Using two approaches, small-angle neutron scattering (SANS) from bulk solutions and nanopore conductance-fluctuation analysis, we studied structural and dynamic features of poly(ethylene glycol) (PEG) water/salt solutions in the dilute and semidilute regimes. SANS measurements on PEG 3400 at the zero-average contrast yielded the single chain radius of gyration (Rg) over 1-30 wt %. We observed a small but statistically reliable decrease in Rg with increasing PEG concentration: at 30 wt % the chain contracts by a factor of 0.94. Analyzing conductance fluctuations of the α-hemolysin nanopore in the mixtures of PEG 200 with PEG 3400, we demonstrated that polymer partitioning into the nanopore is mostly due to PEG 200. Specifically, for a 1:1 wt/wt mixture the smaller polymer dominates to the extent that only about 1/25 of the nanopore volume is taken by the larger polymer. These findings advance our conceptual and quantitative understanding of nanopore polymer partitioning; they also support the main assumptions of the recent "polymers-pushing-polymers" model.

Observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5′-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystalline phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG3(TTAG3)3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG4T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.

We formulate a continuum approach to the equation of state (density dependence of osmotic pressure) of bulk DNA and encapsidated DNA, as well as review the phase diagram of DNA in the regime of densities relevant for DNA packing in bacteriophages. We derive the first integral of the equilibrium equations that connects the behavior of DNA in the bulk and in nanoscale enclosures, and we delineate the changes wrought upon the mesophase equilibria of encapsidated DNA. We show how multiphase equilibria and complicated spatial distribution of DNA density and orientation can emerge due to the curvature contribution to the DNA osmotic pressure within the capsid.

We present a first-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models in different environments. Our study shows that the parallel strand structures are more stable in dry environments and aqueous solutions containing K(+) ions within the tetrad of guanine but conversely, that the anti-parallel structure is more stable in solutions containing the Na(+) ions within the tetrad of guanine. The presence of metal ions within the tetrad of the guanine channel always enhances the stability of the G4-DNA models. The parallel strand structures have larger HOMO-LUMO gaps than antiparallel structures, which are in the range of 0.98 eV to 3.11 eV. Partial charge calculations show that sugar and alkali ions are positively charged whereas nucleobases, PO4 groups and water molecules are all negatively charged. Partial charges on each functional group with different signs and magnitudes contribute differently to the electrostatic interactions involving G4-DNA and favor the parallel structure. A comparative study between specific pairs of different G4-DNA models shows that the Hoogsteen OH and NH hydrogen bonds in the guanine tetrad are significantly influenced by the presence of metal ions and water molecules, collectively affecting the structure and the stability of G4-DNA.

Significance With consequences for the selective partitioning of large molecules in cells, polymer partitioning into nanopores is instructive for single-molecule sensing as well as for polymer-assisted transport and packaging. Here we detect and analyze not only passive but also forced size-dependent partitioning of binary mixtures of differently sized PEGs. We probe three structurally different channels exhibiting forced partitioning that can be understood conceptually as well as quantitatively within a “polymers-pushing-polymers” model, allowing good estimates for the size-dependent pore penetration energy differences. Beyond proof of concept, forced partitioning in cells can now be recognized and used as a new tool for molecule-selective transport and active osmotically regulated packaging.

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems.

The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO43- complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A(260)) or simple purity ratios, such as A(260)/A(230) or A(260)/A(280), and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly.

We have mapped the thermodynamic potentials that drive transitions of DNA in uni- and di-valent salt solutions. The successive mesophases, with measured free energies of deformation and transition, allow computation of interaction potentials as well as transition entropies and enthalpies. We have been able to measure transitions of DNA tetraplexes and duplexes and to compare entropic and enthalpic contributions. Changes in fluctuation free energies are much greater at DNA-ordering transitions for tetraplexes than for duplexes, indicating strong entropic contributions. Disordering due to fluctuations is much greater in the less-ordered (cholesteric) phase, seen in broadening of x-ray scattering peaks. This indicates attraction in the more-ordered phase, where packing is stricter, and the effect of fluctuations is much smaller. This attraction is stronger for quadruplexes than for duplexes. We can read two kinds of information from the x-ray data: the degree of ordering, and the change in density. These changes are much bigger in tetraplexes than in double helical DNA. In addition, we also observe that upon decreasing the applied osmotic stress on the less-ordered phase, there is spontaneous disassembly of tetraplexes. This second transition, from a stack of tetramers to monomers, also depends on temperature, allowing us again to measure transition entropy and free energy. Lowering the temperature in the cholesteric phase favors tetraplex formation. The critical osmotic pressure for the formation of tetraplexes, just as the critical osmotic pressure for inducing the higher-density packing, depends strongly on the temperature. Out next goal is to compare tetraplexes, which lack a linking backbone, with quadruplexes (where the bases are linked) so as to see the stabilizing contributions of a polymer backbone.

The self-assembly of heterogeneous mesoscale systems is mediated by long-range interactions, including van der Waals forces. Diverse mesoscale architectures, built of optically and morphologically anisotropic elements such as DNA, collagen, single-walled carbon nanotubes, and inorganic materials, require a tool to calculate the forces, torques, interaction energies, and Hamaker coefficients that govern assembly in such systems. The mesoscale Lifshitz theory of van der Waals interactions can accurately describe solvent and temperature effects, retardation, and optically and morphologically anisotropic materials for cylindrical and planar interaction geometries. The Gecko Hamaker open-science software implementation of this theory enables new and sophisticated insights into the properties of important organic/inorganic systems: interactions show an extended range of magnitudes and retardation rates, DNA interactions show an imprint of base pair composition, certain SWCNT interactions display retardation-dependent nonmonotonicity, and interactions are mapped across a range of material systems in order to facilitate rational mesoscale design.

The free energies, forces, and torques for all separations and mutual orientations are formulated in the full Lifshitz continuum theory of van der Waals interactions. Angular dependence of interactions is characterized for three different interaction geometries of bodies with morphological and/or material anisotropy, interacting across an isotropic aqueous medium: two infinite half-spaces; two half-spaces of composite media comprising parallel cylinder arrays; and an isolated pair of long, thin cylinders. The contributions to van der Waals interaction energy due to shape anisotropy and material anisotropy are isolated in detailed calculations and examined. Surprisingly, the effect of shape on interactions in the retarded regime results in a torque between arrays of cylinders that is stronger than that between half-spaces.

We consider how membrane fluctuations can modify the miscibility of lipid mixtures, that is to say how the phase diagram of a boundary-constrained membrane is modified when the membrane is allowed to fluctuate freely in the case of zero surface tension. In order for fluctuations to have an effect, the different lipid types must have differing Gaussian rigidities. We show, somewhat paradoxically, that fluctuation-induced interactions can be treated approximately in a mean-field type theory. Our calculations predict that, depending on the difference in bending and Gaussian rigidity of the lipids, membrane fluctuations can either favor or disfavor mixing.

We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background in vacuo Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be explicitly and exactly traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of intrinsically disordered proteins and their analogues.

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

A new method of finely temperature-tuning osmotic pressure allows one to identify the cholesteric → line hexatic transition of oriented or unoriented long-fragment DNA bundles in monovalent salt solutions as first order, with a small but finite volume discontinuity. This transition is similar to the osmotic pressure-induced expanded → condensed DNA transition in polyvalent salt solutions at small enough polyvalent salt concentrations. Therefore there exists a continuity of states between the two. This finding, together with the corresponding empirical equation of state, effectively relates the phase diagram of DNA solutions for monovalent salts to that for polyvalent salts and sheds some light on the complicated interactions between DNA molecules at high densities.

With increasing density imposed by external osmotic pressure, DNA in univalent salt solutions (e.g., NaCl) is known to go through a set of ordered mesophases, eventually crystallizing into an orthorhombic crystal. While the transition from the cholesteric to the line hexatic (LH) phase has been observed before, it has remained unclear whether the transition is of second order or first order. We use the small but accurately measurable temperature dependence of the osmotic pressure of a PEG solution to fine-regulate the osmotic stress with which it acts on the DNA subphase. This allows us to set the osmotic pressure to an accuracy never achieved before. This advance in experimental methodology allows us then to detect small but nevertheless finite changes in the density of DNA as it goes through the cholesteric → LH transition. In this way, we first determine experimentally the small density change that occurs at the cholesteric → LH phase transition. Further, we establish that this small density discontinuity of Na-DNA is merely increased when polyvalent salt Co(NH 3 ) 6 Cl 3 , i.e. CoHex, is added to the solution. Increasing CoHex concentration finally leads to a phase separation at zero imposed osmotic pressure. Establishing a continuity of thermodynamic states for the cholesteric → LH transition and DNA condensation, thought to be completely unrelated before, represents an important advance in our understanding of DNA polymorphism in electrolyte solutions.

At the increasing density imposed by external osmotic pressure, DNA in monovalent salt solutions (e.g., NaCl) to goes through a set of ordered mesophases, finally crystallizing into an orthorhombic crystal. While the transition from the (chiral) nematic to the line-hexatic phase has been observed before, it is still unclear whether the transition is of second order or weak first order. In multivalent salt solutions (e.g., CoHex = Co(NH3)6 Cl3), DNA is known to collapse into an ordered aggregate under osmotic pressure, or even at zero osmotic pressure at large enough concentrations of the multivalent salt. It has remained unclear what is the connection between these two ordering transitions -- with vs. without CoHex. By using a novel method of temperature-regulating the osmotic stress imposed on the DNA subphase, we show that there exists a continuity of states between these two ordering transitions and that they are of the same type. We use the small but accurately measurable temperature dependence of the osmotic pressure of a PEG solution to fine-regulate the osmotic stress with which it acts on the DNA subphase. This allows us to set the osmotic pressure to an accuracy never achieved before. This advance in experimental methodology allows us then to detect small but nevertheless finite changes in the density of DNA as it goes through the ordering transitions. In this way, we first determine experimentally the small density change that occurs at the (chiral) nematic to line-hexatic phase transition. For Na-DNA, this density change can be translated into a ∼1.5 Angstrom change in the interaxial spacing. This density discontinuity at the phase transition either does not depend on the NaCl concentration or varies by < 0.1 Angstrom as the salt concentration is varied.

Gauging the interactions of a natively unfolded Parkinson disease-related protein, alpha-synuclein (alpha-syn) with membranes and its pathways between and within cells is important for understanding its pathogenesis. Here, to address these questions, we use a robust beta-barrel channel, alpha-hemolysin, reconstituted into planar lipid bilayers. Transient, similar to 95% blockage of the channel current by alpha-syn was observed when 1), alpha-syn was added from the membrane side where the shorter (stem) part of the channel is exposed; and 2), the applied potential was lower on the side of alpha-syn addition. While the on- rate of alpha-syn binding to the channel strongly increased with the applied field, the off-rate displayed a turnover behavior. Statistical analysis suggests that at voltages >50 mV, a significant fraction of the alpha-syn molecules bound to the channel undergoes subsequent translocation. The observed on- rate varied by > 100 times depending on the bilayer lipid composition. Removal of the last 25 amino acids from the highly negatively charged C-terminal of alpha-syn resulted in a significant decrease in the binding rates. Taken together, these results demonstrate that beta-barrel channels may serve as sensitive probes of alpha-syn interactions with membranes as well as model systems for studies of channel-assisted protein transport.

Molecular crowding by polyethylene glycols (PEGs) has been employed in a wide range of inquiries into molecular structure and dynamics. Investigating the partitioning of crowded polymers into biological nanopores reveals properties also seen in, e.g., DNA ejection and compaction into viral capsids, as well as in facilitated molecule transport. Capitalizing on our previous work on the partitioning of binary PEG mixtures into the benchmark Alpha-Hemolysin nanopore, we have now studied partitioning of mono- and polydisperse polymer solutions into comparably sized, yet differently structured, diffusion channels. We find that in the presence of large non-partitioning PEG 3400, the small, otherwise equipartitioning PEG 200 partitions disproportionately. Specifically, with 15% PEG 3400, an added 15% PEG 200 reduces channel conductance by 65% (compared with channel conductance in polymer-free solutions), while 15% PEG 200 alone reduces channel conductance by only 45%. We employed open-channel noise analysis to investigate channel diffusion properties of individual polymers, and to compare them with their properties in bulk water solution. In this way we demonstrate and quantify crowding-assisted transport through nanopores in mixed-polymer systems.

Small changes in the dielectric response of a material result in substantial variations in the Hamaker coefficient of the van der Waals interactions, as demonstrated in a simplified approximate model as well as a realistic example of amorphous silica with and without an exciton peak. Variation of the dielectric response spectra at one particular frequency influences all terms in the Matsubara summation, making the total change in the Hamaker coefficient depend on the spectral changes not only at that frequency but also at the rest of the spectrum, properly weighted. The Matsubara terms most affected by the addition of a single peak are not those close to the position of the added peak, but are distributed doubly non-locally over the entire range of frequencies. A possibility of eliminating van der Waals interactions or at least drastically reducing them by spectral variation in a narrow regime of frequencies thus seems very remote.