The structure of triple helical poly(U).poly(A).poly(U) studied by Raman spectroscopy

Using Raman spectroscopy, we examined the ribose-phosphate backbone conformation, the hydrogen bonding interactions, and the stacking of the bases of the poly(U).poly(A).poly(U) triple helix. We compared the Raman spectra of poly(U).poly(A).poly(U) in H2O and D2O with those obtained for single-stranded poly(A) and poly(U) and for double-stranded poly(A).poly(U). The presence of a Raman band at 863 cm-1 indicated that the backbone conformations of the two poly(U) chains are different in the triple helix. The sugar conformation of the poly(U) chain held to the poly(A) by Watson-Crick base pairing is C3' endo; that of the second poly(U) chain may be C2' endo. Raman hypochromism of the bands associated with base vibrations demonstrated that uracil residues stack to the same extent in double helical poly(A).poly(U) and in the triple-stranded structure. An increase in the Raman hypochromism of the bands associated with adenine bases indicated that the stacking of adenine residues is greater in the triple helix than in the double helical form. Our data further suggest that the environment of the carbonyls of the uracil residues is different for the different strands.     

The Z-conformation of poly(dA-dT).poly(dA-dT) in solution as studied by ultraviolet resonance Raman spectroscopy

Poly(dA-dT).poly(dA-dT) structures in aqueous solutions with high NaCl concentrations and in the presence of Ni2+ ions have been studied with resonance Raman spectroscopy (RRS). In low water activity the effects of added 95 mM NiCl2 in solution stabilize the syn geometry of the purines and reorganize the water distribution via local interactions of Ni-water charged complexes with the adenine N7 position. It is shown that RRS provides good marker bands for a left-handed helix: i) a purine ring breathing mode around 630 cm-1 coupled to the deoxyribose vibration in the syn geometry, ii) a 1300-1340 cm-1 region characterizing local chemical interactions of the Ni2+ ions with the adenine N7 position, iii) lines at about 1483- and 1582 cm-1 correlated to the anti/syn reorientation of the adenine residues on B-Z structure transition, iv) marker bands of the thymidine carbonyl group couplings at 1680- and 1733 cm-1 due to the disposition of the thymidine residues in the Z helix specific geometry. Hence poly(dA-dT).poly(dA-dT) can adopt a Z form in solution. The Z form observed in alternate purine-pyrimidine sequences does not require G-C base pairs.     

Water/polymer interactions in a poly(amidoamine) hydrogel studied by NMR spectroscopy

Samples of PAAH1, a cross-linked polymer belonging to the family of poly(amidoamine)s, were investigated at different hydration levels by means of 13C and 1H NMR techniques in order to obtain information on water/polymer interactions. Carbonyl oxygens and amine nitrogens were identified as the main sites of interaction giving hydrogen bonding with water molecules. The polymer turned out to be uniformly plasticized already at moderate degrees of swelling. The hydration process was found to occur in a stepwise manner, with the first batch of water saturating a hydration layer and additional water filling the polymer meshes. The proportion of water in the different states was quantitatively determined.     

Probe diffusion in aqueous poly(vinyl alcohol) solutions studied by fluorescence correlation spectroscopy

We report fluorescence correlation spectroscopy measurements of the translational diffusion coefficient of various probe particles in dilute and semidilute aqueous poly(vinyl alcohol) solutions. The range of sizes of the particles (fluorescent molecules, proteins, and polymers) was chosen to explore various length scales of the polymer solutions as defined by the polymer-polymer correlation length. For particles larger than the correlation length, we find that the diffusion coefficient, D, decreases exponentially with the polymer concentration. This can be explained by an exponential increase in the solution viscosity, consistent with the Stokes-Einstein equation. For probes on the order of the correlation length, the decrease of the diffusion coefficient cannot be accounted for by the Stokes-Einstein equation, but can be fit by a stretched exponential, D approximately exp(-alphacn), where we find n = 0.73-0.84 and alpha is related to the probe size. These results are in accord with a diffusion model of Langevin and Rondelez (Polymer 1978, 19, 1875), where these values of n indicate a good solvent quality.     

Z form of poly d(A-C).poly d(G-T) in solution studied by Raman spectroscopy.

Poly d(A-C).poly d(G-T) structures have been studied in solution by Raman spectroscopy, in presence of Na+, Mn2+ and Ni2+ counterions. Increase of the Na+ concentration or addition of Mn2+ ions up to 1M MnCl2 does not modify the B geometry of the polynucleotide. On the contrary, in conditions of low water activity (4M NaCl), the presence of small amounts of nickel ions (65 mM) induces a left-handed geometry of the DNA. The shift of the guanine line located at 682 cm-1 in B form to 622 cm-1 reflects unambiguously the C2'-endo/anti-greater than C3'-endo/syn reorientation of the deoxyribose-purine entities. Moreover modifications in the phosphate backbone lines indicate that the polymer is in a Z conformation. New or displaced lines corresponding to adenosine vibrations are correlated with the left-handed structure. An interaction of the Ni2+ ions specifically with the N7 site of purines, combined with a low water activity is necessary to promote the B-greater than Z transition.     

pH dependence and protein selectivity of poly(ethyleneimine)/poly(acrylic acid) multilayers studied by in situ ATR-FTIR spectroscopy

The selective interaction between polyelectrolyte multilayers (PEM) consecutively adsorbed from poly(ethyleneimine) (PEI) and poly(acrylic acid) (PAC) and a binary mixture containing concanavalin A (COA) and lysozyme (LYZ) based on electrostatic interaction is reported. The composition and structure of the PEM and the uptake of proteins were analyzed by in situ attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy, and the morphology and thickness were characterized by atomic force microscopy (AFM) and ellipsometry. The PEM dissociation degree and charge state and the protein adsorption were shown to be highly dependent on the outermost layer type and the pH in solution. High protein uptake was obtained under electrostatically attractive conditions. This was used to bind selectively one protein from a binary mixture of LYZ/COA. In detail it could be demonstrated that six-layered PEM-6 at pH = 7.3 showed a preferential sorption of positively charged LYZ, while at PEM-5 and pH = 7.3 negatively charged COA could be selectively bound. No protein sorption from the binary mixture was observed at pH = 4.0 for both PEM, when COA, LYZ, and the outermost PEI layer of PEM-5 were positively charged or the outermost PAC layer of PEM-6 was neutral. Furthermore, from factor analysis of the spectral data the higher selectivity was found for PEM-5 compared to PEM-6. Increasing the ionic strength revealed a drastic decrease in the selectivity of both PEM. Evidence was found that the proteins were predominantly bound at the surface and to a minor extent in the bulk phase of PEM. These results suggest possible working regimes and application fields of PEI/PAC multilayer assemblies related to the preparative separation of binary and multicomponent protein mixtures (biofluids, food) as well as to the design of selective protein-resistant surfaces.     

The mechanical properties and molecular dynamics of plant cell wall polysaccharides studied by Fourier-transform infrared spectroscopy

Polarized one- and two-dimensional infrared spectra were obtained from the epidermis of onion (Allium cepa) under hydrated and mechanically stressed conditions. By Fourier-transform infrared microspectroscopy, the orientation of macromolecules in single cell walls was determined. Cellulose and pectin exhibited little orientation in native epidermal cell walls, but when a mechanical stress was placed on the tissue these molecules showed distinct reorientation as the cells were elongated. When the stress was removed the tissue recovered slightly, but a relatively large plastic deformation remained. The plastic deformation was confirmed in microscopic images by retention of some elongation of cells within the tissue and by residual molecular orientation in the infrared spectra of the cell wall. Two-dimensional infrared spectroscopy was used to determine the nature of the interaction between the polysaccharide networks during deformation. The results provide evidence that cellulose and xyloglucan associate while pectin creates an independent network that exhibits different reorientation rates in the wet onion cell walls. The pectin chains respond faster to oscillation than the more rigid cellulose.     

Substrate recognition by ribosome-inactivating protein studied by molecular modeling and molecular electrostatic potentials

A computer model of dianthin 30, a type 1 ribosome-inactivating protein (RIP), is constructed by homology modeling using two known X-ray structures; a type 1 RIP, pokeweed antiviral protein (PAP), and chain A of a type 2 RIP, ricin. The 3D structure is refined by molecular dynamics and its binding site compared with those of PAP and ricin using molecular electrostatic potential mapping. The differences in the maps obtained clearly show how, despite the similarity of the topology of the binding site, differences in electrostatic potential can account for the experimentally observed differences in substrate recognition and binding. This demonstrates the potential of these techniques for guiding further experimental analyses.     

Variable temperature FTIR study of poly(ethylene-co-vinyl alcohol)-graft-poly(epsilon-caprolactone)

A recently developed technique, i.e., two-dimensional infrared (2D IR) correlation spectroscopy, is used to study the thermal behavior of poly(ethylene-co-vinyl alcohol)-graft-poly(epsilon-caprolactone), a new synthesized highly grafted copolymer. The use of the 2D IR approach to analyze temperature-dependent spectra collected in situ during the temperature elevation process effectively enhanced the spectral resolution and revealed details on the hydrogen bonding and conformational change which are not easily detected in the traditional one-dimensional spectra. The sequence of the spectral changes of different OH and CH(2) fundamental vibrations during heating the polymer was inferred from the signs of the asynchronous peaks. Evidence that the conformational changes of the methylene groups precede the loosening of hydrogen bonds is provided.     

Hydrogen bonding in stereoregular poly(methyl methacrylate)/poly(vinyl chloride) blends as studied by molecular dynamics simulations

In this work, two technically important polymer blends composed of isotactic poly (methyl methacrylate) (iPMMA) or syndiotactic poly (methyl methacrylate) (sPMMA) and isotactic poly (vinyl chloride) (iPVC) have been extensively investigated by molecular dynamics simulations. It is confirmed that sPMMA exhibits stronger interactions with iPVC than does iPMMA, and the non-conventional hydrogen bonds (HBs) occur between the two distinct components. Furthermore, the HBs in sPMMA/iPVC are more than those in iPMMA/iPVC, and the structural relaxation of HBs is closely associated with the backbone chain dynamics, which well explain the experimental trends in miscibility of the two systems and in glass transition temperature of single components. It should be noted that these results cannot be directly obtained by the experiments and single simulations, and the multiscale schemes used to prepare the initial all-atomistic configurations can play an important role. This work provides some key clues to improve the performance of polymer materials.     

Depth profile of free volume in a mixture and copolymers of poly(N-vinyl-pyrrolidone) and poly(ethylene glycol) studied by positron annihilation spectroscopy

Effect of hydrogen bonding on the depth profile of the free-volume in a mixture (weight ratio of 65:35) of poly(N-vinyl-pyrrolidone) (PVP) and poly(ethylene glycol) (PEG) and the copolymers of vinyl pyrrolidone with poly(ethylene glycol) diacrylate (PVP-PEGDA) and monomethacrylate (PVP-PEGMMA) was studied using positron annihilation spectroscopy. Doppler broadening energy spectra of annihilation radiation and positron annihilation lifetime were measured as a function of positron incident energy (0-30 keV). Significant variations of the free-volume depth profile in terms of the S parameter, ortho-positronium lifetime, intensity, and lifetime distribution are observed as a result of the hydrogen-bonding replacement of covalent bonds. The polymer mixture with hydrogen bonding through two sides of PEG short chains has a larger free volume and a wider distribution than the comb-structured PVP-PEGMMA and the network structured PVP-PEGDA. A longer ortho-positronium lifetime is observed near the surface than in the bulk. This is interpreted in terms of surface effect, free volume, and hydrogen bonding for drug delivery applications of polymeric materials.     

Study on fisetin-aluminium(III) interaction in aqueous buffered solutions by spectroscopy and molecular modeling

Spectroscopic (UV/visible and IR) and theoretical studies were used to assess relevant interaction of fisetin, a tetrahydroxylated flavone molecule, and trivalent aluminium in a wide range of buffered aqueous solutions. The chelation sites, stoichiometry, stability and the dependence of the complexes structures on pH and aluminium/fisetin mole ratios were defined. Obtained results implicated successive formation of two complexes with aluminium(III)-fisetin stoichiometries of 1:1 and 2:1. Considering the fisetin molecular structure, results of vibrational analysis and theoretical calculations, it is possible to implicate 3-hydroxyl-4-carbonyl and 3′4′-dihydroxyl groups as those with the possible chelating power. The equilibrium geometries were optimized in vacuum at the B3LYP/6-31G(d) level of theory, which predict structural modifications between the ligand molecule in free state and in the complex structure. The theoretical model has been validated by both vibrational and electronic spectroscopies.     

Interaction of transition metal ions with Z form poly d(A-C).poly d(G-T) and poly d(A-T) studied by I.R. spectroscopy.

Interactions between Ni2+, Co2+ and purine bases have been studied by I.R. spectroscopy in the case of double stranded regularly alternating purine-pyrimidine polynucleotides poly d(A-T), poly d(A-C).poly d(G-T) and poly d(G-C). The spectra of polynucleotide films have been recorded in hydration and salt content conditions which correspond to the obtention of the classical right-handed (A,B) and left-handed (Z) helical conformations. Selective deuteration of the 8C site of purines has been obtained and is used to detect interactions between the transition metal ions and the adenine or guanine bases. The spectral region between 1500 and 1250 cm-1 corresponding to base in-plane vibrations and involving also the glycosidic linkage torsion is discussed in detail. The selective interaction between the transition metal ion and the 7N site of the purine base is considered to be partly responsible for the stabilization of the base in a syn conformation, which favours the adoption by the polynucleotide (poly d(G-C), poly d(A-C).poly d(G-T) or poly d(A-T)) of a Z type conformation.     

Left-handed helical structure of poly[d(A-C)].poly[d(G-T)] studied by infrared spectroscopy

Infrared spectroscopic studies demonstrate the ability of poly[d(A-C)].poly[d(G-T)] to adopt a Z-type conformation. The Z form of the unmodified polynucleotide is induced by Ni2+ counterions and not by Na+. The B----Z equilibrium is shifted at room temperature, in the presence of 1 Ni2+/nucleotide, by an increase in the concentration of poly[d(A-C)].poly[d(G-T)]. The importance of specific binding of Ni2+ ions on the N7 site of purines in the stabilization of the Z form is also discussed.     

Salt-induced conformational transition of poly(d2NH2A-dT) studied by ultraviolet resonance Raman spectroscopy.

The conformational changes of poly(d2NH2A-dT) in aqueous solution, induced by increasing the NaCl concentration from 0.1M to 4M, have been monitored by ultraviolet resonance Raman spectroscopy, in using the 222-, 257- and 281 nm excitation wavelengths. These changes have been interpreted in comparing the polymer spectra to those of the mononucleotide compounds on one hand, and to those of other alternating purine-pyrimidine polymers on the other hand, i.e. poly(dG-dC) and poly(dA-dT) which showed a B to Z transition in going from low- to high salt concentrations. The high salt poly(d2NH2A-dT) spectra do not show any Raman marker line of the Z conformation. The spectroscopic results indicate that most of the ribose puckering goes from C2'-endo/anti to C3'-endo/anti in increasing the salt concentration. In addition the base stacking interactions, to which the resonance Raman effect is very sensitive, are not drastically changed upon salt variations. Thus the high salt structure of poly(d2NH2A-dT) remains a right-handed helix, likely under a dominant A conformation.     

Conformation of DNA in chromatin core particles containing poly(dAdT)-poly(dAdT) studied by 31 P NMR spectroscopy.

We have prepared semi-synthetic chromatin core particles from a complex of chicken erythrocyte inner histones (H2A, H2B, H3 and H4) with double-stranded poly(dAdT).poly(dAdT) and studied the conformation of the phosphodiester backbone using 31P NMR at 109.3 MHz. At 20 degrees C, the core particle spectrum is fit well by a single Lorenzian distribution with a line width of 110 Hz. This signal is significantly broader than that for the 145 base pair poly(dAdT).poly(dAdT) alone; the latter consists of two resonances, approximately equal in intensity, with average line width 41 Hz. Major changes in the spectrum ensue on heating the core particle preparation. In conjunction with other results (1) these data suggest four states for the core particle at increasing temperatures. Additionally, analysis of the spectrum of the unmelted core particle and its differences from protein-free DNA of the same length suggests that the conformation of the phosphodiester backbone and/or its interactions with histones along the length of the core particle DNA segment may not be uniform.     

Properties of invertase immobilized on the poly(ethylene-co-vinyl alcohol) hollow fiber membrane

Invertase was ionically immobilized on the poly(ethylene-co-vinyl alcohol) hollow fiber inside surface, which was aminoacetalized with 2-dimethylaminoacetaldehyde dimethyl acetal. Immobilization and enzyme reaction were carried out by letting the respective solutions pass or circulate through the inside of the hollow fiber, and the activity of invertase was determined by the amount of glucose produced enzymatically from sucrose. Immobilization conditions were examined with respect to the enzyme concentration and to the time, and consequently the preferable conditions at room temperature were found to be 5 mug/mL of enzyme concentration and 4 h of immobilization time. Under those conditions the immobilization yield and the ratio of the activity of the immobilized invertase to that of the native one were 89 and 80%, respectively. For both repeating and continuous usages, the activity fell to ca. 60% of the initial activity in the early stage and after that almost kept that value. The apparent Michaelis constant K(m) (') for the immobilized invertase decreased with increasing the flow rate of the substrate solution, to be close to the value for the native one. Furthermore, the possibility of the separation of the enzymatically formed glucose from the reaction mixture through the hollow fiber membrane was preliminarily examined.