Entropic Trapping and Escape of Long DNA Molecules at Submicron Size Constriction

Abstract

We studied the passage of DNA molecules, driven by an electric field, through a microfabricated channel with 90 nm size constrictions. DNA molecules were entropically trapped at the constriction and escaped with a characteristic lifetime. Counterintuitively, longer DNA were found to escape entropic traps faster than shorter ones. DNA molecules overcome the entropic barrier by stretching their monomers into the constriction, which results in the fact that the energy barrier for DNA escape is independent of the chain length.PACS numbers: 87.14. Gg, 83.10.Nn Recently, the concept of entropic trapping was introduced as a new dynamic regime in gel electrophoresis [1]. A long polymer molecule can be trapped entropically in a random restrictive environment such as a gel, and this effect becomes important when the dimension of pores in a retarding matrix is comparable to the radius of gyration (R 0 ) of the polymer. So far, entropic trapping has been demonstrated by computer simulation [2] and experiment in gel [3]. However, the lack of information on the structure of gel has hindered researchers from obtaining detailed microscopic understanding of the effect. Volkmuth and Austin [4] suggested the use of an artificial structure as a substitute for gel in electrophoresis. Aside from the application to polymer separation [5,6], microfabricated structures provide an ideal environment for studying these polymer dynamics problems, because one can easily control the dimension of obstacles or retarding matrix.The object of this Letter is to characterize the motion of long DNA polymer in an artificial channel with entropic traps. As a model pore-constriction system, we designed a channel with regions of two different depths. Figure 1(a) shows a schematic diagram of the device. The thick regions of the channel are as deep as 1 mm, comparable to the R 0 of the double stranded DNA molecules we used in this experiment. However the depth of the thin region is 90 nm, which is much smaller than R 0 . These thin and thick regions alternate along the channel, and DNA molecules in thick regions are entropically hindered from entering thin regions. Therefore at low electric fields DNA molecules are trapped at the entrance of the thin region and are unable to overcome the trapping barrier. We designed four different channels with different spatial periods of structure (4, 10, 20, and 40 mm). One period is divided by equal lengths of a thick and a thin region, which ensures that the fluid (electrical) resistance of the channel, as well as E s and E l (the electric field in the thin and thick region, respectively), are the same in all four channels. DNA molecules are free to relax while they are traveling in thick regions. By changing the period we can vary the time for DNA to relax before it meets another constriction.The channel was fabricated by standard photolithography techniques on Si substrate, and the front surface was anodically bonded to a Pyrex coverslip. The bonded channels were filled with a buffer solution containing DNA mole...

Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach

“…These results are consistent with observations and in qualitative agreement with those of other simulation studies. 5,6,8 Conclusion CGH-MD showed comparatively good performance in simulating a typical polymer solution, ion distribution in a nanotube, and DNA electrophoresis in polymer solutions and in a nanofluidic device at significantly lower computing cost than those of more rigorous methods. As a computationally efficient explicitsolvent method, CGH-MD is potentially useful for simulating systems of large number of water particles to complement more rigorous methods.…”

“…[8][9][10]58,59 This device is schematically shown in Figure 7. The lengths of one repeating unit of the channel along the x-direction and the ydirection are L x 5 100 r and L y 5 50 r (r is comparable to the persistence length of the DNA chain, 50 nm, or about 150 bp.…”

“…These results are consistent with observations and are comparable to those of other simulation studies. 5,6,[8][9][10] The mobility of DNA chains of lengths N 5 100 and 50 as a function of the electric field is shown in Figure 10. The computed mobility of these DNA chains increases with increasing electric field and saturates at higher electric field.…”

“…6,7 These simulation studies have yielded good agreement with observations. [8][9][10][11] However, some of the explicit solvent effects such as nonuniformly distributed electrostatic interactions, hydrophobic effects, and bound and sequestered water molecules 12,13 cannot be fully considered without using explicit solvent methods. As these effects play important roles in electrophoresis and other processes, it is highly desired to explore explicit solvent methods in practical applications.…”

A nanofluidic device for single molecule studies with in situ control of environmental solution conditions

“…Inside these channels, the DNA molecules are stretched and prevented from exiting due to the entropic barrier provided by the narrower channels. 20,21 The buffer can subsequently be exchanged through the intersecting array of nanochannels in the other direction. The exchange time of the buffer is characterised by monitoring the current through the channels fol-lowing an increase in concentration of salt.…”