Jonas Nyvold Pedersen

DNA confinement in nanochannels: physics and biological applications

DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement--including the effect of varying ionic strength--and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device

We show how a bird’s-eye view of genomic structure can be obtained at ∼1-kb resolution from long (∼2 Mb) DNA molecules extracted from whole chromosomes in a nanofluidic laboratory-on-a-chip. We use an improved single-molecule denaturation mapping approach to detect repetitive elements and known as well as unique structural variation. Following its mapping, a molecule of interest was rescued from the chip; amplified and localized to a chromosome by FISH; and interrogated down to 1-bp resolution with a commercial sequencer, thereby reconciling haplotype-phased chromosome substructure with sequence.

Tunneling through nanosystems: Combining broadening with many-particle states

We suggest an approach for transport through finite systems based on the Liouville equation. By working in a basis of many-particle states for the finite system, Coulomb interactions are taken fully into account and correlated transitions by up to two different contact states are included. This latter extends standard rate equation models by including level-broadening effects. The main result of the paper is a general expression for the elements of the density matrix of the finite size system, which can be applied whenever the eigenstates and the couplings to the leads are known. The approach works for arbitrary bias and for temperatures above the Kondo temperature. We apply the approach to standard models and good agreement with other methods in their respective regime of validity is found.

Coherent transport through an interacting double quantum dot: Beyond sequential tunneling

Various causes for negative differential conductance in transport through an interacting double quantum dot are investigated. Particular focus is given to the interplay between the renormalization of the energy levels due to the coupling to the leads and the decoherence of the states. The calculations are performed within a basis of many-particle eigenstates and we consider the dynamics given by the von Neumann equation taking into account also processes beyond sequential tunneling. A systematic comparison between the levels of approximation and also with different formalisms is performed. It is found that the current is qualitatively well described by sequential processes as long as the temperature is larger than the level broadening induced by the contacts.

Probing the invasiveness of prostate cancer cells in a 3D microfabricated landscape

The metastatic invasion of cancer cells from primary tumors to distant ecological niches, rather than the primary tumors, is the cause of much cancer mortality [Zhang QB, et al. (2010) Int J Cancer 126:2534–2541; Chambers AF, Goss PE (2008) Breast Cancer Res 10:114]. Metastasis is a three-dimensional invasion process where cells spread from their site of origin and colonize distant microenvironmental niches. It is critical to be able to assess quantitatively the metastatic potential of cancer cells [Harma V, et al. (2010) PLoS ONE 5:e10431]. We have constructed a microfabricated chip with a three-dimensional topology consisting of lowlands and isolated square highlands (Tepuis), which stand hundreds of microns above the lowlands, in order to assess cancer cell metastatic potential as they invade the highlands. As a test case, the invasive ascents of the Tepui by highly metastatic PC-3 and noninvasive LNCaP prostate cancer cells were used. The vertical ascent by prostate cancer cells from the lowlands to the tops of the Tepui was imaged using confocal microscopy and used as a measure of the relative invasiveness. The less-metastatic cells (LNCaP) never populated all available tops, leaving about 15% of them unoccupied, whereas the more metastatic PC-3 cells occupied all available Tepuis. We argue that this distinct difference in invasiveness is due to contact inhibition.

Correlation-induced conductance suppression at level degeneracy in a quantum dot.

The large, level-dependent g factors in an InSb nanowire quantum dot allow for the occurrence of a variety of level crossings in the dot. While we observe the standard conductance enhancement in the Coulomb blockade region for aligned levels with different spins due to the Kondo effect, a vanishing of the conductance is found at the alignment of levels with equal spins. This conductance suppression appears as a canyon cutting through the web of direct tunneling lines and an enclosed Coulomb blockade region. In the center of the Coulomb blockade region, we observe the predicted correlation-induced resonance. Our findings are supported by numerical and analytical calculations.

Optical mapping of single-molecule human DNA in disposable, mass-produced all-polymer devices

We demonstrate all-polymer injection molded devices for optical mapping of denaturation–renaturation (DR) patterns on long, single DNA-molecules from the human genome. The devices have channels with ultra-low aspect ratio, only 110 nm deep while 20 μm wide, and are superior to the silica devices used previously in the field. With these polymer devices, we demonstrate on-chip recording of DR images of DNA-molecules stretched to more than 95% of their contour length. The stretching is done by opposing flows Marie et al (2013 Proc. Natl Acad. Sci. USA 110 4893–8). The performance is validated by mapping 20 out of 24 Mbp-long DNA fragments to the human reference genome. We optimized fabrication of the devices to a yield exceeding 95%. This permits a substantial economies-of-scale driven cost-reduction, leading to device costs as low as 3 USD per device, about a factor 70 lower than the cost of silica devices. This lowers the barrier to a wide use of DR mapping of native, megabase-size DNA molecules, which has a huge potential as a complementary method to next-generation sequencing.

A diagrammatic description of the equations of motion, current and noise within the second-order von Neumann approach

We investigate the second-order von Neumann approach from a diagrammatic point of view and demonstrate its equivalence with the resonant tunneling approximation. The investigation of higher order diagrams shows that the method correctly reproduces the equation of motion for the single-particle reduced density matrix of an arbitrary non-interacting many-body system. This explains why the method reproduces the current exactly for such systems. We go on to show, however, that diagrams not included in the method are needed to calculate exactly higher cumulants of the charge transport. This thorough comparison sheds light on the validity of all these self-consistent second-order approaches. We analyze the discrepancy between the noise calculated by our method and the exact Levitov formula for a simple non-interacting quantum dot model. Furthermore, we study the noise of the canyon of current suppression in a two-level dot, a phenomenon that requires the inclusion of electron-electron interaction as well as higher order tunneling processes. (Less)

Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

We investigate the coalescence of two DNA bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.

Modeling of cotunneling in quantum dot systems

Transport through nanosystems is treated within the second-order von Neumann approach. This approach bridges the gap between rate equations which neglect level broadening and cotunneling, and the transmission formalism, which is essentially based on the single-particle picture thereby treating many-particle interactions on an approximate level. Here we provide an alternative presentation of the method in order to clarify the underlying structure. Furthermore we apply it to the problem of cotunneling. It is shown that both elastic and inelastic cotunneling can be described quantitatively, while the transmission approach with a mean-field treatment of the interaction provides an artificial bistability.