DNA Translocation Dynamics Research Articles

Characterization of DNA-Nanopore Interactions by Molecular Dynamics

A major challenge in using solid-state nanopores for DNA detection and sequencing is the molecular selectivity and sensitivity resolution through proper control of DNA-nanopore interface. This paper explores the interaction mechanisms between DNA and nanopores through molecular dynamics simulations. The DNA translocation dynamics through nanopores of various diameters and under various applied biasvoltages are characterized. Such property-function relationship can be used for the optimal designs of the lab-on-chip DNA diagnostic devices.

Escape Dynamics of DNA from a Nanopore under the Influence of an AC Bias

Monitoring the escape of ssDNA from a protein nanopore provides new insight into the dynamics of DNA translocation and a direct means of measuring progress of the escape. New instrumentation has been developed that allows for simultaneous application of an AC and DC bias across a protein nanopore. Initial measurements with the system have focused on the capture and release of ssDNA tails attached to DNA hairpins. Polynucleotide tails attached to 24 nucleotide DNA hairpins are threaded into the beta-barrel of an alpha-hemolysin channel under the influence of a strong DC driving voltage. After the capture of the hairpin, the DC voltage is turned off and the subsequent escape of the hairpin is directly monitored via an AC bias. Escape times were measured as a function of AC amplitude (20 to 250 mV), AC frequency (60-200 kHz), DC drive voltage (0 to 100 mV), and temperature (-10°C to 20°C). The applied AC voltage has been shown to play a significant role in the DNA/nanopore interaction. The results are well described by a one-dimensional diffusion model across an asymmetric, periodic potential.

Single-Molecule Studies of Viral DNA Packaging with Optical Tweezers: Molecular Motor Function and DNA Confinement

A key step in the assembly of many viruses is the packaging of double-stranded DNA into a procapsid shell by the action of an ATP-powered molecular motor. We use optical tweezers to measure the packaging of single DNA molecules into single viral proheads in real time. We can measure DNA binding and initiation of translocation, DNA translocation dynamics, force generated by the motor, and can infer the forces resisting DNA confinement. We have developed approaches to study three different viruses: Bacteriophages phi29, lambda, and T4. These viruses have different capsid sizes and shapes, genome lengths, and structural and biochemical differences in their packaging motors, resulting in differing DNA packaging dynamics. All three motors translocate DNA processively and generate high forces exceeding 50 piconewtons, but the motor velocities vary 10-fold. In the lambda system we have found evidence for an effect of procapsid expansion on the packaging dynamics and evidence for force-induced capsid rupture in the absence of a putative stabilizing protein. We are currently investigating motor structure-function relationships by analyzing effects of point mutations. Amongst the mutants we have identified are one that exhibits a motor velocity roughly one-tenth that of the wild type, and one that exhibits increased pausing and slipping. These studies shed light on the various functional domains of viral packaging motors.

Dynamics of DNA translocation through an attractive nanopore

We investigate the dynamics of single-stranded DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases A and C, having different base-pore interactions, e.g., a strong (weak) attractive force between the pore and the base A (C) inside the pore. From a series of studies on hetero-DNAs with repeat units AmCn, we find that the translocation time decreases exponentially as a function of the volume fraction fC of the base C. For longer A sequences with fC<or=0.5, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length N with repeat units AmCn, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of m, n, and N, respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection.

DNA Translocation Governed by Interactions with Solid-State Nanopores

We investigate the voltage-driven translocation dynamics of individual DNA molecules through solid-state nanopores in the diameter range 2.7–5 nm. Our studies reveal an order of magnitude increase in the translocation times when the pore diameter is decreased from 5 to 2.7 nm, and steep temperature dependence, nearly threefold larger than would be expected if the dynamics were governed by viscous drag. As previously predicted for an interaction-dominated translocation process, we observe exponential voltage dependence on translocation times. Mean translocation times scale with DNA length by two power laws: for short DNA molecules, in the range 150–3500 bp, we find an exponent of 1.40, whereas for longer molecules, an exponent of 2.28 dominates. Surprisingly, we find a transition in the fraction of ion current blocked by DNA, from a length-independent regime for short DNA molecules to a regime where the longer the DNA, the more current is blocked. Temperature dependence studies reveal that for increasing DNA lengths, additional interactions are responsible for the slower DNA dynamics. Our results can be rationalized by considering DNA/pore interactions as the predominant factor determining DNA translocation dynamics in small pores. These interactions markedly slow down the translocation rate, enabling higher temporal resolution than observed with larger pores. These findings shed light on the transport properties of DNA in small pores, relevant for future nanopore applications, such as DNA sequencing and genotyping.

The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores

In this work, we investigate the effect of hydrodynamic interactions on the dynamics of DNA translocation through micropores. We simulate DNA as a bead-spring chain and use a lattice Boltzmann method to simulate the flow field that arises from the motion of the molecule. We investigate the free-draining entrance of DNA to the pore by diffusion and find that, consistent with experiments, molecules have a higher probability of entering the pore from one end. We then consider the electric-field driven translocation of 21-210 microm DNA with and without hydrodynamic interactions. Consistent with experiments, we study translocation events that are much shorter than the relaxation time of DNA. We find that the effect of hydrodynamic interactions on this process is to cause different regions of a molecule, other than the ones pulled by voltage or chain connectivity into the pore, to move toward the pore. We quantify this effect and show that it is smaller than the difference in the translocation dynamics of chains that arises from different initial configurations of the molecules. A power-law scaling of translocation time with chain length is observed, with exponents of 1.28+/-0.03 and 1.31+/-0.03 in simulations with and without hydrodynamic interactions, respectively. Our results are in good agreement with recent translocation experiments conducted in small pores and show that, for the regime considered in this work, hydrodynamic interactions play a minor role in the relation of the translocation time to chain length. For fast translocation processes, the effect of hydrodynamic interactions is local and the main factor determining the dynamics of DNA is the initial configuration of the molecules.

Sequence Dependence of DNA Translocation through a Nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.