DNA stretching on the wall surfaces in curved microchannels with different radii
© Hsieh et al.; licensee Springer. 2014
Received: 9 July 2014
Accepted: 27 July 2014
Published: 7 August 2014
DNA molecule conformation dynamics and stretching were made on semi-circular surfaces with different radii (500 to 5,000 μm) in microchannels measuring 200 μm × 200 μm in cross section. Five different buffer solutions - 1× Tris-acetate-EDTA (TAE), 1× Tris-borate-EDTA (TBE), 1× Tris-EDTA (TE), 1× Tris-phosphate-EDTA (TPE), and 1× Tris-buffered saline (TBS) solutions - were used with a variety of viscosity such as 40, 60, and 80 cP, with resultant 10−4 ≤ Re ≤ 10−3 and the corresponding 5 ≤ Wi ≤ 12. The test fluids were seeded with JOJO-1 tracer particles for flow visualization and driven through the test channels via a piezoelectric (PZT) micropump. Micro particle image velocimetry (μPIV) measuring technique was applied for the centered-plane velocity distribution measurements. It is found that the radius effect on the stretch ratio of DNA dependence is significant. The stretch ratio becomes larger as the radius becomes small due to the larger centrifugal force. Consequently, the maximum stretch was found at the center of the channel with a radius of 500 μm.
KeywordsDNA stretching Microchannel μPIV Curve effect
Fully stretched DNA molecules are very important with regard to advancing the genomic sciences and analyses in order to understand the physical and biological properties of DNA, including the ability to directly manipulate and visualize single DNA molecules. In fact, engineering DNA stretching would be a key step in the development of the next generation of biological microfluidic devices [1, 2].
Microfluidics is the study of behavior manipulation and control of fluids confined to micrometer dimensions, typically 1 to 100 μm. Transport in the microchannels is the major phenomenon; it includes flow detections, liquid transport, control of molecular transport like DNA molecule conformation dynamics, measurement of bulk-level rheological properties, and separation techniques with biophysical and genomic applications because they generate defined fluid flows that manipulate large DNA molecules . In addition, understanding the complex behavior of DNA molecules flowing in microchannels is essential to the realization of lap-on-a-chip (LOC) and micro total analysis system (μTAS) intended to systematically manipulate, process, and analyze these molecules. The presence of DNA molecules gives the fluid viscoelastic behavior that may change the base flow pattern in curved channels .
Two general approaches to DNA stretching are in common use: DNA is stretched in a solution as it flows through a microchannel, or it is stretched on a solid surface. For the latter, the conditions required for significant DNA stretching include high shear rates and high pressure gradient operations with a pressure-driven flow, due to non-slip boundary conditions on the wall. The shear flow existing at the channel walls could stretch DNA molecules. The degree of stretching is correlated with the Weissenberg number of the flow, Wi = τ, where τ is a characteristic relaxation time for the molecule in the solution and is a characteristic shear rate based on the flow in the channel. For the past two decades, DNA molecules have served as a model system for single molecule semi-flexible polymer (larger persistence length of approximately 65 mm) dynamics and can be fluorescently labeled for direct observation with videomicroscopy , revealing a DNA solution non-equilibrium microstructure, DNA- solvent interactions, and DNA macromolecular transport phenomena. Moreover, increased interactions between DNA molecules and channel surfaces result in non-Newtonian flow behavior, even in a dilute DNA molecule solution.
When the laminar flow passes through the curved channels/ducts, the centrifugal force pushes the fluid from the center of the channel when the bulk fluid flows with high velocity to the outer side, while the fluid at the outer wall is pressed either upwards or downwards, thus producing two vortices to fill the entire channel at a cross section along the downstream . The mean flow velocity and the curvature of the channel can determine the centrifugal force, which is governed by an important dimensionless parameter of Dean number (Dn = Re (dh/R)0.5), including the flow Reynolds number (Re) and the duct hydraulic diameter (dh) to the curvature of the channel/duct (R). Here, the Reynolds number is defined as , where ρ is the solution density, U is the average velocity, μ is the solution viscosity, and is the solution shear rate.
Research on shear flow [3, 7, 8] has been conducted in order to model the conformation of DNA molecules for an extended time. These studies reported that the stretching of the DNA molecules subject to shear flow is a function of Wi and τ in the flow. In this study, λDNA molecules were stretched on curved wall surfaces in different curved ducts in pressure-driven flows and visualized as well as measured via micro particle image velocimetry (μPIV) and an optical system. Special attention will be paid to examining the effect of different radii of the curved duct (i.e., Dn), buffer solutions, and the viscosity of the solution. Moreover, viscoelastic (i.e., non-Newtonian) flow in dilute DNA solution will also be examined.
PDMS flow cell fabrication
Fabrication parameters of curved microchannel
SU-8 fabrication processes
550 rpm (80 s)
800 rpm (70 s)
65°C (3 min)
95°C (21 min)
65°C (3 min)
Room temperature (30 min)
Total time 30 s
Post exposure bake
65°C (3 min)
95°C (12 min)
65°C (3 min)
95°C (3 min)
Substrate type: silicon wafer
Photoresist: SU8-2100 (MicroChem)
Depth: 200 μm
Photomask: film mask
(FUJI HPB-S 7mil, 20,000 DPI)
PDMS fabrication processes
10:1 Sylgard-184 A/Sylgard-184 B mixture
70°C (21 min)
For the tested channels, precise information on their dimensions is extremely important to obtain an accurate evaluation of this microchannel. The depth, width, and length were measured optically within an accuracy of ±0.2%. The surface roughness of the channel was measured with a surface profilometer. During the experiments, the surface of the flow channel was so designed that the surface was kept hydrophilic in order to have the buffer solution flow through the microchannels with a definite surface resistance. Pressure gradients in the present curved channels generated modified (due to centrifugal force) parabolic flow, such that shear flow occurred near the channel walls. Furthermore, microfluidic semi-circular curved ducts created a periodic oscillating flow, in which flow pressure gradient alternated directions at a definite time and extended observations of DNA molecules.
DNA visualization and buffer solution preparation
Shear flow system
Buffer solution used in the study
Tris base concentration (mM)
EDTA concentration (mM)
Other ion concentration
5.2 mM of hydrochloric acid
20 mM of acetic acid
90 mM of boric acid
26 mM of phosphoric acid
150 mM of sodium chloride
Lambda DNA (μg/ml)
JOJO-1 concentration (mM)
Relevant parameters of the flow under study
34 Pa, 44 Pa, 57 Pa
0.06 W, 0.068 W, 0.08 W
DNA molecular concentration
Working fluid viscosity, μ (cP)
Reynolds number, Re (×10−3)
1.2 to 1.87
0.561 to 0.828
0.326 to 0.486
Dean number (×10−4)
1.7 to 8.4
0.8 to 4.1
0.4 to 2.4
Relaxation time, τR (Rouse model)
Relaxation time, τZ (Zimm model)
Relaxation time, τ (present study)
Weissenberg number, Wi
6.7 to 11
7.2 to 11.3
8 to 12
The μPIV utilizes flow-tracing particles (stained DNA molecules) to map the flow in the microchannels. The setup shown in Figure 2 was based on two-pulsed Nd:YAG lasers (New Wave SoloII, 30 mJ, double cavity; New Wave Research, Inc., Fremont, CA, USA) firing on the second harmonic (green 532 nm). A detailed description of the μPIV setup can be found in . The concentration of the stained DNA molecules, based on the interrogation volume, was less than 8 × 107 particles/ml. The images were recorded using a Dantec 80C77 Hisense PIV 1,344 × 1,024 × 12 bit interface transfer camera (Dantec Dynamics A/S, Skovlunde, Denmark). A total of five images were taken for each flow field with a spatial resolution of 64 × 64 pixels. The interrogation cell overlay was 50%. The background noise effect was removed by subtracting the background intensity from captured images. In addition, an ensemble averaging 20 images consecutively captured in 4 s was used to obtain the velocity measurements and to avoid the Brownian motion of the stained DNA molecules. A total of 800 sets of data were taken at each location for a specified Re. The selection of 800 datasets was based on the examination of the data convergence. Each measurement was repeated at least five times under specific conditions.
Results and discussion
DNA mean stretching rate
Input voltage (DC)
Buffer viscosity (cP)
Radius effect was significantly noted with maximum stretch ratio occurring at the center of the semi-circle (θ = 90°) with a radius of 500 μm.
The oscillatory/recovery nature of the present stretching behavior was found.
The buffer solution type seems to have no significant influence on the stretch ratio, with no viscosity effect.
The correlation of x/L c was developed for parameters of Wi and Pe, respectively, with different functional relationships.
SSH is a professor at the Department of Mechanical and Electro Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan, Republic of China. FHW is a student working towards a master's degree at the Department of Mechanical and Electro Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan, Republic of China. MJT is a student working towards a master's degree at the Department of Mechanical and Electro Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan, Republic of China.
micro total analysis system.
This work was supported by the National Science Council (NSC) of Taiwan under contract number NSC 101-2221-E-110-043-MY3.
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