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Solid-state nanopores are promising tools for single molecule detection of both DNA and proteins. In this study, we investigate the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of such conically shaped pores. We studied how the geometry of a nanopore affects the detected ionic current signal of a translocating DNA molecule over a wide range of salt concentration. The blockade level in the ionic current depends on the translocation direction at a high salt concentration, and at lower salt concentrations we find a non-intuitive ionic current decrease and increase within each single event for the DNA translocations exiting from confinement. We use recently developed DNA rulers with markers and finite element calculations to explain our observations. Our calculations explain the shapes of the signals observed at all salt concentrations and show that the unexpected current decrease and increase are due to the competing effects of ion concentration polarization and geometric exclusion of ions. Our analysis shows that over a wide range of geometry, voltage and salt concentrations we are able to understand the ionic current signals of DNA in asymmetric nanopores enabling signal optimization in molecular sensing applications.
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Nanopores that exhibit ionic current rectification (ICR) behave like diodes, such that they transport ions more efficiently in one direction than the other. Conical nanopores have been shown to rectify ionic current, but only those with at least 500 nm in length exhibit significant ICR. Here, through the finite element method, we show how ICR of conical nanopores with length below 200 nm can be tuned by controlling individual charged surfaces i.e. inner pore surface (surface_inner), and exterior pore surfaces on the tip and base side (surface_tip and surface_base). The charged surface_inner and surface_tip can induce obvious ICR individually, while the effects of the charged surface_base on ICR can be ignored. The fully charged surface_inner alone could render the nanopore counterion-selective and induces significant ion concentration polarization in the tip region, which causes reverse ICR compared to nanopores with all surface charged. In addition, the direction and degree of rectification can be further tuned by the depth of the charged surface_inner. When considering the exterior membrane surface only, the charged surface_tip causes intra-pore ionic enrichment and depletion under opposite biases which results in significant ICR. Its effective region is within ~40 nm beyond the tip orifice. We also found that individual charged parts of the pore system contributed to ICR in an additive way due to the additive effect on the ion concentration regulation along the pore axis. With various combinations of fully/partially charged surface_inner and surface_tip, diverse ICR ratios from ~2 to ~170 can be achieved. Our findings shed light on the mechanism of ionic current rectification in ultra-short conical nanopores, and provide a useful guide to the design and modification of ultra-short conical nanopores in ionic circuits and nanofluidic sensors.
Nanopores in solid state membranes are a tool able to probe nanofluidic phenomena or can act as a single molecular sensor. They also have diverse applications in filtration, desalination or osmotic power generation. Many of these applications involve chemical, or hydrostatic pressure differences, which act on both the supporting membrane and the ion transport through the pore. By using pressure differences between the sides of the membrane, and an alternating current approach to probe ion transport, we investigate two distinct physical phenomena: the elastic deformation of the membrane through the measurment of strain at the nanopore, and the growth of ionic current rectification with pressure due to pore entrance effects.
The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using 1 microsecond molecular dynamics (MD) computer simulations. The peptide displays 71 alpha-helical structure without salt and destabilizes with the addition of NaCl in agreement with experiments of a somewhat longer version. It is mainly stabilized by direct and indirect (i+4)EK salt bridges between the Lys and Glu side chains and a concomitant backbone shielding mechanism. NaI is found to be a stronger denaturant than NaCl, while the potassium salts hardly show influence. Investigation of the molecular structures reveals that consistent with recent experiments Na+ has a much stronger affinity to side chain carboxylates and backbone carbonyls than K+, thereby weakening salt bridges and secondary structure hydrogen bonds. At the same time the large I- has a considerable affinity to the nonpolar alanine in line with recent observations of a large propensity of I- to adsorb to simple hydrophobes, and thereby assists Na+ in its destabilizing action. In the denatured states of the peptide novel long-lived (10-20 ns) loop-configurations are observed in which single Na+ ions and water molecules are hydrogen-bonded to multiple backbone carbonyls. In an attempt to analyze the denaturation behavior within the preferential interaction formalism, we find indeed that for the strongest denaturant, NaI, the protein is least hydrated. Additionally, a possible indication for protein denaturation might be a preferential solvation of the first solvation shell of the peptide backbone by the destabilizing cosolute (sodium).
We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. We observe a complex transition path from the initial state to the final state of the AND gate. This path is strongly influenced by non-ideal effects due to transient bubbles revealing undesired toeholds and thermal melting of whole strands. We have also characterized the bound and unbound kinetics of single strands, and in particular the kinetics of the total AND operation and the three distinct distinct DNA transitions that it is based on. We observe a exponential kinetic dependence on the toehold length of the competitive displacement operation, but that the gate operation time is only weakly dependent on both the toehold and adjacent domain length. Our gate displays excellent logical fidelity in three input states, and quite poor fidelity in the fourth input state. This illustrates how non-ideality can have very selective effects on fidelity. Simulations and detailed analysis such as those presented here provide molecular insights into strand displacement computation, that can be also be expected in chemical implementations.
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop formation, and salt effects. Using an iterative expression for the partition function that neglects pseudoknots, we calculate folding free energies and minimum free energy configurations based on the experimentally derived base pairing free energies. The configurational entropy of loop formation is modeled by the asymptotic expression -c ln m, where m is the length of the loop and c the loop exponent, which is an adjustable constant. Salt effects enter in two ways: first, we derive salt induced modifications of the free energy parameters for describing base pairing and, second, we include the electrostatic free energy for loop formation. Both effects are modeled on the Debye-Hueckel level including counterion condensation. We validate our theory for two different RNA sequences: For tRNA-phe, the resultant heat capacity curves for thermal denaturation at various salt concentrations accurately reproduce experimental results. For the P5ab RNA hairpin, we derive the global phase diagram in the three-dimensional space spanned by temperature, stretching force, and salt concentration and obtain good agreement with the experimentally determined critical unfolding force. We show that for a proper description of RNA melting and stretching, both salt and loop entropy effects are needed.
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