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Video clips of DNA motion in entropic channels (fast connection recommended)
Link to the Science paper ("Separation of Long DNA Molecules in a Microfabricated Entropic Trap Array", J. Han and H. G. Craighead, Science 288, 1026 (2000))
J. Han and H. G. Craighead
School of Applied and Engineering Physics, Cornell University, Ithaca, NY
Microfabricated devices for separating or sieving biomolecules like DNA or protein draws a lot of attention, because its technical importance.[1][2] We have demonstrated a new device for the separation of long polymer like double strand DNA molecules. This initial structure, patterned by multi-level photolithography, is a 30 µm wide channel with repeated, alternating regions of different depths. (typically ~ 90 nm and ~ 1.4 µm, See figure below) When driven by an electric field, DNA molecules go from "thick" to "thin" region many times. Since the radius of gyration is usually larger than ~ 90 nm, the thin region poses an entropic barrier, and can act as a size filter for DNA molecules. Every time a DNA enters into a thin region, its motion is affected by this effect.
Nanofluidic sieving structure for DNA molecules.
Since the radius of gyration is larger than thin gaps,
DNA is trapped entropically in the thick region.
The first result of lambda DNA movement in this channel shows the possibility of a new kind of sieving device for polymers and macromolecules. In a flow of very low concentration of DNA, individual DNA molecules were retarded by the entropic barriers posed by the interface between thin and thick region of channel. Below a certain driving electric field, this effect decreases the mobility of DNA drastically, suggesting a trapping of DNA molecule.
Recent experimental results shows that there is actually a difference in mobility between larger and smaller DNA molecules. In contrary to our intuition from conventional gel electrophoresis, larger DNA molecules turned out to move faster than smaller ones in this channel.[3] This is due to the fact that DNA molecules are heavily deformed and stretched when they enter the thin gap, and this deformation energy barrier, not the entropic free energy difference between spherical and compressed molecule, is the relevant energy barrier in the escape of DNA molecule.[4]
This separation device is a very promising candidate for an alternative of gel electrophoresis,
Several advantages over gel electrophoresis or other newely emerging technologies include,
(1) It is not a time-consuming pulsed-field technique but requires only a dc field to control the device.
(2) It is peculiar because one can recover
the longer DNA molecules first, in contrast with the gel electrophoresis where longer molecules
are generally 'stuck' at the first part of the gel.
(3) It is very easy to control
the gap size (or etch depth) and there is no practical limit in terms of how
narrow they can be made. Therefore one can easily optimize the device for a desired length
range of DNA for an efficient separation.
(4) Since we are making use of only z-directional
size constriction, we could make a large area of this structure on a Si wafer for a
paralleled operation of many samples.
To see a video clip of the DNA molecules moving in the channel, click here. This page will load two large avi files which requires appropriate plug-in to see.
Motion of lambda phage DNA in the sieving channel. This is a
continuous video frames separated by 0.1 seconds. DNA molecule forms a spherical
blob when it is fully relaxed (under no external force). For lambda phage DNA, the
diameter of DNA blob is about 1.4 µm. Therefore, under an electric field,
DNA should deform itself to fit into the thin gap(bright region). In this video
sequences, one can see the stretching of DNA when it is 'jumping' to the next
thick region. Click here for video clips of the DNA motion in entropic channels. (fast connection recommended)
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References
[1] T. A. J. Duke, R. H. Austin, Phys. Rev. Lett. 80, 1552 (1998)
[2] W. D. Volkmuth, T. Duke, M. C. Wu et. al., Phys. Rev. Lett.
72, 2117 (1994)
[3] J. Han and H. G. Craighead, J. Vac. Sci. Technol. A, in press (1999)
[4] J. Han, S. W. Turner, and H. G. Craighead, Phys. Rev. Lett. in press (1999)
Last modified 17 March 1999
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