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From the Cover
BIOPHYSICS
The dynamics of genomic-length DNA molecules in 100-nm channels







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*Department of Physics, Lund University, SE-221 00 Lund, Sweden; Departments of
Electrical Engineering,
Physics, and
Molecular Biology, Princeton University, Princeton, NJ 08544; and ¶Institut Curie, Centre National de la Recherche Scientifique, 75231 Paris, France
Contributed by Robert H. Austin, June 2, 2004
| Abstract |
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We show that genomic-length DNA molecules imaged in nanochannels have an extension along the channel that scales linearly with the contour length of the polymer, in agreement with the scaling arguments developed by de Gennes for self-avoiding confined polymers. This fundamental relationship allows us to measure directly the contour length of single DNA molecules confined in the channels, and the statistical analysis of the dynamics of the polymer in the nanochannel allows us to compute the SD of the mean of the extension. This statistical analysis allows us to measure the extension of
DNA multimers with a 130-nm SD in 1 min.
Confinement elongation of genomic-length DNA has several advantages over alternative techniques for extending DNA, such as flow stretching and/or stretching relying on a tethered molecule. Confinement elongation does not require the presence of a known external force because a molecule in a nanochannel will remain stretched in its equilibrium configuration, and hence, the mechanism is in equilibrium. Second, it allows for continuous measurement of length.
Some fundamental statistical mechanical problems are associated with confinement of a polymer in a channel whose width D is much less than the radius of gyration of the unconfined polymer, such as (i) the dependence of the end-to-end length Lz of the confined polymer on the length L of the polymer and (ii) the dependence of the effective spring constant k of the confined polymer on the length L. The spring constant sets the scale of end-to-end length fluctuations for the confined polymer because of thermal effects. For the measurement process, an understanding of the relaxation time
is also crucial. A key element for understanding these questions is the influence of the self-avoiding nature of random walk of the polymer in the channel, as we show in Fig. 1.
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(pL)1/2. Thus, self-avoidance for a freely coiled polymer has the following two effects: it adds a weak dependence on the molecule width and it "puffs out" the coil slightly by giving rise to a stronger dependence on the contour length. These equations are, in fact, roughly in agreement with existing data for freely coiled DNA (5). Benzothiazolium-4-quinolinium dimer (TOTO-1)-dyed DNA molecules in the range of 3094.36 kbp are well fit by the form Rg = 80 nm·n[kbp]0.6. Compare this experimentally measured prefactor to the prefactor predicted by the FloryPincus result, which turns out to be
90 nm if we use a DNA diameter of 2 nm, a persistence length of 60 nm (6), and a base pair spacing of 0.34 nm (7).
Things change dramatically if the polymer is confined in a channel whose width D is less than its free-solution radius of gyration Rg. Self-avoidance increases the scaling exponent for the contour length because the polymer is prevented from back-folding. As de Gennes demonstrated (8), self-avoidance effectively divides the confined polymer into a series of noninterpenetrating blobs, distributing the polymer mass along the channel in such a way that the monomer density is uniform. Consequently, the extension of the polymer in the channel Lz must scale linearly with the contour length L. Assuming that the rms end-to-end length of each blob follows the FloryPincus scaling, de Gennes showed that
![]() | [1] |
Note that this formula gives us a numerical estimate of how much a DNA molecule should stretch in a nanochannel, given that the stretching is purely due to self-exclusion. For example, in a 100-nm-wide channel, we would expect an extension factor, defined as the ratio
= Lz/L, of
0.20; in a 400-nm-wide channel, we would expect
0.15. It is not clear, however, that the de Gennes theory actually holds in the regime in which the channel width is on the order of or less than the persistence length, and hence we do not attempt to predict extension factors for channels <100 nm in width.
The polymer extension also exhibits thermal fluctuations
Lz around the mean value Lz. Fluctuations set the lower bound for the error in a single "snapshot" of the polymer extension. The de Gennes scaling theory can be adopted to predict how the rms fluctuation
should scale with L and D. We use the free energy of a confined polymer, also predicted by the de Gennes theory, to derive an effective spring constant k for small fluctuations around Lz. We find that
![]() | [2] |
The rms length variance
is then given by the following equation:
![]() | [3] |
The SD of
, and defining the resolving power
as the ratio Lz/
t, we obtain the following equation:
![]() | [4] |
Thus, we expect
to increase with the square root of the length of the polymer L, and we should expect a greater resolving power for narrower channels.
Averaging of independent measurements of Lz allows one to compute the SD of the mean length Lz and, thus, achieve even higher resolution. In order for a measurement to be independent from a previous measurement, it is necessary to wait a time twait longer than the mean relaxation time of the length fluctuations. The de Gennes theory can be used to show how the polymer relaxation time should scale with the channel width and length (9). De Gennes argued that the friction factor of the chain can be written as follows:
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Lz, where
is the viscosity of the solvent. The relaxation time for the lowest vibrational mode should scale as
/k, so we expect the following:
![]() | [5] |
This formula can be used to make a direct numerical estimate of the relaxation time of confined DNA. For
-DNA, assuming a channel diameter of 100 nm and a buffer viscositity of 1 mPa, we get a relaxation time of
1.6 s.
| Experimental Methods |
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-ladder consisting of concatemers of the 48.5-kbp-long
monomer (cI857 ind1 Sam7) embedded in low-melting-point agarose (product no. N0340S, New England Biolabs) as a DNA standard to test the feasibility of the nanochannel technique (Fig.3). The total contour length of a
monomer is 16.3 µm (12). The intercalating dye at our concentration increases the contour length to 22 µm (1315). The DNA molecules were extracted from the gel plug directly on the chip by using electrophoresis from a 10-mm3 piece of gel. When the molecules were extracted from the gel, a second set of electrodes was used to move molecules into the nanochannels.
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-ladder DNA was moved by electrophoresis into the imprinted channel array, the electrophoretic field was turned off, and 100-ms-duration frames from the camera were captured to memory. Fig. 4 shows a typical frame capture. The intensity I(z) of the elongated molecule was assumed to be a convolution of a step function Io of length Lz, with a Gaussian point-spread function
, yielding the following fitting function:
![]() | [6] |
where Erf is the error function and Lz and
o are fitting parameters denoting the true end-to-end distance and the point-spread function resolution of the optics, respectively. The resolution
o of the x60 numerical aperture 1.4 oil-immersion objective was determined by curve fitting to be 0.4 µm. An example of such a fit is shown in Fig. 5.
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| Results and Discussion |
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-DNA dyed with benzothiazolium-4-quinolinium dimer (TOTO-1)] (14) and Lz = 8 µm, the extension factor is
= 0.36 for monomers in 100-nm-wide channels. Ligation numbers of n = 5, 6, 7, 8, 18, and 24 were assigned to the additional peaks under the assumption that a
monomer in a 100-nm-wide nanochannel has a end-to-end length Lz of 8 µm. The linear relation between Lz of the observed histogram maxima for n = 14, as shown in Fig. 7, indicates that Lz
L, as predicted by the de Gennes theory for self-avoiding confined polymers (8).
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o of Eq. 6 is not the limit for single-molecule techniques because the uncertainty in the ensemble average (i.e., the SD of the mean) is not limited by the width of the point-spread function
o of Eq. 6. By collecting enough photons, the location of a point source of light can be determined to arbitrary precision (16, 17). We do not look at point sources of light here but, rather, extended molecules. In this case, thermal fluctuations of the end-to-end distance of the molecule allow us to overcome the pixelation error that is inherent in any digital technology for imaging. Thus, the SD of the mean end-to-end distance of a single molecule can, in principle, be made arbitrarily small.
The fluctuations set the error in a single snapshot of the polymer extension. We first test the predictions of Eq. 3, namely, that the SD
t of the length of a confined molecule should vary as the square root of the contour length L. Fig. 8 gives a plot of the observed SD of single molecules of known length L as a length fit to an L1/2 length dependence. The SD of the mean extension
Lz
of a given molecule should scale as
after M independent measurements, where the
t refers to the SD due to thermal fluctuations of the individual molecule and is shown in Fig. 8. This analysis allows us to determine the mean length
Lz
of a molecule in a nanochannel to arbitrary precision simply by making enough measurements. For example, in Fig. 9 we show a histogram made of measurements of the fluctuating end-to-end distance of a single confined
monomer. A Gaussian fit yields a
t of 0.6 µm. After 20 measurements, or a measurement time on the order of 1 min, the SD of the mean extension (8.38 µm) is ±0.15 µm. This means that we know the extension of the
monomer to an accuracy of ±400 bp within 1 min of observation.
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| Conclusions |
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| Acknowledgements |
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|| To whom correspondence should be addressed. E-mail: austin{at}princeton.edu.
© 2004 by The National Academy of Sciences of the USA
| References |
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