are acquired
between silicon-wires and DNA layer. Additionally, the level
of field intensity in sensing measurand layer increases when
dsDNA gets separated into two ssDNA, therefore the intensity
inside sensing layer for 100% ssDNA is higher than that
of 100% dsDNA. However, increment in the refractive index
contrast between silicon nanorods and measurand layer results
in decrement of field intensity inside linker layer.
B. Impact of ‘h’ on Power Confinement
The next parametric variable of SNORW is height of
silicon nanorods (h). Height of nanorods are varied from
200nm to 340nm while keeping other parameters at its opti-
mum value (i.e. k = 15, d = 30nm and g = 10nm). Impact of
h on power confinement of SNORW with 100% ssDNA and
100% dsDNA as sensing layer is shown in Fig. 4.
The increase in h value results in increase in power con-
finement value. Because of lower refractive index of ssDNA
 
n 2ab − 1 n 2a − 1
= φa
n 2ab + 2 n 2a + 2
 
(n 2a + 2)(n 2b + 2) + 2 φa (n 2a − 1)(n 2b + 2) + φb (n 2a + 2)(n 2b − 1)
n ab = 
(n 2a + 2)(n 2b + 2) − φa (n 2a − 1)(n 2b + 2) + φb (n 2a + 2)(n 2b − 1)
1125
Fig. 4. Power confinement in DNA versus nanorod height of SNORW with
d = 30nm, g = 10nm and k = 15.
than dsDNA as a sensing layer, former having high power
confinement than the latter. For silicon nanorod height ranging
from 200nm to 340nm, 220nm and 330nm are Standard silicon
height technologies for SOI fabrication. So, both these heights
are taken into consideration for better analysis. Power con-
finement of 43.30% and 54.19% is obtained for ssDNA with
h = 220nm and 330nm respectively. After complete renatura-
tion to dsDNA, power confinement decreases to 41.22% and
50.64% for h = 220nm and 330nm respectively.
C. Separation of dsDNA
The conversion of dsDNA to ssDNA progressively modifies
the refractive index of dsDNA–ssDNA concoction. The refrac-
tive index for different percentage fraction of dsDNA–ssDNA
composition is acquired by Lorentz-Lorenz mixing rule [15]
given in Eq. (2), as shown at the bottom of this page, which
is rearranged to get composition refractive index by Eq. (3),
as shown at the bottom of this page.
Here φa and φb are volume fractions correspond to refrac-
tive index na and nb respectively. Notation ‘a’ and ‘b’ are used
for representing ssDNA and dsDNA respectively. In integrated
optical bio-sensors, any change in chemical parameter of
measurand will vary the refractive index. This variation in
refractive index affects the effective mode propagation. The
probability of detecting various levels of dsDNA–ssDNA in a
composition can be estimated by evaluating guided power in
cladding region with change in refractive index due to the mix-
ture. Likewise, the variation in field distribution profile affects
the sensitivity performance of the waveguide. So, an optical
waveguide to work as a bio-sensor, variation in effective index
should vary its guiding power and sensitivity. The normal-
ized power in measurand zone is the ratio of electric field
intensity in nano-slot of SNORW for DNA composition to the
field intensity in nano-slots for initial DNA type. However,
waveguide sensitivity is the ratio of change of waveguide
effective refractive index to the refractive index of initial DNA.
Fig. 5(a) shows that for SOI standard height technology of
h = 220nm, normalized power increases by 3.70% for 50%
change in fraction from pure dsDNA to ssDNA–dsDNA com-
position. The normalized power level significantly increases by
 
n 2b − 1
+ φb (2)
n 2b + 2
(3)
1126
Fig. 5. (a) Normalized power, and (b) sensitivity dependence on percentage
separation of dsDNA.
Fig. 6. (a) Normalized power, and (b) sensitivity dependence on percentage
renaturation of ssDNA for h = 220nm and 330nm.
8% when dsDNA completely separate into ssDNA. However,
in SOI standard height technology of h = 330nm, 50% change
in fraction will lead to increase in normalized power by 5.8%.
The normalized power level increases by 12% for complete
separation of dsDNA. Waveguide sensitivity correspond to
the separation process is shown in Fig. 5(b). By careful
observation it can be concluded that SOI technology with
330nm height is more sensitive towards change in refractive
index of DNA sensing layer than that of 220nm height.
D. Renaturation of ssDNA
Renaturation is a process in which denatured DNA (ssDNA)
can reformulate hydrogen bonds between complementary
strands of ssDNA, making it likely to reform double helix
dsDNA structure. The renaturation of ssDNA to dsDNA
will slowly modify the refractive index of ssDNA–dsDNA
composition. The probability of detecting various levels of
ssDNA–dsDNA composition is estimated by calculating the
guided power for effective change in refractive index of
cladding due to mixture.
Change in fraction from pure ssDNA to dsDNA–ssDNA
mixture and its corresponding power levels are shown
in Fig. 6(a). For SOI standard height technology of h =
220nm, the normalized power level decreases by 8% when
ssDNA completely renature to dsDNA. While, in SOI standard
height technology of h = 330nm, the normalized power level
decreases by 12% for complete renaturation. Sensitivity of
SNORW towards renaturation is shown in Fig. 6(b). The
waveguide sensitivity in renaturation process decreases with
the increase in percentage renaturation. However, in case of
renaturation, 220nm height technology is more sensitive than
that of 330nm height technology. Precise and fast detection
of DNA hybridization are very crucial for which proposed
SNORW will be extremely compelling.
V. C ONCLUSION
Silicon nanowire optical rectangular waveguide based
biosensor with advanced characteristics has been proposed
to detect DNA hybridization. Characteristic properties like
IEEE PHOTONICS TECHNOLOGY LETTERS, VOL. 30, NO. 12, JUNE 15, 2018
power confinement, mode field intensity and normalized power
have been studied by applying full vectorial finite element
method. The optimum power confinement has been obtained
by appropriately designing the structure parameters inside
water as a cladding material. For high power confinement and
physical compactness, k = 15, d = 30nm and g = 10nm were
obtained as optimized SNORW parameters.
Mode field intensity has been obtained by adding linker and
DNA layer to SNORW structure, which shows that any change
in refractive index is detected with corresponding change in
field intensity level. Silicon wires of height 220nm and 330nm
correspond to standard silicon fabrication technology used
for DNA hybridization. The change in normalized power is
ascertained in case of separation of dsDNA strands when
double strand DNA splits into two single strand DNA. Also,
the case of renaturation when two single strand DNA combines
to form a double strand DNA has been thoroughly investigated
with a change in the fractional composition of ssDNA and
dsDNA. The difference in the power confinement in presence
of 100% ssDNA and 100% dsDNA have been found as 8%
for 220nm and 12% for 330nm SOI technology, respectively.
Renaturation and separation of DNAs are slow processes,
the power confinement when different percentages of dsDNA
and ssDNA coexist has also been evaluated.
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