DNA Hybridization in Microfluidics

Systems – Transport Mechanisms

Overview
!  Introduction to DNA Microarray Technology
!  Physico–chemical model
!  Mathematical model
!  FEM numerical model
!  Results and discussion
!  Conclusions
!  References
DNA Structure
"  DNA is the genetic material of
living organisms that carries
information for the direct synthesis
of proteins.

"  DNA structure comprises two

helical strings named nucleotides,
chained together.

"  Each nucleotide in formed of a

string of molecules, phosphate,
sugar, and one of the four bases:
adenine (A), guanine (G), cytosine
(C), and thymine (T).
 Introduction – DNA

"  Genomics is an emerging scientific discipline

concerned with the analysis, diagnosis, and treatment
of genetic conditions as well as research of genome
particularities.

"  A series of technologies for DNA sampling, processing,

and analysis such as gene chips and microarrays are
currently under development.
 Microarrays and gene Chips
"  Micro arrays are based on Watson-Crick hybridization
rule, in which two DNA strands with complementary
base sequences react and form a double helix
structure.

"  Known DNA sequences are used to target specific

DNA configurations that characterize diseases or
particularities.

"  The known DNA molecules (probes) are usually

combined with a fluorescent molecule to aid optical
detection using an excitation-detection mechanism.
Microarrays and gene chips
"  Microarrays use a
technology based on a
silicon or quartz base
plate, on which the probe
molecules are fixed.

"  Microarrays are printed

using a special machine,
shown in the picture to
the left.
 Motivation
DNA Hybridization in Microfluid Channel
"  For the DNA microarray in a microfluidic channel, the single stranded
DNA is immobilized on a solid surface known as DNA Probe.

"  DNA hybridization occurs when the DNA in the sample is captured on
the probes with a similar complementary sequence.
•  Target will refer to the material which is hybridized to the array.
•  Probe will refer to the material which comprises the array
(oligonucleotides).
This study aims at developing a theoretical framework for the
analysis of transport effects on DNA hybridization reaction in
microfluidic-based, flow-through microarray assays.
 Physico-chemical model
•  The coupled convection, diffusion of a
species (free, target DNA suspension),
and its consumption through the reaction
with a second species (probe DNA) at
one of the confining channel side walls
are investigated.

•  The forced flow of the working fluid is y⎛ y⎞

steady, fully developed, laminar, at low ux ( y ) = 4umax ⎜1− ⎟
H⎝ H⎠
Reynolds number, with parabolic velocity
profile (Hagen–Poiseuille). Re H = uav H ν << 2000

€
•  The reaction between the target and probe DNA molecules is assumed
reversible, of second order, with known characteristic
€ parameters.
kon

T+P ↔H
koff
 Mathematical model
Convection-diffusion transport processes of a species (free, target
DNA suspension) is governed by mass conservation law:

∂c ⎛ ∂2c ∂2c ⎞ ∂c
= Dmol ⎜ 2 + 2 ⎟ −ux
∂t ⎝ ∂x ∂y ⎠ ∂x
Boundary conditions Initial conditions

c (0, y,t ) = C0 (Specified species concentration) c ( x, y,t = 0) = C0

c s ( x,t = 0) = 0
= 0, € = 0 (Impermeable surface)
∂c ∂c
∂x x= L ∂y y= H
€ € c ( mol /m 3 ) -  Concentration of species (free,
∂c ∂c target DNA suspension)
Dmol = s
∂y y= 0 ∂t €
(On the bottom, reactive surface)
€ Dmol ( m 2 /s) -  Diffusion coefficient
€ Velocity field
ux ( m / s) - 
∂c s
= k on c (Cs0 − c s )− koff c s
€ ∂t !#"# $ c s ( mol /m 2 ) -  Concentration of DNA
€
CP hybridization species
€
 The nondimensional model
"  Mass conservation
2
∂C 2 ∂ C ∂2C ∂C
= γ + − Pe γU
∂τ ∂X 2 ∂Y 2 ∂X
Boundary condition Initial conditions
∂C ∂C 1 ∂Cs
C (0,Y ) = 1, = 0, =− C ( τ = 0) = 0
∂X €
X =1 ∂Y Y = 0 ε ∂τ
Cs ( τ = 0) = 0
∂Cs
€ € € ∂τ
[
= Da ε C (1 − Cs ) − K d Cs ] €
The scaling rules
"  €γ = H L - Aspect ratio
c x y D c u
C= , X€ = , Y = , τ = t mol2 , Cs = s , U = x Pe H = umax H Dmol - Peclet number
C0 L H H Cs0 umax
Da = k on Cs0 H Dmol - Damkohler number
ε = C0 H Cs0 - Absorption rate of the €
reactive surface
€ €
K d = koff (konC0 )
€
 Numerical model

"  The mathematical model was

implemented and solved in Comsol –
a finite element environment.

"  The mesh is unstructured, triangular,

Delaunay – 3028 Lagrange quadratic
elements and 6708 degrees of
freedom.

Detail of FEM Mesh

 Results and discussion
The rate of the DNA hybridization process is affected by three physico–
chemical processes that evolve at different time scales

!  Convection t c = L uav
!  Diffusion t d = H 2 Dmol
!  Reaction −1
(
t r = k on Cs0 H )
€
The optimization goal: € t r →t d , t c < t r
"  The mass transfer mechanisms € by diffusion and convection do not affect
the velocity of the reaction.
"  The increase in time of DNA hybridization concentration on surface
€
reaction of the microchannel is given by the analytical solution of eq. (1)
k CC
(
c s = on 0 s 1− e ( on 0 off )
kon C0 + k off
− k C +k t
)
 Results and discussion
"  Typical values used in DNA microarray system in a microfluidic channel for
DNA hybridization.

H = 10µm t r ≅1s
Cs0 = 10 −8 mol/m2
3
kon = 10 mol/m s 3
⇒ t d ≅10s
t
Da = r = kon CP L (uav H) = 10
Dmol = 10 −7 cm2 /s td

"  For Da = 10 (second Damköhler number) the diffusion transfer process

limits the reaction rate and forms a concentration gradient or a
€ concentration boundary layer€ across the surface of reaction.
Results and discussion
Simulation Parameters
Da = 10
Pe = 500
ε = 0.01
K D = 0.1
γ =2

Time evolution of the mass

€ boundary layer – fig.1 a, b, c
depicts the gradients concentration
distribution of DNA species in the
working solution at:

τ = 20, τ = 25, τ = 40

Fig. 1,d shows the kinetics

reaction of DNA hybridization at
(X = 1, Y = 0) location.
 Results and discussion

Pe = 5000
ε = 0.05
k D = 0.01 Simulation
γ = 0.1
Parameters

Pe H = 5000
ε = 0.05
K D = 0.01
γ = 0.1
tr
Da =
td
€
Time evolution of DNA hybridization species DNA hybridization species concentration across
concentration at (X = 1, Y = 0) location at reactive surface for Da = 5 and Da =
€ 50 at τ = 5.
different Da numbers.
 Results and discussion
Propagation of concentration wave in the case of the DNA hybridization process limited by convection.

Simulation
Parameters

Da = 1
Da c = 5
Pe = 25
ε = 0.01
K D = 0.1
γ = 0.02

DNA molecular species target concentration C in working Distribution of DNA hybridization species
€ concentration
solution across reactive surface (Y = 0) in time Cs across reactive surface (Y = 0) at different time
moments. moments.

"  The hybridization process can be limited by convection when t c > t r.

"  To compare the two phenomena we introduce a second Damkohler number
Da c = t c t r = k on CP L (uav H)
 Results and discussion

Simulation
Parameters
Da = 1
Pe = 1000
ε = 0.01
K D = 0.1
γ = 0.02

Influence of adimensional parameter (ε) on Influence of adimensional parameter € (KD)

hybridization rate at (X = 1, Y = 1) location. on hybridization efficiency at (X = 1, Y=1)
location.
 Conclusions

"  In this study we present a simple, Cartesian, yet efficient

mathematical model of microfluidic channel device aimed at
assessing physico-chemical phenomena associated with DNA
hybridization.

"  The numerical results provide for a better understanding of the

influence that the transfer phenomena have on the hybridization
processe.
"  Optimization criteria for microarray systems may be deviced.
 References
"  Alberts, B. 2002. The molecular biology of the cell. Garland Science.

"  Ambreen Abdullah-Sayani, J. M. B.-d. M., Marc J van de Vijver. 2006. Technology
insight: tuning into the genetic orchestra using microarrays. Nature Clinical Practice
Oncology 3:16.

"  Almut, S., and D. Julian. 2001. Navigating gene expression using microarrays - a
technology review. Nature Cell Biology 3 E190-E195.

"  Ralf, L., H. L. Robin, A. Mahesh, C. Zhijian, G. Dale, Y. Jianing, R. Cory, and L. Yingje.
2002. Plastic biochannel hybridization devices: a new concept for microfluidic DNA
arrays. Analytical Biochemistry 311 40-49.

"  Regis, P., R. R. Frederic, G. Dominic, J. P. Francois, J. Guangyao, Z. Jum, M. Marc, B.

Karel, B. Maurice, B. Luc, O. Marc, and G. B. Michel. 2005. Microfluidic device for rapid
(<15 min) automated microarray hybridization Clinical Chemistry 51 1836-1844.

"  Hyun Ho, L., S. James, M. Zack, A. S. David, and Y. Paul. 2006. Recirculating flow
accelerates DNA microarray hybridization in a microfluidic device. Lab on a Chip 6
1163-1170.

"  Joshua Hyong-Seok, K., M. Alia, J. Xi-Yu, V. Z. Jim, and J. M. Marc. 2006.
Characterization of DNA hybridization kinetics in a microfluidic flow channel. Sensors
and Actuators B 113 281-289.