Helical Charge Distribution Research Articles

Lyotropic meso-phase behavior of supra-molecular nanotubes with helical charge distribution.

We report diverse meso-phase arrangements of supra-molecular nanotubes assembled by ionic benzene-1,3,5-tricarboxamide (BTA) molecules in water; their transition pathway and equilibrium structure are controlled by the helical structure. Besides, the different sensitivity to the condition of initial solutions is revealed for the final rectangular phase and the intermediate phase.

Role of geometrical shape in like-charge attraction of DNA.

While the phenomenon of like-charge attraction of DNA is clearly observed experimentally and in simulations, mean-field theories fail to predict it. Kornyshev et al. argued that like-charge attraction is due to DNA's helical geometry and hydration forces. Strong-coupling (SC) theory shows that attraction of like-charged rods is possible through ion correlations alone at large coupling parameters, usually by multivalent counterions. However for SC theory to be applicable, counterion-counterion correlations perpendicular to the DNA strands need to be sufficiently small, which is not a priori the case for DNA even with trivalent counterions. We study a system containing infinitely long DNA strands and trivalent counterions by computer simulations employing varying degrees of coarse-graining. Our results show that there is always attraction between the strands, but its magnitude is indeed highly dependent on the specific shape of the strand. While discreteness of the charge distribution has little influence on the attractive forces, the role of the helical charge distribution is considerable: charged rods maintain a finite distance in equilibrium, while helices collapse to close contact with a phase shift of π, in full agreement with SC predictions. The SC limit is applicable because counterions strongly bind to the charged sites of the helices, so that helix-counterion interactions dominate over counterion-counterion interactions. Thus DNA's helical geometry is not crucial for like-charge DNA attraction, but strongly enhances it, and electrostatic interactions in the strong-coupling limit are sufficient to explain this attraction.

Spin-Dependent Effects in Helical Molecular Systems with Rashba-Like Spin-Orbit Interaction

Strong spin-selective e ects have been recently observed in both photoemission and electrical transport experiments in biomolecular systems, opening fascinating possibilities for interfacing semiconductor and biomolecular systems to create highly e cient spintronics devices. From the theoretical and experimental point of view there are strong suggestions that molecular chirality is playing a crucial role. In this study we extend a previously formulated model (R. Gutierrez, E. Diaz, R. Naaman, G. Cuniberti, Phys. Rev. B 85, 081404 (2012)) describing the linear propagation of a charge with spin along the axis of a helical charge distribution. We explore di erent parameter regions and show that a strong negative spin polarization as observed in the previously mentioned experiments can be obtained with reasonable values of both the electronic coupling elements and the helical eld induced spin orbit interaction.

Cholesteric order in systems of helical Yukawa rods

We consider the interaction potential between two chiral rod-like colloids which consist of athin cylindrical backbone decorated with a helical charge distribution on the cylindersurface. For sufficiently slender helical rods a simple scaling expression is derived whichrelates the chiral ‘twisting’ potential to the microscopic properties of the particles, such asthe internal helical pitch, charge density and electrostatic screening parameter. To predictthe behaviour of the macroscopic cholesteric pitch of the fluid bulk phase we invoke asimple second-virial theory generalized to treat anisotropic states with weakly twisteddirector fields. It is shown that, while particles with weakly coiled helices always form acholesteric phase whose helical sense is commensurate with that of the internalhelix, more strongly coiled rods lead to the formation of a cholesteric state ofopposite sense. The correlation between the helical symmetry at the microscopic andmacroscopic scale is found to be very sensitive to the pitch of the Yukawa helix. Mixinghelical particles of sufficiently disparate length and internal pitch may give rise toa demixing of the uniform cholesteric phase into two fractions with a differentmacroscopic pitch. Our findings could be relevant to the interpretation of experimentalobservations in systems of cellulose and chitin microfibres, DNA and fd virus rods.

Counterion-mediated electrostatic interactions between helical molecules

We study the interaction of two cylinders with helical charge distribution mediated by neutralizing counterions, by analyzing the separation as well as the azimuthal angle dependence of the interaction force in the weak and strong coupling limit. While the azimuthal dependence of the interaction in the weak coupling limit is overall small and mostly negligible, the strong coupling limit leads to qualitatively new features of the interaction, among others also to an orientationally dependent optimal configuration that is driven by angular dependence of the correlation attraction. We investigate the properties of this azimuthal ordering in detail and compare it to existing results.

Lattice-Boltzmann Simulations of Ionic Current Modulation by DNA Translocation.

We present a numerical study of the effect of DNA translocation on the ionic current through a nanopore. We use a coarse-grained model to solve the electrokinetic equations at the Poisson-Boltzmann level for the microions, coupled to a lattice-Boltzmann equation for the solvent hydrodynamics. In most cases, translocation leads to a reduction in the ionic current. However, at low salt concentrations (large screening lengths) we find ionic current enhancement due to translocation. In an unstructured pore, translocation of the helical charge distribution of the DNA has no effect on the ionic current. However, if a localized charge probe is placed on the wall of the nanopore, we observe ionic current modulations that, though weak, should be experimentally observable.

Structure of DNA toroids and electrostatic attraction of DNA duplexes

DNA–DNA electrostatic attraction is considered as the driving force for the formation ofDNA toroids in the presence of DNA condensing cations. This attraction comes from theDNA helical charge distribution and favours hexagonal toroidal cross-sections. The latter isin agreement with recent cryo-electron microscopy studies on DNA condensed with cobalthexammine. We treat the DNA–DNA interactions within the modern theory ofelectrostatic interaction between helical macromolecules. The size and thickness of thetoroids is calculated within a simple model; other models of stability of DNA toroids arediscussed and compared.

Simple Model for Overcharging of a Sphere by a Wrapped Oppositely Charged Asymmetrically Neutralized Polyelectrolyte: Possible Effects of Helical Charge Distribution

We investigate the complexation of a polyelectrolyte bendable rod with an oppositely charged spherical macroion. We take into account electrostatic bending of the rod and its asymmetric charge neutralization by sphere charges. The spontaneous curvature of the rod toward the sphere results in a substantial overcharging of such polyelectrolyte complex with a possible phase transition. Assuming a discrete helical charge distribution on the rod surface, we calculate the electrostatic energy of the helix and the electrostatic contribution to its bending and twisting elasticity. We show that the latter may change sign when the helical pitch is changed. For a DNA-relevant case, these corrections appear to be small compared to the corresponding mechanical elastic moduli. We discuss possible applications of our results to the description of overcharging of the nucleosome core particles.

The Role of Apolipoprotein A-I Helix 10 in Apolipoprotein-mediated Cholesterol Efflux via the ATP-binding Cassette Transporter ABCA1

Recent studies of Tangier disease have shown that the ATP-binding cassette transporter A1 (ABCA1)/apolipoprotein A-I (apoA-I) interaction is critical for high density lipoprotein particle formation, apoA-I integrity, and proper reverse cholesterol transport. However, the specifics of this interaction are unknown. It has been suggested that amphipathic helices of apoA-I bind to a lipid domain created by the ABCA1 transporter. Alternatively, apoA-I may bind directly to ABCA1 itself. To better understand this interaction, we created several truncation mutants of apoA-I and then followed up with more specific point mutants and helix translocation mutants to identify and characterize the locations of apoA-I required for ABCA1-mediated cholesterol efflux. We found that deletion of residues 221-243 (helix 10) abolished ABCA1-mediated cholesterol efflux from cultured RAW mouse macrophages treated with 8-bromo-cAMP. Point mutations in helix 10 that affected the helical charge distribution reduced ABCA1-mediated cholesterol efflux versus the wild type. We noted a strong positive correlation between cholesterol efflux and the lipid binding characteristics of apoA-I when mutations were made in helix 10. However, there was no such correlation for helix translocations in other areas of the protein as long as helix 10 remained intact at the C terminus. From these observations, we propose an alternative model for apolipoprotein-mediated efflux.

Counterion exchange reactions on DNA: Monte Carlo and Poisson-Boltzmann analysis.

AbstractIn solutions containing DNA and cations of more than one type, the competitive interactions of these cations with DNA can be modeled as an ion exchange process that can be described quantitatively by means of the theoretical approach reported in this paper. Under conditions of experimental interest the radial distribution function of each type of counterion is calculated from the results of canonical Monte Carlo (MC) simulations using the primitive model for DNA (having a helical charge distribution) and for the electrolyte ions. These ions consist of monovalent coions, monovalent counterions intended to represent Na+, and counterions of a second type designated Mz+, having variable size and charge (z ≥ 1). The competitive association of these counterions with DNA is described in terms of D, a parameter analogous to an ion exchange equilibrium quotient. Values of D are calculated from the results of our MC simulations and compared with corresponding predictions of the Poisson–Boltzmann (PB) cell model and with results inferred from analyses of previously published nmr measurements. Over typical experimental concentration ranges (0.02M < [Na+] < 0.20M, 0.001 < [Mz+] < 0.160M), DMC and DPB both are predicted to be relatively independent of the bulk ion concentrations. For various specifications of the size and charge of the competing cation (Mz+), DMC and DPB exhibit similar trends, although the MC simulations consistently predict that the cations bearing a higher charge density than that of Na+ are somewhat stronger competitors than indicated by the PB calculations. For monovalent and divalent competitors of varying radii, theoretical predictions of D are compared with values obtained by fitting nmr measurements. If the hard‐sphere radii specified in the simulations are the (hydrated) ionic radii determined from conductance measurements, then the MC predictions and the corresponding nmr results are in reasonable agreement for various monovalent competitors and for a divalent polyamine, but not for Ca2+ and Mg2+.

Monte carlo simulations of counterion accumulation near helical DNA

For a model of DNA having a helical charge distribution, the number of adjacent counterions is calculated from the Monte Carlo (MC) simulations at various salt concentrations. These results are compared with corresponding MC simulations for an axial polyion charge distribution and with the predictions of other polyelectrolyte theories.