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School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853
Correspondence: Address reprint requests to H. G. Craighead, E-mail: hgcl{at}cornell.edu.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONACKNOWLEDGEMENTSREFERENCES |
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONACKNOWLEDGEMENTSREFERENCES |
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–4), micro- and nanopillar arrays (5–9), nanopores (10–14), and nanochannels (15–18). Each has shown promise as either a tool for the analysis of statistical mechanical properties of long biopolymers or as a tool for sorting biomolecules according to their length. For example, the contour lengths of molecules that were driven into a 100-nm channel have been measured by Tegenfeldt et al. (16). They were able to determine the length of a single 
-DNA strand to within 400 bp in 1 min. Using nanochannels it is also possible to observe the action of an enzyme on a single DNA molecule and consequently map its restriction sites (17).
It has been demonstrated that DNA molecules inserted partly into a nanopillar array with an applied electric field experience a confinement-induced entropic force, causing them to recoil from the array, when the field is turned off (8). This effect, termed entropic recoil, was used to sort two DNA populations of different lengths with a resolution of 11% by length (7). The resolution of pillar arrays is blurred by the fact that DNA molecules entering the array at a distinct point may enter the array diagonally, wrap around pillars, or even form sideways loops. All these different conformations probably have different friction and lead to different recoil times. We have therefore investigated entropic recoil from nanochannels, a geometry that allows only one direction of insertion. Nanochannels also simplify the optical analysis (17) and allow a better comparison to well-known theoretical models like de Gennes' blob model for confined polymers (19).
Here, for the first time, we investigate the motion and conformation of single DNA molecules in 
channels while they are manipulated with both electric fields and confinement-induced entropic forces. Fig. 1 A illustrates the recoil experiment. In addition to the basic recoil process we investigate several new types of motion in nanochannels. Sometimes as shown in Fig. 1 B, when a molecule is electrophoretically driven into a nanochannel, its leading end is folded over on itself. We show that in our experiments the looped DNA strands can be unfolded by the recoil process. Note that folding of DNA has already been observed as quantized resistance changes during DNA translocation through artificial nanopores (12,20). The term "folded DNA" just refers to a transient loop formation and should not be confused with protein folding, for example.
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). A molecule undergoing entropic recoil speeds up over time. In contrast, one expects that the contraction due to entropic elasticity would slow down over time. Here we cause molecules to undergo either elastic contraction or entropic recoil. Fig. 1 C illustrates the contraction of a stretched molecule inside a nanochannel. As shown in Fig. 1 D, we also demonstrate that under certain initial conditions it is possible for a molecule to undergo both the contraction and entropic recoil processes simultaneously.
A basic theory (8) can be derived by neglecting the self-avoidance effects of the persistent DNA. A molecule at the interface has the entropy per unit length 
inside the nanochannel and entropy per unit length 
in the microchannel. Thus the entropy is 
where 
and 
are the lengths in the two regions. The length of the molecule that resides in the microchannel can be rewritten as 
where 
is the full extended length of the DNA strand in the nanochannel. The entropic force 
results from the free energy 
and is found to be independent of the inserted length inside the nanochannel. The molecule retraction at velocity 
is only hindered by the hydrodynamic drag force 
inside a confined environment (21). Here 
is the hydrodynamic drag per unit extended length in the nanochannel. Solving the resulting differential equation 
under the condition 
leads to:
 | (1) |
is the time of complete extraction. |
MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONACKNOWLEDGEMENTSREFERENCES |
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(MarkOptics, Santa Ana, CA) using a combination of electron beam and optical lithography. Initially, a layer of gold, 
thick, was evaporated onto poly(methyl-methacrylate) (PMMA) electron-beam resist to help draw current during the electron-beam process. Negative patterns of the nanochannel regions were exposed using a JBX-9300FS electron beam lithography system (JEOL, Peabody, MA). After removal of gold and PMMA development, the patterns were transferred to a chrome mask by evaporation and lift off. Microchannel patterns were then added to the mask using optical lithography and the same lift-off process. Both micro- and nanochannels were etched simultaneously using a Plasmalab 80Plus REI (Oxford Instruments, Eynsham, UK) with a CHF3/O2 mixture at 50 Watts for 20 min. Access holes were created by alumina powder blasting from the backside of the wafer. Finally a 
fused silica cover wafer (MarkOptics) was touch bonded and annealed at 1050°C to the device wafer, enclosing the channels. Nanoports (Upchurch Scientific, Oak Habor, WA) were sealed to the access holes forming buffer reservoirs. A schematic of the completed device can be seen in Fig. 2. Several electron micrographs of the nanostructures before bonding are shown in Fig. 3.
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The contour length of single T4-DNA (169 kbp) can be calculated from the basepair spacing of 
to 
But recent studies have shown that the dye TOTO-1, which is similar to YOYO-1, increases the contour length 
by 30–35% at a dye to basepair ratio of 1:4 (21,22). Thus at our dye ratio of 1:5 is expected to rise by 23% to 
Although in the past, the persistence length of the DNA was assumed to increased from 
when stained (21,22), recent investigations indicate that staining reduces the persistence length to 
(23). The two protonated amino and two protonated imino groups of YOYO-1 also decrease the average charge of the negative DNA backbone. Given our buffer concentrations, we assume a counterion shielding of 60% (24,25) and calculate a charge per unit length of 
As changes in the properties are all less than an order of magnitude, we expect that the behavior of unstained DNA would be similar to the observed dynamics of the DNA/dye complex. The buffer consisted of 445 mM Tris-borate and 10 mM EDTA (5xTBE, pH 8.3, Sigma, St. Louis, MO) with 5% (v/v) ß-mercaptoethanol (Sigma) as an antiphotobleaching agent and 2.5% (w/w) poly(n-vinylpyrrolidone) (PVP; molecular weight = 10,000; Sigma) to reduce both electroosmotic flow and unspecific binding of DNA to channel walls (18,26,27). Electrical contact was made with platinum electrodes inserted into the reservoirs.
Microscopy
The individual molecules were observed with an IX70 inverted microscope (Olympus, Melville, NY), which was equipped with a 100x/0.93 NA oil immersion objective (Olympus) and illuminated by a 100-W mercury arc lamp. An XF100 filter set (Omega Optical, Brattleboro, VT) was used for fluorescence imaging. Images were acquired using an ICCD-350F camera (Videoscope, Dulles, VA) connected to a DVD recorder at a rate of 29.97 frames per second. DNA molecule movement was extracted from the videos by using a combination of thresholding and morphological algorithms programmed in MATLAB (The Mathworks, Natick, MA).
Experimental protocol
DNA molecules were driven from the reservoirs into the microchannel with a bias of 30 V. To drive a molecule from the microchannel into a nanochannel, a 3-V bias was always applied. This bias resulted in 
in nanochannels and 
in the loading channel. Any further manipulations within the nanochannel were conducted under electric fields of either 
or 
Three types of experiments were conducted for each molecule that we observed. First, the molecules were driven entirely into the nanochannel, and the field was then switched off. Their relaxation to equilibrium extension length in the nanochannel was studied. Once they had contracted, they were slowly driven back down the nanochannel until a small portion of the molecule had reached the microchannel. At this point the field was again switched off and the molecules were observed to undergo a pure recoil process. Finally, after exiting the nanochannel, molecules were driven back in electrophoretically. This time, however, the field was switched off before the DNA strands had completely entered the nanochannel. As a result, they were observed to both recoil and unstretch simultaneously.
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONACKNOWLEDGEMENTSREFERENCES |
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) or stretching by microbead techniques (28). Upon fully entering a nanochannel, a molecule begins to relax and finally reaches its equilibrium extension length inside the channel. Though the dynamics of this contraction in nanochannels has not yet been modeled, as far as the authors are aware, DNA contraction in nanoslits was tested by Bakajin et al. (21) and treated numerically by Stigter (24). We assume that the end-to-end length 
of a contracting molecule in a nanochannel can be roughly characterized with an exponential fitting function:
 | (2) |
Here is the equilibrium length in the channel, 
the measured initial extended length, and 
is the time constant of contraction. The contraction of several T4 DNA strands was fit with this function fixing to the measured length at 
The results were 
and 
with n = 8, where n is the number of measurements. The ratio of extension was 
An example of one of these fits is plotted in Fig. 5. The equilibrium extended length of -DNA molecules in channels was measured to be 
by Tegenfeldt et al. (16). They also found that the extended length scales linearly with the contour length 
which leads to an expected length of 
for a T4 molecule. This is in close agreement with our measured value. In all experiments molecules drifted at 
inside the nanochannels. This was compensated for either mathematically or with an electric field offset of 
The origin of the drift might be an electrochemical or osmotic gradient due to different DNA or dye concentrations in the fluid reservoirs.
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were 
(n = 23) and 
(n = 18) for molecules recoiling from the two sides of the nanochannel array. The ambient drift, responsible for the difference between the two values, can be compensated for by averaging the two, resulting in a corrected value of 
In addition, a set of experiments with an electrical offset correction resulted in 
Fig. 6 shows this set of experiments as well as a fit to all of the curves. The theory accurately describes the data. Our values for are three times higher than the value of 
determined by Turner et al. (8) for DNA recoil from nanopillar arrays. This is probably due to an increased entropic force 
due the higher confinement in 100-nm nanochannels compared to nanopillar arrays with 125-nm spacing.
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To formulate a recoil theory that accommodates contracting, we introduce a stretching factor 
which describes the degree to which the inserted part of the molecule is stretched compared to the equilibrium extension inside our nanochannels. As in Eq. 2, we assume an exponential dependence on the time 
:
 | (3) |
and the initial stretching factor 
at the beginning of the recoil. Therefore we may write, for the insertion length of a molecule that begins to both recoil and contract at the instant the electric field is turned off,
 | (4) |
Fig. 7 compares a stretched recoil process with a relaxed recoil process for the same molecule in the same channel. Each has been fit using the appropriate model. As a result we obtain 
for an offset corrected set of experiments (n = 13), which is close to the value we obtained for relaxed recoil experiments. This indicates that the modified recoil model, which accounts for the entropic force as well as the stretching, is a good first approximation.
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) is a powerful tool for investigating the unfolding behavior of DNA molecules. This is important for us as many of the recoil experiments showed a folded conformation upon entry, two examples of which are shown in Fig. 8. Folded portions of DNA molecules are brighter than unfolded portions in the time trace plots. The possibility that the brighter portion of the molecule has simply been compressed can be ruled out by observing its evolution through time. We would expect compressed regions to decompress and reach equilibrium with the rest of the molecule over a period of time on par with the timescale of the observed contraction processes. Instead, the border between the bright and the dim sections does not become less defined through time. Only the observed lengths of the bright and dim portions change during the recoil process. Finally, when a certain threshold is reached the molecule suddenly becomes uniform in intensity and slightly longer. This event may correspond to the final act in an unfolding process where the energy required to bend the end of the DNA molecule is released. Note that molecules that appeared to be folded were discarded from all pure recoil and stretch-recoil measurements.
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the observed length will be larger than 
when it is folded in half. Therefore the folded configuration is entropically unfavorable in comparison with the straight configuration, so that given enough time any folded molecules should spontaneously unfold. For molecules with a significant degree of folding (more than several microns), there were no observable decreases in length of the folded segment of the molecule during our experiments. We therefore assume that spontaneous unfolding must occur over a much larger timescale than that of the unfolding process that we induce using the recoil force.
DNA friction determination
To determine hydrodynamic drag of DNA in the nanochannels, molecules were repeatedly driven by an electric field of in both directions. Fig. 9 shows a portion of two time traces demonstrating molecules driven in both directions. Folded molecules could easily be distinguished, and only unfolded molecules were used for velocity measurements. Velocities were measured by a linear fit of the molecule position versus time. Fig. 10 displays the distribution of the measurement values as well as two Gaussian fits, one for each direction. The average velocity of all measurements was 
which corresponds to a mobility of 
This value is slightly higher than 
measured for -DNA in silicon/polydimethylsiloxane nanochannels (29). In these measurements an overall linear relation between velocity and electric field was measured. This linearity was also confirmed for DNA translocation through nanopores at high electric fields of the order of 
(20). This is in agreement with theoretical models of confined polymers (30) and confined DNA (21) that predict hydrodynamic friction coefficients that are dependent on channel diameter and viscosity but not on the electric field.
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with the viscous drag coefficient 
As the channel diameter is on the order of the persistence length 
most of the hydrodynamic interactions between molecule segments are screened (21). Thus, the drag coefficient is assumed to be 
with the friction coefficient per unit length 
and the contour length 
For a nonaccelerating DNA strand of charge 
and charge per unit contour length the friction force and the electrical force 
are in equilibrium. Therefore, the friction coefficient per unit contour length is 
Assuming a charge per unit length of 
we calculate a friction coefficient of 
This is five times higher than the pure hydrodynamic friction coefficient 
of a solid tube with the DNA diameter 
inside another PVP solution-filled tube with diameter 
The calculation is a lower bound as it neglects the average DNA segment tilt in the channel as well as frictional interactions with the channel walls. Additionally, although electroosmotic backflow was minimized by the dynamic PVP coating, it may not have been completely eliminated. Future studies with different surface coatings may isolate the relative contributions of hydrodynamic friction, DNA-wall interactions, and electroosmotic backflow to the overall friction. The friction coefficient can be converted to drag per unit extended length by scaling with the previously determined extended length 
The result is 
Calculation of entropic recoil force
From the determined drag coefficient and the fitted ratio of the entropic force to the drag coefficient 
we calculate an entropic force of 
Note that this force is specific for DNA molecules at the interface between a nanochannel and the microchannel in our device. To obtain a theoretical estimate for comparison with the measured entropic recoil force, we calculated the free energy difference between a DNA strand in a 100-nm channel and in free solution. This was done using Schaefer's polymer model for persistent polymers (31). Inside the nanochannel, this model was combined with de Gennes' "blob" model (19) as has been described elsewhere in detail (15,16,32). Dividing the free energy change by half the extended length, which is approximately the distance the center of mass moves during recoil, leads to an estimate for the entropic recoil force of 
The difference between the measured and estimated values for force might be due to the uncertainty of the shielding of the DNA backbone charge which influences the calculation of the drag. A better theoretical estimate might also be achieved by using a more sophisticated numerical polymer model such as the worm-like chain model, though such a calculation would require numerical simulations. Note also that our approach attributes the free energy change to the difference in configuration space accessible to a molecule, and assumes that electrical interaction between DNA and the walls is negligible. This is a valid assumption considering that the Debye screening length at the buffer concentration used is less than 
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CONCLUSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONACKNOWLEDGEMENTSREFERENCES |
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This work is relevant for both the statistical physics and the applied biophysics fields. From a statistical mechanics perspective, further insight into the nature of the entropic force might be gained by investigating single molecule retraction from nanochannels of different widths. Stretching and relaxation experiments using molecules of different sizes could lead to a better understanding of the elastic forces for DNA strands, as theory suggests that longer polymer molecules have smaller spring constants (33). As we have shown, elongation of molecules in nanochannels enables researchers to optically visualize molecule folding. Further studies in this area may lead to a better understanding of DNA packaging into bacteriophage heads or chromatin (34), which is an important topic in biology. Devices combining nanochannels with nanopore-like constrictions will give us the opportunity to combine optical and electrical DNA investigations. The entropically driven process of DNA recoil from nanopatterned geometries has already proven its potential to separate DNA by length (7). Our work will lead to an improved device geometry to achieve higher separation resolution for DNA molecules in the kilobase to megabase pair range.
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ACKNOWLEDGEMENTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONACKNOWLEDGEMENTSREFERENCES |
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FOOTNOTES |
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Submitted on September 19, 2005; accepted for publication March 8, 2006.
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REFERENCES |
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2. Han, J. Y., and H. G. Craighead. 2002. Characterization and optimization of an entropic trap for DNA separation. Anal. Chem. 74:394–401.[Medline]
3. Slater, G. W., Y. Gratton, M. Kenward, L. McCormick, and F. Tessier. 2003. Deformation, stretching, and relaxation of single-polymer chains: fundamentals and examples. Soft Matter. 1:365–391.[CrossRef]
4. Tessier, F., J. Labrie, and G. W. Slater. 2002. Electrophoretic separation of long polyelectrolytes in submolecular-size constrictions: a Monte Carlo study. Macromolecules. 35:4791–4800.[CrossRef]
5. Huang, L. R., J. O. Tegenfeldt, J. J. Kraeft, J. C. Sturm, R. H. Austin, and E. C. Cox. 2002. A DNA prism for high-speed continuous fractionation of large DNA molecules. Nat. Biotechnol. 20:1048–1051.[CrossRef][Medline]
6. Kaji, N., Y. Tezuka, Y. Takamura, M. Ueda, T. Nishimoto, H. Nakanishi, Y. Horiike, and Y. Baba. 2004. Separation of long DNA molecules by quartz nanopillar chips under a direct current electric field. Anal. Chem. 76:15–22.[Medline]
7. Cabodi, M., S. W. P. Turner, and H. G. Craighead. 2002. Entropic recoil separation of long DNA molecules. Anal. Chem. 74:5169–5174.[Medline]
8. Turner, S. W. P., M. Cabodi, and H. G. Craighead. 2002. Confinement-induced entropic recoil of single DNA molecules in a nanofluidic structure. Phys. Rev. Lett. 88:128103.[CrossRef][Medline]
9. Bakajin, O., T. A. J. Duke, J. Tegenfeldt, C. F. Chou, S. S. Chan, R. H. Austin, and E. C. Cox. 2001. Separation of 100-kilobase DNA molecules in 10 seconds. Anal. Chem. 73:6053–6056.[Medline]
10. Chang, H., F. Kosari, G. Andreadakis, M. A. Alam, G. Vasmatzis, and R. Bashir. 2004. DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels. Nano Lett. 4:1551–1556.[CrossRef]
11. Heng, J. B., C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. 2004. Sizing DNA using a nanometer-diameter pore. Biophys. J. 87:2905–2911.
12. Li, J. L., M. Gershow, D. Stein, E. Brandin, and J. A. Golovchenko. 2003. DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2:611–615.[CrossRef][Medline]
13. Storm, A. J., C. Storm, J. H. Chen, H. Zandbergen, J. F. Joanny, and C. Dekker. 2005. Fast DNA translocation through a solid-state nanopore. Nano Lett. 5:1193–1197.[CrossRef][Medline]
14. Li, J., D. Stein, C. McMullan, D. Branton, M. J. Aziz, and J. A. Golovchenko. 2001. Ion-beam sculpting at nanometre length scales. Nature. 412:166–169.[CrossRef][Medline]
15. Reisner, W., K. J. Morton, R. Riehn, Y. M. Wang, Z. N. Yu, M. Rosen, J. C. Sturm, S. Y. Chou, E. Frey, and R. H. Austin. 2005. Statics and dynamics of single DNA molecules confined in nanochannels. Phys. Rev. Lett. 94:196101.[CrossRef][Medline]
16. Tegenfeldt, J. O., C. Prinz, H. Cao, S. Chou, W. W. Reisner, R. Riehn, Y. M. Wang, E. C. Cox, J. C. Sturm, P. Silberzan, and R. H. Austin. 2004. The dynamics of genomic-length DNA molecules in 100-nm channels. Proc. Natl. Acad. Sci. USA. 101:10979–10983.
17. Riehn, R., M. C. Lu, Y. M. Wang, S. F. Lim, E. C. Cox, and R. H. Austin. 2005. Restriction mapping in nanofluidic devices. Proc. Natl. Acad. Sci. USA. 102:10012–10016.
18. Ueda, M., T. Hayama, Y. Takamura, Y. Horiike, T. Dotera, and Y. Baba. 2004. Electrophoresis of long deoxyribonucleic acid in curved channels: the effect of channel width on migration dynamics. J. Appl. Phys. 96:2937–2944.[CrossRef]
19. de Gennes, P. G. 1979. Scaling Concepts in Polymer Physics. Cornell University Press, Ithaca, NY.
20. Chen, P., J. J. Gu, E. Brandin, Y. R. Kim, Q. Wang, and D. Branton. 2004. Probing single DNA molecule transport using fabricated nanopores. Nano Lett. 4:2293–2298.[CrossRef]
21. Bakajin, O. B., T. A. J. Duke, C. F. Chou, S. S. Chan, R. H. Austin, and E. C. Cox. 1998. Electrohydrodynamic stretching of DNA in confined environments. Phys. Rev. Lett. 80:2737–2740.[CrossRef]
22. Perkins, T. T., D. E. Smith, R. G. Larson, and S. Chu. 1995. Stretching of a single tethered polymer in a uniform-flow. Science. 268:83–87.
23. Sischka, A., K. Toensing, R. Eckel, S. D. Wilking, N. Sewald, R. Ros, and D. Anselmetti. 2005. Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophys. J. 88:404–411.
24. Stigter, D. 2002. Wall effects on DNA stretch and relaxation. Biophys. Chem. 101:447–459.[CrossRef][Medline]
25. Schellman, J. A., and D. Stigter. 1977. Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA. Biopolymers. 16:1415–1434.[CrossRef][Medline]
26. Gao, Q. F., and E. S. Yeung. 1998. A matrix for DNA separation: genotyping and sequencing using poly(vinylpyrrolidone) solution in uncoated capillaries. Anal. Chem. 70:1382–1388.[Medline]
27. Kang, S. H., M. R. Shortreed, and E. S. Yeung. 2001. Real-time dynamics of single-DNA molecules undergoing adsorption and desorption at liquid-solid interfaces. Anal. Chem. 73:1091–1099.[Medline]
28. Smith, S. B., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA-molecules by using magnetic beads. Science. 258:1122–1126.
29. Campbell, L. C., M. J. Wilkinson, A. Manz, P. Camilleri, and C. J. Humphreys. 2004. Electrophoretic manipulation of single DNA molecules in nanofabricated capillaries. Lab Chip. 4:225–229.[CrossRef][Medline]
30. Brochard, F., and P. G. de Gennes. 1977. Dynamics of confined polymer-chains. J. Chem. Phys. 67:52–56.[CrossRef]
31. Schaefer, D. W., J. F. Joanny, and P. Pincus. 1980. Dynamics of semiflexible polymers in solution. Macromolecules. 13:1280–1289.
32. Reccius, C. H., J. T. Mannion, J. D. Cross, and H. G. Craighead. 2005. Compression and free expansion of single DNA molecules in nanochannels. Phys. Rev. Lett. 95:268101.
33. Bueche, F. 1962. Physical Properties of Polymers. Interscience, New York, NY.
34. Smith, D. E., S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, and C. Bustamante. 2001. The bacteriophage phi 29 portal motor can package DNA against a large internal force. Nature. 413:748–752.[CrossRef][Medline]
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wide. The wall separating the two channels is 
wide. (C) Closer view of a nanochannel entrance. Floor roughness is 
and is attributed to the etching process.
the molecule is stretched while being driven with 21 V/cm from the microchannel (x < 0) into the nanochannel (x > 0). It is then allowed to sit in the nanochannel and contract until it reaches its equilibrium length. At 
a 0.5 V/cm pulse moves the molecule to the channel entrance (a). A small part straddles the interface and the molecule begins to recoil from the nanochannel into the microchannel. At 
DNA is driven partially into channel with a 
which is the measurement value at 
results in 
and 
Both experiments are done with the same molecule. The curves were fit with the appropriate model (
for the pure recoil event and 
for the combined process. The strand was stretched by 18% in the combined process and relaxed with a time constant of 
and 
which are equal to within the measurement error.