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.T he location of landmark restriction sites on chromosomallength DNA molecules is a powerful way to guarantee that the assembled DNA sequences in shotgun DNA sequencing represent the native genome faithfully. The restriction sites can be determined by measuring the length of restriction fragments by gel electrophoresis (1). Alternatively, they can be located by using optical mapping of stretched DNA molecules trapped on a surface (2). To measure the contour length of a single molecule by using optical techniques directly, it is necessary to extend the polymer such that a one-to-one mapping can be established between the spatial position along the polymer and position within the genome.Confinement elongation of genomic-length DNA has several advantages over alternative techniques for extending DNA, such as flow stretching and͞or 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 L z 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 selfavoiding nature of random walk of the polymer in the channel, as we show in Fig. 1.The effect of self-avoidance on flexible polymers that are freely coiled in solution was first understood by Flory (3) and later generalized to the semiflexible case by Schaefer et al. (4). The rms radius of gyration R g of a self-avoiding persistent polymer in solution scales according to Flory-Pincus with the persistence length p, molecule width w, and contour length L, such that (pw) 1/5 L 3/5 . Compare this form with the result expected for an ideal, non-self-avoiding polymer R g Ϸ (pL) 1/2 . Thus, self-av...

Miniaturization to the micrometer and nanometer scale opens up the possibility to probe biology on a length scale where fundamental biological processes take place, such as the epigenetic and genetic control of single cells. To study single cells the necessary devices need to be integrated on a single chip; and, to access the relevant length scales, the devices need to be designed with feature sizes of a few nanometers up to several micrometers. We will give a few examples from the literature and from our own research in the field of miniaturized chip-based devices for DNA analysis, including dielectrophoresis for purification of DNA, artificial gel structures for rapid DNA separation, and nanofluidic channels for direct visualization of single DNA molecules.

Dissociated sensory neurons were cultured on epitaxial gallium phosphide (GaP) nanowires grown vertically from a gallium phosphide surface. Substrates covered by 2.5 microm long, 50 nm wide nanowires supported cell adhesion and axonal outgrowth. Cell survival was better on nanowire substrates than on planar control substrates. The cells interacted closely with the nanostructures, and cells penetrated by hundreds of wires were observed as well as wire bending due to forces exerted by the cells.

Nanowires are commonly used as tools for interfacing living cells, acting as biomolecule-delivery vectors or electrodes. It is generally assumed that the small size of the nanowires ensures a minimal cellular perturbation, yet the effects of nanowires on cell migration and proliferation remain largely unknown. Fibroblast behaviour on vertical nanowire arrays is investigated, and it is shown that cell motility and proliferation rate are reduced on nanowires. Fibroblasts cultured on long nanowires exhibit failed cell division, DNA damage, increased ROS content and respiration. Using focused ion beam milling and scanning electron microscopy, highly curved but intact nuclear membranes are observed, showing no direct contact between the nanowires and the DNA. The nanowires possibly induce cellular stress and high respiration rates, which trigger the formation of ROS, which in turn results in DNA damage. These results are important guidelines to the design and interpretation of experiments involving nanowire-based transfection and electrical characterization of living cells.

We used epitaxially grown monodisperse nanowire arrays to measure cellular forces with a spatial resolution of 1 mum. Nerve cells were cultured on the array and cellular forces were calculated from the displacement of the nanowire tips. The measurements were done in situ on live cells using confocal microscopy. Forces down to 15 pN were measured on neural growth cones, showing that this method can be used to study the fine details of growth-cone dynamics.

We have established long-term cultures of postnatal retinal cells on arrays of gallium phosphide nanowires of different geometries. Rod and cone photoreceptors, ganglion cells and bipolar cells survived on the substrates for at least 18 days in vitro. Glial cells were also observed, but these did not overgrow the neuronal population. On nanowires, neurons extended numerous long and branched neurites that expressed the synaptic vesicle marker synaptophysin. The longest nanowires (4 μm long) allowed a greater attachment and neurite elongation and our analysis suggests that the length of the nanowire per se and/or the adsorption of biomolecules on the nanowires may have been important factors regulating the observed cell behavior. The study thus shows that CNS neurons are amenable to gallium phosphide nanowires, probably as they create conditions that more closely resemble those encountered in the in vivo environment. These findings suggest that gallium phosphide nanowires may be considered as a material of interest when improving existing or designing the next generation of implantable devices. The features of gallium phosphide nanowires can be precisely controlled, making them suitable for this purpose.

We demonstrate high-fidelity guidance of axons using rows of nanowires. The axons are prevented from crossing the rows, making it possible to guide and sort a large number of axons as opposed to when chemical patterns are used. Focal adhesion forms at the nanowires establishing a possible site of information transfer between the surface and the cells. Rows of gallium phosphide (GaP) nanowires were epitaxially grown on GaP(111) substrates in patterns defined by electron beam lithography.

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