Effective charge and free energy of DNA inside an ion channel

Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin channel in a lipid membrane driven by applied transmembrane voltage V was extensively studied recently. While the bare charge of the ssDNA piece inside the channel is approximately 12 (in units of electron charge) measurements of different effective charges resulted in values between one and two. We explain these challenging observations by a large self-energy of a charge in the narrow water filled gap between ssDNA and channel walls, related to large difference between dielectric constants of water and lipid, and calculate effective charges of ssDNA. We start from the most fundamental stall charge $q_s$, which determines the force $F_s= q_s V/L$ stalling DNA against the voltage V (L is the length of the channel). We show that the stall charge $q_s$ is proportional to the ion current blocked by DNA, which is small due to the self-energy barrier. Large voltage V reduces the capture barrier which DNA molecule should overcome in order to enter the channel by $|q_c|V$, where $q_c$ is the effective capture charge. We expressed it through the stall charge $q_s$. We also relate the stall charge $q_s$ to two other effective charges measured for ssDNA with a hairpin in the back end: the charge $q_u$ responsible for reduction of the barrier for unzipping of the hairpin and the charge $q_e$ responsible for DNA escape in the direction of hairpin against the voltage. At small V we explain reduction of the capture barrier with the salt concentration.Comment: Typos are correcte

Dynamics of a bubble formed in double stranded DNA

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let

Effect of shear force on the separation of double stranded DNA

Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and approaches to the asymptotic value in accordance with the experiment. The qualitative nature of these curves almost remains same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (back bone) under the shear force.Comment: 4 pages, 4 figure

Bubble generation in a twisted and bent DNA-like model

The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally distributed initial conditions to simulate thermal fluctuations, a relationship between bubble generation, twist and curvature is established. An analytical approach supports the numerical results.Comment: 7 pages, 8 figures. Accepted for Phys. Rev. E (in press

Energy Localization in the Peyrard-Bishop DNA model

We study energy localization on the oscillator-chain proposed by Peyrard and Bishop to model the DNA. We search numerically for conditions with initial energy in a small subgroup of consecutive oscillators of a finite chain and such that the oscillation amplitude is small outside this subgroup for a long timescale. We use a localization criterion based on the information entropy and we verify numerically that such localized excitations exist when the nonlinear dynamics of the subgroup oscillates with a frequency inside the reactive band of the linear chain. We predict a mimium value for the Morse parameter $(\mu >2.25)$ (the only parameter of our normalized model), in agreement with the numerical calculations (an estimate for the biological value is $\mu =6.3$). For supercritical masses, we use canonical perturbation theory to expand the frequencies of the subgroup and we calculate an energy threshold in agreement with the numerical calculations

Reversible Metal-Semiconductor Transition of ssDNA-Decorated Single-Walled Carbon Nanotubes

A field effect transistor (FET) measurement of a SWNT shows a transition from a metallic one to a p-type semiconductor after helical wrapping of DNA. Water is found to be critical to activate this metal-semiconductor transition in the SWNT-ssDNA hybrid. Raman spectroscopy confirms the same change in electrical behavior. According to our ab initio calculations, a band gap can open up in a metallic SWNT with wrapped ssDNA in the presence of water molecules due to charge transfer.Comment: 13 pages, 6 figure

Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Helix-dependent Spin Filtering through the DNA Duplex

Recent work suggests that electrons can travel through DNA and other chiral molecules in a spin-selective manner, but little is known about the origin of this spin selectivity. Here we describe experiments on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. Our results show that the two spins migrate through duplex DNA with different yield, and that spin selectivity requires charge transport through the DNA duplex. Significantly, shifting the same duplex DNA between right-handed B- and left-handed Z-forms leads to a diode-like switch in spin-selectivity; which spin moves more efficiently through the duplex depends upon the DNA helicity. With DNA, the supramolecular organization of chiral moieties, rather than the chirality of the individual monomers, determines the selectivity in spin, and thus a conformational change can switch the spin selectivity

Effects of finite curvature on soliton dynamics in a chain of nonlinear oscillators

We consider a curved chain of nonlinear oscillators and show that the interplay of curvature and nonlinearity leads to a number of qualitative effects. In particular, the energy of nonlinear localized excitations centered on the bending decreases when curvature increases, i.e. bending manifests itself as a trap for excitations. Moreover, the potential of this trap is double-well, thus leading to a symmetry breaking phenomenon: a symmetric stationary state may become unstable and transform into an energetically favorable asymmetric stationary state. The essentials of symmetry breaking are examined analytically for a simplified model. We also demonstrate a threshold character of the scattering process, i.e. transmission, trapping, or reflection of the moving nonlinear excitation passing through the bending.Comment: 13 pages (LaTeX) with 10 figures (EPS

Numerical Calculations of the B1g Raman Spectrum of the Two-Dimensional Heisenberg Model

The B1g Raman spectrum of the two-dimensional S=1/2 Heisenberg model is discussed within Loudon-Fleury theory at both zero and finite temperature. The exact T=0 spectrum for lattices with up to 6*6 sites is computed using Lanczos exact diagonalization. A quantum Monte Carlo (QMC) method is used to calculate the corresponding imaginary-time correlation function and its first two derivatives for lattices with up to 16*16 spins. The imaginary-time data is continued to real frequency using the maximum-entropy method, as well as a fit based on spinwave theory. The numerical results are compared with spinwave calculations for finite lattices. There is a surprisingly large change in the exact spectrum going from 4*4 to 6*6 sites. In the former case there is a single dominant two-magnon peak at frequency w/J appr. 3.0, whereas in the latter case there are two approximately equal-sized peaks at w/J appr. 2.7 and 3.9. This is in good qualitative agreement with the spinwave calculations including two-magnon processes on the same lattices. Both the Lanczos and the QMC results indicate that the actual infinite-size two-magnon profile is broader than the narrow peak obtained in spinwave theory, but the positions of the maxima agree to within a few percent. The higher-order contributions present in the numerical results are merged with the two-magnon profile and extend up to frequencies w/J appr. 7. The first three frequency cumulants of the spectrum are in excellent agreement with results previously obtained from a series expansion around the Ising limit. Typical experimental B1g$ spectra for La2CuO4 are only slightly broader than what we obtain here. The exchange constant extracted from the peak position is J appr. 1400K, in good agreement with values obtained from neutron scattering and NMR experiments.Comment: 15 pages, Revtex, 13 PostScript figure