Conformation and Dynamics of DNA Confined in Slitlike Nanofluidic Channels

Abstract

Using laser fluorescence microscopy, we study the shape and dynamics of individual DNA molecules in slitlike nanochannels confined to a fraction of their bulk radius of gyration. With a confinement size spanning 2 orders of magnitude, we observe a transition from the de Gennes regime to the Odijk regime in the scaling of both the radius of gyration and the relaxation time. The radius of gyration and the relaxation time follow the predicted scaling in the de Gennes regime, while, unexpectedly, the relaxation time shows a sharp decrease in the Odijk regime. The radius of gyration remains constant in the Odijk regime. Additionally, we report the first measurements of the effect of confinement on the shape anisotropy. DOI: 10.1103/PhysRevLett.101.108303 PACS numbers: 82.35.Àx, 87.80.Fe A detailed understanding of the static and dynamic properties of DNA in confined environments is essential for the design of devices for single-molecule analysis and manipulation [1,2]. In addition, it provides better insight in natural processes like DNA packaging in viruses [3] and DNA segregation in bacteria [4]. In bulk, DNA molecules form random coils that are sphere shaped on average, with radius of gyration R bulk . Upon confining DNA to a nanochannel, different regimes of confinement can be distinguished. The important length scales are the bulk radius R bulk , the height of the confining channel h, and the persistence length of the molecule a. In the de Gennes regime, where 2a < h < 2R bulk , the molecule still has threedimensional orientational freedom at a short length scale, forming three-dimensional blobs, while at larger scales the molecule is flattened; see Fig. 1(c). The effect of confinement on the diffusion constant in this regime has been investigated optically in slitlike nanochannels [5]. Using the same technique, the extension, diffusion constant, and relaxation time were measured in tubelike confinement [6,7]. When the height of the nanochannel reaches the persistence length (h % 2a), the orientation of the molecule becomes restricted even at the shortest length scales, drastically affecting the response of the molecule to confinement. The onset of this Odijk regime has been reported for tubelike nanochannels [6], while truly two-dimensional polymers were investigated much earlier, by adsorbing them on a lipid membrane [8]. However, an assessment of the radius of gyration of DNA in slitlike confinement, which is crucial for size separation schemes [5,9], has been lacking so far.In this Letter, we present measurements of the radius of gyration and shape anisotropy of DNA confined to slitlike nanochannels varying in height from 33 nm to 1:3 m. Our measurements show three regimes of DNA conformations: compression, elongation, and saturation. At h % 100 nm, we see a strong discontinuity in the scaling of the radius of gyration and the relaxation time, which we interpret as the transition from the de Gennes to the Odijk regime.We studied -phage DNA (48 kb, double-strand), stained with YOYO-1 (Molecular Probes), a...

Wall depletion length of a channel-confined polymer

“…DNA has played a key role in the experimental tests of theories of a polymer confined to a slit [1][2][3][4][5][6][7][8][9][10][11][12][13][14] or a channel [15][16][17][18][19][20][21][22][23][24][25][26][27], in particular the models by de Gennes and coworkers for weak confinement [28,29] and Odijk for strong confinement [30,31]. The key results of this body of work have been summarized in several recent reviews [32][33][34].…”

Numerical Study of Linear and Circular Model DNA Chains Confined in a Slit: Metric and Topological Properties

“…In fact, the width of presently-available confining nano-devices (a channel, a slit, a pit etc.) can be set to compete with one or more of the characteristic lengths of a DNA molecule and hence allow for probing different physical regimes [8,[11][12][13][14][15][16][17][18].…”

“…To the best of our knowledge there exist only * Electronic address: michelet@sissa.it † Electronic address: orlandini@pd.infn.it a limited number of experimental and numerical studied of the size and shape of DNA molecules in nanoslits [8,18,[31][32][33]. These seminal studies have addressed the interesting issue of whether multiple scaling regimes exist in linear DNA filaments inside slits.…”

Size and shape of excluded volume polymers confined between parallel plates

“…A number of single molecule fluorescence microscopy studies have recently investigated the structure and dynamics of confined DNA trapped between parallel * Electronic address: chaudhuri@amolf.nl † Electronic address: mulder@amolf.nl plates [8][9][10][11] or within cylindrical geometries [12][13][14] with the confining dimensions typically of the order of, or smaller than, the bulk radius of gyration of the polymer.…”

“…In particular Bonthuis et al [10] have recently observed DNA confined to parallel-plate nanochannels, showing among others an interesting non-monotonic variation of the two-dimensional (2d) projected radius of gyration with the distance between channel walls.…”