Water Clustering and Percolation in Low Hydration DNA Shells

Does the addition of a heteropoly acid change the water percolation threshold of PFSA membranes?

A large system containing heteropoly acids (HPAs) and Nafion® 117 was simulated and studied to verify whether the additive particles affect the formation of the water percolating network or not. Two structures of HPA particles were considered as dopants, i.e. H₉AlW₆O₂₄ and H₃PW₁₂O₄₀. The SAXS simulation revealed that HPA particle addition to the membrane matrix leads to an increased order in the abundance and size of the hydrophilic region beside an expansion of the distance between the ionic domains. The morphological assessment shows that the hydrophilic phase domains in the HPA-doped Nafion® were spaced further apart than in the undoped membrane. These results show that adding HPA particles to the PFSA membrane reduces the so-called dead-pockets and makes the water channels more interconnected. For undoped Nafion®, the so-called percolating hydration level (λ_p) was 5.63. In other words, according to these results, approximately 8 wt% of water molecules are required to establish a spanning water network. The H₉AlW₆O₂₄ and H₃PW₁₂O₄₀ particles directly influence the morphology of water clusters and reduce by 10.12% and 17.41% the required hydration level to reach the percolation threshold, respectively.

Changes in Microenvironment Modulate the B- to A-DNA Transition

B- to A-DNA transition is known to be sensitive to the macroscopic properties of the solution, such as salt and ethanol concentrations. Microenvironmental effects on DNA conformational transition have been broadly studied. Providing an intuitive picture of how DNA responds to environmental changes is, however, still needed. Analyzing the chemical equilibrium of B-to-A DNA transition at critical concentrations, employing explicit-solvent simulations, is envisioned to help understand such microenvironmental effects. In the present study, free-energy calculations characterizing the B- to A-DNA transition and the distribution of cations were carried out in solvents with different ethanol concentrations. With the addition of ethanol, the most stable structure of DNA changes from the B- to A-form, in agreement with previous experimental observation. In 60% ethanol, a chemical equilibrium is found, showing reversible transition between B- and A-DNA. Analysis of the microenvironment around DNA suggests that with the increase of ethanol concentration, the cations exhibit a significant tendency to move toward the backbone, and mobility of water molecules around the major groove and backbone decreases gradually, leading eventually to a B-to-A transition. The present results provide a free-energy view of DNA microenvironment and of the role of cation motion in the conformational transition.

Pf1 bacteriophage hydration by magic angle spinning solid-state NMR

High resolution two- and three-dimensional heteronuclear correlation spectroscopy ((1)H-(13)C, (1)H-(15)N, and (1)H-(13)C-(13)C HETCOR) has provided a detailed characterization of the internal and external hydration water of the Pf1 virion. This long and slender virion (2000 nm × 7 nm) contains highly stretched DNA within a capsid of small protein subunits, each only 46 amino acid residues. HETCOR cross-peaks have been unambiguously assigned to 25 amino acids, including most external residues 1-21 as well as residues 39-40 and 43-46 deep inside the virion. In addition, the deoxyribose rings of the DNA near the virion axis are in contact with water. The sets of cross-peaks to the DNA and to all 25 amino acid residues were from the same hydration water (1)H resonance; some of the assigned residues do not have exchangeable side-chain protons. A mapping of the contacts onto structural models indicates the presence of water "tunnels" through a highly hydrophobic region of the capsid. The present results significantly extend and modify results from a lower resolution study, and yield a comprehensive hydration surface map of Pf1. In addition, the internal water could be distinguished from external hydration water by means of paramagnetic relaxation enhancement. The internal water population may serve as a conveniently localized magnetization reservoir for structural studies.

Two-dimensional percolation at the free water surface and its relation with the surface tension anomaly of water

The percolation temperature of the lateral hydrogen bonding network of the molecules at the free water surface is determined by means of molecular dynamics computer simulation and identification of the truly interfacial molecules analysis for six different water models, including three, four, and five site ones. The results reveal that the lateral percolation temperature coincides with the point where the temperature derivative of the surface tension has a minimum. Hence, the anomalous temperature dependence of the water surface tension is explained by this percolation transition. It is also found that the hydrogen bonding structure of the water surface is largely model-independent at the percolation threshold; the molecules have, on average, 1.90 ± 0.07 hydrogen bonded surface neighbors. The distribution of the molecules according to the number of their hydrogen bonded neighbors at the percolation threshold also agrees very well for all the water models considered. Hydrogen bonding at the water surface can be well described in terms of the random bond percolation model, namely, by the assumptions that (i) every surface water molecule can form up to 3 hydrogen bonds with its lateral neighbors and (ii) the formation of these hydrogen bonds occurs independently from each other.

Highly efficient quencher-free molecular beacon systems containing 2-ethynyldibenzofuran- and 2-ethynyldibenzothiophene-labeled 2'-deoxyuridine units

We have prepared two fluorescent DNA probes--UDBF and UDBT, containing 2-ethynyldibenzofuran and 2-ethynyldibenzothiophene moieties, respectively, covalently attached to the base dU--and incorporated them in the central positions of oligodeoxynucleotides (ODNs) so as to develop new types of quencher-free linear beacon probes and investigate the effect of functionalization of the fluorene scaffold on the photophysical properties of the fluorescent ODNs. The ODNs containing adenine flanking bases (FBs) displayed a selective fluorescence "turn-off" response to mismatched targets with guanine bases; this suggests that these probes could be used as base-discriminating fluorescent nucleotides. On the other hand, we observed a "turn-on" response to matched targets when the UDBF and UDBT units of ODNs containing pyrimidine-based FBs were positioned opposite the four natural nucleobases. In particular, an ODN incorporating UDBT and cytosine FBs has potential use in single-nucleotide polymorphism typing.

Electric conductivity percolation in naturally dehydrating, lightly wetted, hydrophilic fumed silica powder

In studying the dehydration of surface-moistened fumed silica Aerosil powders, we found a conductivity percolation transition at low hydration levels. Both the percolation exponent and the threshold are typical for correlated site-bond transitions in complex two-dimensional (2D) systems. The exponent values, 0.94-1.10, are indicative of severe heterogeneity in the conducting medium. The surface moisture at the percolation threshold takes on a universal value of 0.65 mg([H2O])/m(2)([silica]), independent of the silica grain size, and equivalent to twice the first hydration monolayer. This level is just sufficient to sustain a quasi-2D, hydrogen-bonded water network spanning the silica surface.

Power-law trapping of water molecules on the lipid-membrane surface induces water retardation

Cell membranes provide unique local environments for biological reactions, where the diffusion of biomolecules as well as water molecules plays critical roles. Translational and rotational motions of water molecules near membranes are known to be slower than those in bulk. Using all-atom molecular dynamics simulations of a membrane, we show that the temperature dependence of the water molecular motions on the membrane surface is different from that in bulk. Decreasing temperature enhances the water retardation on the membrane surface, and the lateral motions of water molecules are correlated with the vertical motions. We find that trapping times of water molecules onto membrane surfaces are distributed according to a power-law distribution and that the power-law exponents depend linearly on temperature, suggesting a random energy landscape picture. Moreover, we find that water molecules on the membrane surfaces exhibit subdiffusions in translational motions.

Popping the cork: mechanisms of phage genome ejection

Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and the mechanisms and energetics of packaging a phage genome are beginning to be better understood. Condensing DNA subjects it to high osmotic pressure, which has been suggested to provide the driving force for its ejection during infection. However, forces internal to a phage capsid cannot, alone, cause complete genome ejection into cells. Here, we describe the structure of the DNA inside mature phages and summarize the current models of genome ejection, both in vitro and in vivo.

Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments

DNA sequence analyzing and base pair separation techniques have attracted much attention, such as denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and capillary electrophoresis. However, details of sequence separation mechanisms in electrophoresis are not clarified enough. Understanding and controlling flow characteristics of DNA are important not only for fundamental research but also for further developments of bio-nano technologies. In the present study, we theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B-DNA decamer 5'-dCGTATATATA-3'. Consequently, it is found that water molecules that concentrate on dissociated base pairs form hydrated structures and change the diffusivity of DNA decamers. The diffusion coefficients are affected by the substitution of GC for AT because of the different manner of interactions between the base molecules and water solvent. This result predicts a possibility of base pair separation according to differences in the diffusivity.

Molecular level properties of the free water surface and different organic liquid/water interfaces, as seen from ITIM analysis of computer simulation results

Molecular dynamics simulations of the interface of water with four different apolar phases, namely water vapour, liquid carbon tetrachloride, liquid dichloromethane (DCM) and liquid dichloroethane (DCE) are performed on the canonical ensemble at 298 K. The resulting configurations are analysed using the novel method of identification of the truly interfacial molecules (ITIM). Properties of the first three molecular layers of the liquid phases (e.g. width, spacing, roughness, extent of the in-layer hydrogen bonding network) as well as of the molecules constituting these layers (e.g., dynamics, orientation) are investigated in detail. In the analyses, particular attention is paid to the effect of the polarity of the non-aqueous phase and to the length scale of the effect of the vicinity of the interface on the various properties of the molecules. The obtained results show that increasing polarity of the non-aqueous phase leads to the narrowing of the interface, in spite of the fact that, at the same time, the truly interfacial layer of water gets somewhat broader. The influence of the nearby interface is found to extend only to the first molecular layer in many respects. This result is attributed to the larger space available for the truly interfacial than for the non-interfacial molecules (as the shapes of the two liquid surfaces are largely independent of each other, resulting in the presence of voids between the two phases), and to the fact that the hydrogen bonding interaction of the truly interfacial water molecules with other waters is hindered in the direction of the interface.

The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation

In an effort to develop unnatural DNA base pairs we examined six pyridine-based nucleotides, d3MPy, d4MPy, d5MPy, d34DMPy, d35DMPy and d45DMPy. Each bears a pyridyl nucleobase scaffold but they are differentiated by methyl substitution, and were designed to vary both inter- and intra-strand packing within duplex DNA. The effects of the unnatural base pairs on duplex stability demonstrate that the pyridine scaffold may be optimized for stable and selective pairing, and identify one self pair, the pair formed between two d34DMPy nucleotides, which is virtually as stable as a dA:dT base pair in the same sequence context. In addition, we found that the incorporation of either the d34DMPy self pair or a single d34DMPy paired opposite a natural dA significantly increases oligonucleotide hybridization fidelity at other positions within the duplex. Hypersensitization of the duplex to mispairing appears to result from global and interdependent solvation effects mediated by the unnatural nucleotide(s) and the mispair. The results have important implications for our efforts to develop unnatural base pairs and suggest that the unnatural nucleotides might be developed as novel biotechnological tools, diagnostics, or therapeutics for applications where hybridization stringency is important.

The electrostatic origin of low-hydration polymorphism in DNA

In recent years, significant progress has been made towards uncovering the physical mechanisms of low-hydration polymorphism in double-helical DNA. The effect appears to be mechanistically similar in different biological systems, and it is due to the ability of water to form spanning H-bonded networks around biomacromolecules via a quasi-two-dimensional percolation transition. In the case of DNA, disintegration of the spanning H-bonded network leads to electrostatic condensation of DNA strands because, below the percolation threshold, water loses its high dielectric permittivity, whereas the concentration of neutralizing counterions becomes high. In this Concept article arguments propose that this simple electrostatic mechanism represents the universal origin of low-hydration polymorphism in DNA.

Ion dynamics and water percolation effects in DNA polymorphism

The dynamics of ions and water at the surface of DNA are studied by computer simulations in a wide range of hydrations involving the zone of low-hydration polymorphism in DNA. The long-range mobility of ions exhibits a stepwise increase at three distinct hydration levels. The first of them is close to the midpoint of the water percolation transition as well as the midpoint of the transition between A- and B-DNA forms. It coincides with the onset of the dissociation of ion pairs on the DNA surface probably caused by the increase in the water dielectric permittivity due to the appearance of the spanning hydrogen-bonding network. The other two steps are attributed to the formation of percolating water layers on the surface of DNA accompanied by the progressive escape of ions from the DNA surface. The results agree with earlier experimental data and further corroborate the suggested universal mechanism of the low hydration polymorphism in DNA including intraduplex electrostatic condensation close to the water percolation threshold.