How are small ions involved in the compaction of DNA molecules?

DNA is a genetic material found in all life on Earth. DNA is composed of four types of nucleotide subunits, and forms a double-helical one-dimensional polyelectrolyte chain. If we focus on the microscopic molecular structure, DNA is a rigid rod-like molecule. On the other hand, with coarse graining, a long-chain DNA exhibits fluctuating behavior over the whole molecule due to thermal fluctuation. Owe to its semiflexible nature, individual giant DNA molecule undergoes a large discrete transition in the higher-order structure. In this folding transition into a compact state, small ions in the solution have a critical effect, since DNA is highly charged. In the present article, we interpret the characteristic features of DNA compaction while paying special attention to the role of small ions, in relation to a variety of single-chain morphologies generated as a result of compaction.     

Single polyelectrolyte macromolecule in the salt solution: Effect of escaped counter ions

We developed simplest theory of swelling of polyelectrolyte macromolecules in the solution of low‐molecular salts. The novel feature taken into account is the electrostatic interaction between the macro‐ion and counter ions which escaped from the interior of the macromolecular coil and distributed in the whole volume of solution. The phase diagram in the variables solvent quality vs. salt concentrationis derived. One of the unexpected findings is that the total charge within the sphere surrounding the macro‐ion changes in a non‐monotonical manner with the increase of the salt concentration. In particular, our calculations predict that the electrophoretic mobility of a polyelectrolyte macromolecule can demonstrate non‐monotonic behavior with an increase of salt concentration. The results of the calculations are compared with those obtained under the assumption of electroneutrality of the macromolecule when all of the counter ions are kept within the effective volume of macromolecule.     

Relationships between chemical structures and solubility,diffusivity, and permselectivity of 1,3-butadiene and n-butane in 6FDA-based polyimides

The solubility, diffusivity, and permselectivity of 1,3-butadiene and n-butane in seven different polyimides synthesized from 2,2-bis (3,4-carboxyphenyl) hexafluoropropane dianhydride (6FDA) were determined at 298 K. The influence of chemical structures on physical and gas permeation properties of 6FDA-based polyimides was studied. Solubility of 1,3-butadiene in 6FDA-based polyimides can be described by a dual-mode sorption model. 1,3-Butadiene-induced plasticization is considered to be associated with the increasing permeabilities of 1,3-butadiene and n-butane and the decreasing permselectivity of 1,3-butadiene vs. n-butane in the mixed gas system containing a high concentration of 1,3-butadiene. It was found that controlling the solubility of 1,3-butadiene in an unrelaxed volume in 6FDA-based polyimides is very important to maintain the high permselectivity of 1,3-butadiene vs. n-butane in the mixed gas system. Changing the  C(CF₃)₂ linkage to a  CH₂ ,  O linkage, removing methyl substituents at the ortho position of the imide linkage, and changing the p-phenylene linkage to an m-phenylene linkage in the main chains in some 6FDA-based polyimides are effective to decrease fractional free volume and restrict the solubility of 1,3-butadiene in the unrelaxed volume of a polymer matrix. The 6FDA-based polyimides restricting the solubility of 1,3-butadiene in an unrelaxed volume exhibit high separation performance in the 1,3-butadiene/n-butane mixed gas system compared with conventional glassy polymers and, therefore, are potentially useful membrane materials for the separation of 1,3-butadiene and n-butane in the petrochemical industry. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2941–2949, 1999     

Two-dimensional near-infrared correlation spectroscopy studies of polymer blends I: Composition-dependent spectral variations of blends of atactic polystyrene and poly[2,6-dimethyl-1,4-phenylene ether]

Generalized two-dimensional (2D) near-infrared (NIR) correlation spectroscopy has been applied to study the conformational changes and molecular interactions in blends of atactic polystyrene (PS) and poly[2,6-dimethyl-1,4-phenylene ether] (PPE). NIR diffuse reflectance spectra have been measured for PS, PPE and their blends of different compositions, i.e., PS/PPE=90/10, 70/30, 50/50, 30/70, 10/90. The 2D synchronous correlation analysis of these composition-dependent NIR spectral variations separates the bands of PS from those of PPE. The 2D asynchronous analysis identifies spectral features indicative of the conformational changes or the specific interaction of PS and PPE. It can also detect “blend bands” whose origin is attributed to the formation of the polymer blends. Two “blend bands” of PS are identified at 6887 and 4836 cm⁻¹, and three “blend bands” of PPE are observed at 5752, 5679 and 4647 cm⁻¹. These “blend bands” are due to vibrations of the aromatic rings of PS or PPE and of the CH₃ of PPE. Thus, not only the aromatic rings of PS and PPE but also the CH3 groups of PPE play important roles in the formation of the blends.     

Mixing of triply degenerated molecular orbitals in C602− and C603−

Mixing of triply degenerated lowest unoccupied molecular orbitals (LUMO; t_1u) and the next LUMO (NLUMO; t_1g) of a neutral C₆₀ molecule was estimated when it becomes dianionic (C₆₀²⁻) and trianionic (C₆₀³⁻) species. The electronic structure of the basic C₆₀ was obtained by a semiempirical (INDO type) Hartree-Fock scheme and the mixing of the t_1u and t_1g MOs by the conventional configuration interaction (CI) method assuming I_h structural symmetry of a C₆₀ for the sake of simplicity. The most favorable electronic states of C₆₀²⁻ and C₆₀³⁻ are predicted to be triplet and doublet, respectively. Furthermore, in C₆₀²⁻, the energy difference of this triplet state and the first excited singlet state is very close, which agrees well with the experimental observation. © 1997 John Wiley & Sons, Inc.     

Theoretical study of the π→π* excited states of linear polyenes: The energy gap between 11Bu+ and 21Ag− states and their character

Multireference perturbation theory with complete active space self-consistent field (CASSCF) reference functions is applied to the study of the valence π→π* excited states of 1,3-butadiene, 1,3,5-hexatriene, 1,3,5,7-octatetraene, and 1,3,5,7,9-decapentaene. Our focus was put on determining the nature of the two lowest-lying singlet excited states, 1¹B_u⁺ and 2¹A_g⁻, and their ordering. The 1¹B_u⁺ state is a singly excited state with an ionic nature originating from the HOMO→LUMO one-electron transition while the covalent 2¹A_g⁻ state is the doubly excited state which comes mainly from the (HOMO)²→(LUMO)² transition. The active-space and basis-set effects are taken into account to estimate the excitation energies of larger polyenes. For butadiene, the 1¹B_u⁺ state is calculated to be slightly lower by 0.1 eV than the doubly excited 2¹A_g⁻ state at the ground-state equilibrium geometry. For hexatriene, our calculations predict the two states to be virtually degenerate. Octatetraene is the first polyene for which we predict that the 2¹A_g⁻ state is the lowest excited singlet state at the ground-state geometry. The present theory also indicates that the 2¹A_g⁻ state lies clearly below the 1¹B_u⁺ state in decapentaene with the energy gap of 0.4 eV. The 0–0 transition and the emission energies are also calculated using the planar C_2h relaxed excited-state geometries. The covalent 2¹A_g⁻ state is much more sensitive to the geometry variation than is the ionic 1¹B_u⁺ state, which places the 2¹A_g⁻ state significantly below the 1¹B_u⁺ state at the relaxed geometry. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 157–175, 1998     

Motion of large DNA molecules traveling from solution to gel under steady field

Direct observation of individual T4 DNA molecules at the interface between gel and pure solvent under steady electric field was carried out with fluorescence microscopy. Statistical analyses of the image data show that (1) when a DNA arrives at the gel surface, it remains there for a short time before the DNA stretches its arms to enter the gel, and (2) the time spent on the gel surface increases with an increase of the agarose percentage in the gel. © 1996 John Wiley & Sons, Inc.