Structural correlations and melting of B-DNA fibers

Melting transition of oriented Li-DNA fibers submerged in ethanol solutions

The melting transition of Li-DNA fibers immersed in ethanol-water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard-Bishop-Dauxois model to determine the strengths of the intra- and inter-base pair potentials. The data and analysis show that the potentials are weaker than those for DNA in water. They become weaker still and the DNA less stable as the ethanol concentration increases but, conversely, the fibers become more compact and the distances between base pairs become more regular. The results show that the melting transition is relatively insensitive to local confinement and depends more on the interaction between the DNA and its aqueous environment.

Thermal Conductivity of B-DNA

The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical molecular dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D model or a coarse-grained model of DNA to reduce simulation times, full atomistic simulations are employed to understand the thermal conduction in B-DNA. Thermal conductivities at different temperatures from 100 to 400 K are investigated using the Einstein-Green-Kubo equilibrium and Müller-Plathe non-equilibrium formalisms. The thermal conductivity of B-DNA at room temperature is found to be 1.5 W/m·K in equilibrium and 1.225 W/m·K in the non-equilibrium approach. In addition, the denaturation regime of B-DNA is obtained from the variation of thermal conductivity with temperature. It is in agreement with previous studies using the Peyrard-Bishop-Dauxois model at a temperature of around 350 K. The quantum heat capacity (C_vq) has given additional clues regarding the Debye and denaturation temperature of 12-bp B-DNA.

Chromosome aberration in typical biological systems under exposure to low- and high-intensity magnetic fields

The aim of this study was to investigate the response of chromosomes in typical human and plant cells under applied low-frequency magnetic fields at low and high intensities. Neuronal-like cells and roots of Allium sativum and Vicia faba were used to investigate chromosome's response to a static and 50 Hz magnetic fields at intensities ranging from 1 mT to 0.8 T, generated by two Helmholtz coils driven by direct current or alternate current voltage. Vertex spectrometer and Olympus microscope with camera were used. A significant decrease in intensity of the phosphate bands in the DNA infrared region was observed by FTIR spectroscopy analysis after exposure of neuronal-like cells to static and 50 Hz magnetic field at low intensity of 1 mT, which can be explained assuming that uncoiling and unpackaging of chromatin constituents occurred after exposure. This effect was directly observed by microscope in roots of Allium sativum and Vicia faba under exposure to a static magnetic field at high intensity of 0.8 T. These findings can be explained assuming that exposure to both low- and high-intensity magnetic fields of chromosomes in typical human and plant cells induces uncoiling and unpackaging of chromatin constituents, followed by chromosome alignment towards the direction of applied magnetic field, providing further demonstration that magnetic fields can induce the orientation of organic macromolecules even at low-intensity values.

Sulfur-substitution-induced base flipping in the DNA duplex

Base flipping is widely observed in a number of important biological processes. The genetic codes deposited inside the DNA duplex become accessible to external agents upon base flipping. The sulfur substitution of guanine leads to thioguanine, which alters the thermodynamic stability of the GC base pairs and the GT mismatches. Experimental studies conclude that the sulfur substitution decreases the lifetime of the GC base pair. In this work, under three AMBER force fields for nucleotide systems, we firstly performed equilibrium and nonequilibrium free energy simulations to investigate the variation of the thermodynamic profiles in base flipping upon sulfur substitution. It is found that the bsc0 modification, the bsc1 modification and the OL15 modification of AMBER force fields are able to qualitatively describe the sulfur-substitution dependent behavior of the thermodynamics. However, only the two last-generation AMBER force fields are able to provide quantitatively correct predictions. The second computational study on the sulfur substitutions focused on the relative stability of the S6G-C base pair and the S6G-T mismatch. Two conflicting experimental observations were reported by the same authors. One suggested that the S6G-C base pair was more stable, while the other concludes that the S6G-T mismatch was more stable. We answered this question by constructing the free energy profiles along the base flipping pathway computationally.

Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification

Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free-energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free-energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for the efficient calculation of the free-energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free-energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of the equilibrium umbrella sampling and the nonequilibrium stratification is given. The results show that nonequilibrium free-energy simulation achieves similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size.

Understanding PIM-1 kinase inhibitor interactions with free energy simulation

The proviral integration site of the Moloney leukemia virus (PIM) family includes three homologous members. PIM-1 kinase is an important target in effective therapeutic interventions of lymphomas, prostate cancer and leukemia. In the current work, we performed free energy calculations to calculate the binding affinities of several inhibitors targeting this protein. The alchemical method with integration and perturbation-based estimators and the end-point methods were compared. The computational results indicated that the alchemical method can accurately predict the binding affinities, while the end-point methods give relatively unreliable predictions. Decomposing the free energy difference into enthalpic and entropic components with MBAR reweighting enabled us to investigate the detailed thermodynamic parameters with which the entropy-enthalpy compensation in this protein-ligand binding case is identified. We then studied the conformational ensemble, and the important protein-ligand interactions were identified. The current work sheds light on the understanding of the PIM-1-kinase-inhibitor interactions at the atomic level and will be useful in the further development of potential drugs.

Ionic mobility in DNA films studied by dielectric spectroscopy

Double-helix DNA molecules can be found under different conformational structures driven by ionic and hydration surroundings. Usually, only the B-form of DNA, which is the only form stable in aqueous solution, can be studied by dielectric measurements. Here, the dielectric responses of DNA molecules in the A- and B-form, oriented co-linearly within fibres assembled in a film have been analyzed. The dielectric dispersion, permittivity and dissipation factor, have been measured as a function of frequency, strength voltage, time, temperature and nature of the counter-ions. Besides a high electrode polarization component, two relaxation peaks have been observed and fitted by two Cole-Cole relaxation terms. In the frequency range that we investigated (0.1 Hz to 5 ·10(6) Hz) the dielectric properties are dominated by the mobility and diffusivity of the counter-ions and their interactions with the DNA molecules, which can therefore be characterized for the A- and B-forms of DNA.

Phase-dependent premelting of self-assembled phosphonic acid multilayers

Melting and premelting phenomena in self-organized organic systems have been extensively explored in the literature, exploring distinct behaviors of different molecule lengths and morphologies. Nevertheless, the influence of the supramolecular assembly configuration on the occurrence of premelting remains poorly explored. Here we use phosphonic acids as model systems for self-organized molecular assemblies. These molecules exhibit long-range order on different types of substrates. The balance between chain-to-chain and head-to-head interactions leads to distinct types of stackings. Although their structural configurations are well understood, very little is known about their behavior near the melting transition. We show here that premelting occurs in lamellar structures and that its behavior depends directly on the ordered configuration assumed in the studied multilayers. Two molecules with different chain lengths were investigated: octadecyl phosphonic and octyl phosphonic acids. Although almost no dependence on the molecule length was observed, the occurrence of premelting is strongly influenced by their lamellar packing configuration. For tilted packings premelting is unfavored while in straight configurations, where alkyl chain interactions are weakened with respect to head-to-head interactions, strong premelting is observed. We find that the onset of premelting occurs at the domain boundaries with straight lamellar configurations and the domain sizes exhibit power law temperature dependences.

Base pair openings and temperature dependence of DNA flexibility

The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.