Visualizing the entire DNA from a chromosome in a single frame.

The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1 mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds.

Model for melting of confined DNA.

When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, in part caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behavior and that the effect of confinement is stronger than in the ideal case.

Fast size-determination of intact bacterial plasmids using nanofluidic channels.

We demonstrate how nanofluidic channels can be used as a tool to rapidly determine the number and sizes of plasmids in bacterial isolates. Each step can be automated at low cost, opening up opportunities for general use in microbiology labs.

Extension of nanoconfined DNA: Quantitative comparison between experiment and theory.

The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.

Diffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics.

We solve a nonequilibrium statistical-mechanics problem exactly, namely, the single-file dynamics of N hard-core interacting particles (the particles cannot pass each other) of size Delta diffusing in a one-dimensional system of finite length L with reflecting boundaries at the ends. We obtain an exact expression for the conditional probability density function rhoT(yT,t|yT,0) that a tagged particle T (T=1,...,N) is at position yT at time t given that it at time t=0 was at position yT,0. Using a Bethe ansatz we obtain the N -particle probability density function and, by integrating out the coordinates (and averaging over initial positions) of all particles but particle T , we arrive at an exact expression for rhoT(yT,t|yT,0) in terms of Jacobi polynomials or hypergeometric functions. Going beyond previous studies, we consider the asymptotic limit of large N , maintaining L finite, using a nonstandard asymptotic technique. We derive an exact expression for rhoT(yT,t|yT,0) for a tagged particle located roughly in the middle of the system, from which we find that there are three time regimes of interest for finite-sized systems: (A) for times much smaller than the collision time t<>taucoll but times smaller than the equilibrium time t<>taue , rhoT(yT,t|yT,0) approaches a polynomial-type equilibrium probability density function. Notably, only regimes (A) and (B) are found in the previously considered infinite systems.

Single-file diffusion in a box.

We study diffusion of (fluorescently) tagged hard-core interacting particles of finite size in a finite one-dimensional system. We find an exact analytical expression for the tagged particle probability density function using a Bethe ansatz, from which the mean square displacement is calculated. The analysis shows the existence of three regimes of drastically different behavior for short, intermediate, and large times. The results are in excellent agreement with stochastic simulations (Gillespie algorithm).

Electromagnetic response of a dipole-coupled ellipsoidal bilayer.

We derive an expression for the polarizability of an ellipsoidally shaped cell-like structure at field frequencies where membrane molecular resonances (vibrational and electronic) are important. We first present analytical results for the dielectric function of a flat, dipole coupled, bilayer consisting of molecules with one prominent resonance frequency. Due to the nature of the dipole coupling the dielectric function is different for the field being parallel or perpendicular to the bilayer normal with two new resonance frequencies omega=omega;(0 parallel) and omega=omega;(0 perpendicular ). We then combine this anisotropic bilayer dielectric function with the analytical solution of Gauss equation for an ellipsoid with an anisotropic coating (the coating dielectric function being different parallel and perpendicular to the coating normal) in order to find the polarizability of an ellipsoidal bilayer membrane. In particular, we find that for a thin-walled (compared to the size of the cell) membrane the resonance frequencies of the polarizability are the same as for a flat bilayer (independent of the cell shape). However, our analytic result for the geometric weights for the oscillator strengths is sensitive to the shape; the geometric weight for the omega=omega;(0 perpendicular ) (omega=omega;(0 parallel)) peak is largest when the external field is along the largest (smallest) axis. The geometric weights are shown to be constrained by three sum rules.

Ellipsoidal particles driven by intensity gradients through viscous fluids.

We investigate the drift velocity v(drift) of ellipsoidal polarizable particles (ellipsoids and coated ellipsoids), driven through a viscous fluid by an electric or electromagnetic field intensity gradient. At low Reynolds number and in the dipole approximation v(drift) is proportional to the square of the principal axis along the direction of motion multiplied by a form factor, which is weakly depending on the shape of the particle, and by a frequency and shape dependent factor f(omega). Near frequencies where the real part of epsilon (m)f(omega) changes sign ( epsilon (m) is the relative dielectric function of the medium in which the partcle is immersed), v(drift) is sensitive to the shape of the particle. We suggest that our results can be used for the experimental separation of neutral polarizable particles with respect to size or shape.