On the stability of double stranded nucleic acids

We present the first pressure-versus-temperature phase diagram for the helix-to-coil transition of double stranded nucleic acids. The thermodynamic stability of a nucleic acid duplex is a complex function of temperature and pressure and strongly depends on the denaturation temperature, T(M), of the duplex at atmospheric pressure. Depending upon T(M), pressure, and temperature, the phase diagram shows that pressure may stabilize, destabilize, or have no effect on the conformational state of DNA. To verify the phase diagram, we have conducted high-pressure UV melting experiments on poly(dIdC)poly(dIdC), a DNA duplex, poly(rA)poly(rU), an RNA duplex, and poly(dA)poly(rU), a DNA/RNA hybrid duplex. The T(M) values of these duplexes have been modulated by altering the solution ionic strength. Significantly, at low salt, these three duplexes have helix-to-coil transition temperatures of 50 degrees C or less. In agreement with the derived phase diagram, we found that the polymeric duplexes were destabilized by pressure if the T(M) is < approximately 50 degrees C. However, these duplexes were stabilized by pressure if the T(M) is > approximately 50 degrees C. The DNA/RNA hybrid duplex, poly(dA)poly(rU), with a T(M) of 31 degrees C in 20 mM NaCl undergoes a pressure-induced helix-to-coil transition at room temperature. This is the first report of pressure-induced denaturation of a nucleic acid duplex and provides new insights into the molecular forces stabilizing these structures.     

Proton transfer in small model systems: A density functional study

The structures, interaction energies, and proton-transfer features of some representative intermolecular complexes are determined by using a density functional which incorporates gradient corrections and, as recently suggested by Becke, some Hartree–Fock exchange. The results are compared with those obtained by high-order many-body perturbation theory and by a number of more conventional density functionals. Hydrogen-bond strengths and interatomic distances between heavy atoms are well reproduced by several density functionals. However, inclusion of some Hartree–Fock exchange is mandatory to improve XH bond lengths, and, especially, energy barriers governing proton transfer. Use of the new functional significantly improves the agreement with experimental and post-Hartree–Fock results. This paves the route for a detailed theoretical study of proton-transfer processes in large, biologically significant systems. © 1995 John Wiley & Sons, Inc.     

The interaction of poly(ethylenimine) with nucleic acids and its use in determination of nucleic acids based on light scattering

For the first time, poly(ethylenimine) (PEI) was used to determine nucleic acids with a light scattering technique using a common spectrofluorometer. The interaction of PEI with DNA results in greatly enhanced intensity of light scattering at 300 nm, which is caused by the formation of the big particles between DNA and PEI. Based on this, a new quantitative method for nucleic acid determination in aqueous solutions has been developed. Under the optimum conditions, the enhanced intensity of light scattering is proportional to the concentration of nucleic acid in the range of 0.01-10.0 microg ml(-1) for herring sperm DNA (hsDNA), 0.02-10.0 microg ml(-1) for calf thymus DNA (ctDNA), 0.02-20.0 microg ml(-1) for yeast RNA (yRNA). The detection limits are 5.3, 9.9, and 13.7 ng ml(-1), respectively. Synthetic samples were determined satisfactorily. At the same time, the light scattering technique has been successfully used to obtain the information on the effects of pH and ionic strength on the formation and the stability of the DNA/PEI complex, which is important in some fields such as genetic engineering and gene transfer. Using ethidium bromide (EB) as a fluorescent probe, the binding of PEI with hsDNA was studied. Both the binding constant of EB with DNA and the number of binding sites per nucleotide decrease with increasing concentration of PEI, indicating noncompetitive inhibition of EB binding to DNA in the presence of PEI. And the association constant of PEI to DNA obtained is 1.2 x 10(5) M(-1). IR-spectra show that PEI interacts with DNA through both the phosphate groups and the bases of DNA and the formation of DNA/PEI complex may cause the change of the conformation of the DNA secondary structure, which is also proved by UV-spectra.     

Molecular electrotatic potential of a triple stranded helix: Poly(dT)·poly(dA)·poly(dT)

The molecular electrostatic potential of the triple helix poly(dT)·tpoly(dA)·poly(dT) is calculated, and the results are examined in relation to those obtained for its component double and single helical parts. For the double helix presenting the standard Watson–Crick hydrogen bonds, the deepest potentials are formed on the side of the major groove, a situation similar to that observed in the A-DNA duplex. For the double helix presenting Hoogsteen-type hydrogen bonds the deepest potentials lie in the major groove, on the side of the pyrimidine strand. In the triple helix the deepest potentials are located in the major groove in a narrow zone over the thymine bases of the Watson–Crick pair.     

Towards Stereoselective Synthesis of the C(31)–C(39) and C(20)–C(27) Fragments of Phorboxazole A

The stereoselective synthesis of the C(31)–C(39) and C(20)–C(27) fragments of phorboxazole A ( 1 ) was achieved from commercially available and inexpensive D ‐mannitol. Crimmins aldol reaction and a decarboxylative Claisen‐type reaction are the key steps for the C(31)–C(39) fragment, and L ‐proline‐catalyzed aldol reaction, Sharpless asymmetric epoxidation, and epoxide ring opening reaction with Gilman's reagent are the key steps for the C(20)–C(27) fragment of phorboxazole.     

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.     

Structure formation in systems involving poly(ethylene oxide) and small molecules

The structure of the intercalates in which poly(ethylene oxide), PEO, is the host component and para-disubstituted benzenes are the guest molecules is completely elucidated by X-ray diffractometry, polarized FTIR spectrography, and calorimetry. It is shown that the association of these molecules results from the adaptation of the shape of their external surfaces. On this basis the possibility of formation of structure involving PEO and small molecules is discussed.     

Synthesis of poly(propylene glycol)-block-polyethylenimine triblock copolymers for the delivery of nucleic acids

LPEIs, which are efficient DNA transfection agents, were found to be far less effective for the delivery of siRNAs. Here, two amphiphilic triblock copolymers LPEI(50) -b-PPG(36) -b-LPEI(50) (2) and LPEI(14) -b-PPG(68) -b-LPEI(14) (4) have been synthesized. The transfection assays showed that compound 2 was efficient for DNA transfection whilst it was almost inactive for siRNA delivery. In contrast, polymer 4 was inefficient for DNA transfection while it showed capabilities for siRNA delivery. Taken together, our results indicate that the properties required for DNA and siRNA delivery are different. Moreover, we show that introduction of a hydrophobic segment that allows self-assembly confers siRNA delivery capacities.     

A dielectric study of poly(ethylene-co-vinylacetate)–poly(vinyl chloride) blends. I. Miscibility and phase behavior

Measurements of the complex permittivity were used to study miscibility and phase behavior in blends of poly(vinyl chloride) (PVC) with two random ethylene—vinyl acetate (EVA) copolymers containing 45 and 70 wt % of vinyl acetate. The dielectric β relaxation of the pure polymers and blends was followed as a function of temperature and frequency for different blend compositions and thermal treatments. Blends of EVA 70/PVC were found to be miscible for compositions of about 25% EVA 70 and higher. Blends of lower EVA 70 content showed evidence of two-phase behavior. EVA 45/PVC blends were found to be miscible only at the composition extremes; at intermediate compositions these blends were two-phase, partially miscible. Both blend systems showed lower critical solution temperature behavior. Phase separation studies revealed that in the EVA 45/PVC blends, PVC was capable of diffusing into the higher T_g phase at temperatures below the T_g of the upper phase. In the blends, ion transport losses were significant above the loss peak temperatures, and in the two-phase systems, often obscured the upper temperature loss process. It was shown possible, however, to correct the loss curves for this transport contribution.     

Synthesis and micellization of amphiphilic poly(sebacic anhydride)–poly(ethylene glycol)–poly(sebacic anhydride) block copolymers

Amphiphilic biodegradable block copolymers [poly(sebacic anhydride)–poly(ethylene glycol)–poly(sebacic anhydride)] were synthesized by the melt polycondensation of poly(ethylene glycol) and sebacic anhydride prepolymers. The chemical structure, crystalline nature, and phase behavior of the resulting copolymers were characterized with ¹H NMR, Fourier transform infrared, gel permeation chromatography, and differential scanning calorimetry. Microphase separation of the copolymers occurred, and the crystallinity of the poly(sebacic anhydride) (PSA) blocks diminished when the sebacic anhydride unit content in the copolymer was only 21.6%. ¹H NMR spectra carried out in CDCl₃ and D₂O were used to demonstrate the existence of hydrophobic PSA domains as the core of the micelle. In aqueous media, the copolymers formed micelles after precipitation from water‐miscible solvents. The effects on the micelle sizes due to the micelle preparation conditions, such as the organic phase, dropping rate of the polymer organic solution into the aqueous phase, and copolymer concentrations in the organic phase, were studied. There was an increase in the micelle size as the molecular weight of the PSA block was increased. The diameters of the copolymer micelles were also found to increase as the concentration of the copolymer dissolved in the organic phase was increased, and the dependence of the micelle diameters on the concentration of the copolymer varied with the copolymer composition. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1271–1278, 2006     

Synthesis and block‐specific complexation of poly(ethylene oxide)–poly(tetrahydrofuran)–poly(ethylene oxide) triblock copolymers

Well‐defined ABA triblock copolymers in which A stands for poly(ethylene oxide) (PEO) and B for poly(tetrahydrofuran) (PTHF) were synthesized by end‐capping bifunctionally living PTHF with different polyethylene glycol–monomethylethers. Differential scanning calorimetry analysis of these copolymers showed two melting points: one around 55 °C due to the PEO blocks, and one around 30 °C due to the PTHF segments, demonstrating that these block copolymers show extensive phase separation. Upon addition of sodium thiocyanate, crystalline complexes with PEO were formed and as a consequence, the melting points of the PEO segments had shifted to approximately 170 °C, whereas the melting points of the PTHF segments decreased slightly. The obtained materials behave as thermoplastic elastomers up to 160–175 °C. The influence of the relative lengths of the PEO and the PTHF segments on the thermal and mechanical properties of the materials have been investigated. Copyright © 1999 John Wiley & Sons, Ltd.     

Thermodynamic studies of some complexation systems involving methacrylic acid-acrylamide copolymer,poly(vinyl pyrrolidone) and poly(ethylene oxide)

Interpolymer complexes of methacrylic acid-acrylamide copolymer have been prepared by the interaction of its comonomer units with two different homopolymers, and also with a single homopolymer. The stability constants and related thermodynamic parameters (e.g., ΔH⁰ and ΔS⁰) of the mixed complex were found to be significantly different from the single homopolymer complexes. This has been attributed to neighboring group influence and destabilization of various interacting forces at different temperatures. © 1994 John Wiley & Sons, Inc.     

Joule heating and heat transfer in poly(dimethylsiloxane) microfluidic systems

Joule heating is a significant problem in electrokinetically driven microfluidic chips, particularly polymeric systems where low thermal conductivities amplify the difficulty in rejecting this internally generated heat. In this work, a combined experimental (using a microscale thermometry technique) and numerical (using a 3D "whole-chip" finite element model) approach is used to examine Joule heating and heat transfer at a microchannel intersection in poly(dimethylsiloxane)(PDMS), and hybrid PDMS/Glass microfluidic systems. In general the numerical predictions and the experimental results agree quite well (typically within +/- 3 degree C), both showing dramatic temperature gradients at the intersection. At high potential field strengths a nearly five fold increase in the maximum buffer temperature was observed in the PDMS/PDMS chips over the PDMS/Glass systems. The detailed numerical analysis revealed that the vast majority of steady state heat rejection is through lower substrate of the chip, which was significantly impeded in the former case by the lower thermal conductivity PDMS substrate. The observed higher buffer temperature also lead to a number of significant secondary effects including a near doubling of the volume flow rate. Simple guidelines are proposed for improving polymeric chip design and thereby extend the capabilities of these microfluidic systems.     

Energy transfer and radical formation in the system poly(methyl methacrylate)–2-methyltetrahydrofuran

ESR spectra of γ-irradiated poly(methyl methacrylate) (PMMA) at 77°K and the effect of additives have been studied. γ-Irradiation of PMMA containing a small amount of 2-methyltetrahydrofuran as an additive at 77°K gives MTHF radical. Yields of MTHF radical increase with increasing MTHF concentration and reach a plateau value, and are independent of photobleaching with visible light. Yeilds of polymer radical are reduced by the addition of MTHF. Some elementary processes for the MTHF radical formation are proposed on the basis of the experimental results.     

A novel acrylonitrile–butadiene–styrene/poly(ethylene glycol) membrane: preparation,characterization, and gas permeation study

Polymeric membranes were prepared by blending different grades of poly(ethylene glycol) (PEG) as the added polymer with acrylonitrile–butadiene–styrene as the backbone structure. The membranes were characterized by Fourier transform infrared, X‐ray diffractometry, dynamic mechanical thermal analysis, differential scanning calorimetry, and scanning electron microscopy. Furthermore, the gas permeation and separation properties of CO₂/CH₄ were studied. In addition, the effect of pressure (1–8 bar) and the effect of PEG content (0–40 wt%) on CO₂ and CH₄ permeability/selectivity were investigated. The results showed that, in more cases, with the introduction of PEG molecules, CO₂/CH₄ selectivity increases without significant changes in CH₄ permeability, indicating that the incorporation of intermolecular interaction is suitable for the separation of gas pairs with no molecular size domination but the solution–diffusion. From the viewpoint of gas separation applications, the resultant data are in the commercially attractive region. Copyright © 2011 John Wiley & Sons, Ltd.     

Voltammetric study of the interaction of ciprofloxacin-copper with nucleic acids and the determination of nucleic acids

The behavior of the ciprofloxacin (CPFX) complex with copper, Cu(II)L₂, at a mercury electrode has been investigated in borax–boric acid buffer. The adsorption phenomena were observed by linear sweep voltammetry. The mechanism of the electrode reaction was found to be reduction of Cu(II)L₂ adsorbed on the surface of the electrode by an irreversible charge transfer to metal amalgam, Cu(0)(Hg). In the presence of DNA, the formation of the electrochemically non-active complexes Cu(II)L₂–DNA results in the decrease of the equilibrium concentration of Cu(II)L₂ and its peak current. Under the optimum conditions, the decrease of the peak current is proportional to DNA concentration. The linear ranges are 6.67×10⁻⁸ to 1.20×10⁻⁵ g ml⁻¹ for calf thymus DNA (ctDNA), 3.30×10⁻⁸ to 2.33×10⁻⁶ g ml⁻¹ for fish sperm DNA (fsDNA) and 1.0×10⁻⁸ to 1.2×10⁻⁶ g ml⁻¹ for yeast RNA. The detection limits are 5.00×10⁻⁹, 3.00×10⁻⁹ and 2.50×10⁻⁹ g ml⁻¹, respectively. This method exhibits good recovery and high sensitivity.     

Crystallization of poly(tetramethyl-p-silphenylene–dimethylsiloxane) (TMPS–DMS) block copolymers: Morphology and kinetics

The crystallization behavior of random block copolymers of (tetramethyl-p-silphenylenesiloxane) and dimethylsiloxane has been studied over a wide range of temperature and composition. The copolymer melting temperature, glass transition temperature, rate of crystallization, crystallinity, and density decrease in magnitude as the dimethylsiloxane block content are raised in this two-component system. The crystal end-surface (interfacial) energy increases as the dimethylsiloxane mole fraction decreases in accord with other morphological observations. The morphological changes observed in these copolymers are consistent with the conclusions deduced from the crystallization kinetics. Negatively, birefringent spherulites are observed over the entire crystallization range investigated.     

Organic–inorganic hybrid hydrogels involving poly(N‐isopropylacrylamide) and polyhedral oligomeric silsesquioxane: Preparation and rapid thermoresponsive properties

3‐Acryloxypropylhepta(3,3,3‐trifluoropropyl) polyhedral oligomeric silsesquioxane (POSS) was synthesized and used as a modifier to improve the thermal response rates of poly(N‐isopropylacrylamide) (PNIPAM) hydrogel. The radical copolymerization among N‐isopropylacrylamide (NIPAM), the POSS macromer and N,N′‐methylenebisacrylamide was performed to prepare the POSS‐containing PNIPAM cross‐linked networks. Differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) showed that the POSS‐containing PNIPAM networks displayed the enhanced glass transition temperatures (T_g's) and improved thermal stability when compared with plain PNIPAM network. The POSS‐containing PNIPAM hydrogels exhibited temperature‐responsive behavior as the plain PNIPAM hydrogels. It is noted that with the moderate contents of POSS, the POSS‐containing PNIPAM hydrogels displayed much faster response rates in terms of swelling, deswelling, and re‐swelling experiments than plain PNIPAM hydrogel. The improved thermoresponsive properties of hydrogels have been interpreted on the basis of the formation of the specific microphase‐separated morphology in the hydrogels, that is, the POSS structural units in the hybrid hydrogels were self‐assembled into the highly hydrophobic nanodomains, which behave as the microporogens and promote the contact of PNIPAM chains and water. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 504–516, 2009     

Förster energy transfer from poly(arylene–ethynylene)s to an erbium–porphyrin complex

We study the infrared emission at 1.54 μm of an organolanthanide complex, Er(III)-tetraphenylporphyrin [Er(TPP)acac], both as a result of direct optical excitation and via energy transfer from host π-conjugate polymers of type poly(arylene–ethynylene) [PAE]. In the first case, the emission of the neat complex is characterized in inert transparent materials and a value of the quantum yield at 1.54 μm φ_IR=4×10⁻⁴ is measured. Then, fluorescence resonance transfer is investigated in blends of Er(TPP)acac with PAEs by monitoring the quenching of the polymer fluorescence along with the enhancement of both the visible emission of the ligand and the near-infrared band of Er³⁺. These different procedures allow a detailed analysis of the transfer efficiency within a specific implementation of the Förster model for polymeric donors. The experimental values of the critical radius R₀, ranging from 1.3 to 2.5 nm for the different blends, are in good agreement with theory for a wide interval of the physical and spectroscopic parameters. This suggests that other mechanisms for excitation transfer do not play a significant role in these materials.     

Photoinduced dissociative electron transfer (DET) interactions in methoxycalixarene–chloroalkane systems

Fluorescence quenching of methoxycalixarenes (MOCX) by chloroalkanes (CA) has been investigated in acetonitrile solutions. Observed quenching is attributed to photoinduced dissociative electron transfer (DET) interaction, which is supported by the characterization of the Cl⁻ ions and by the radical scavenging experiments. Comparing the Cl⁻ yields with different DET systems, it is inferred that both concerted and stepwise DET mechanisms operate simultaneously in MOCX–CA systems. A correlation of the quenching constants with the free-energy changes following a suitable DET theory supports the above inference.