Structure of Poly (dT)·Poly (dA)·Poly (dT)

Abstract

The molecular structure of poly (dT)·poly (dA)·poly (dT) has been determined and refined using the continuous x-ray intensity data on layer lines in the diffraction pattern obtained from an oriented fiber of the DNA. The final R-value for the preferred structure is 0.29 significantly lower than that for plausible alternatives. The molecule forms a 12-fold right- handed triple-helix of pitch 38.4 Å and each base triplet is stabilized by a set of four Crick-Watson-Hoogsteen hydrogen bonds. The deoxyribose rings in all the three strands have C2′-endo conformations. The grooveless cylindrical shape of the triple-helix is consistent with the lack of lateral organization in the fiber.     

The Structure of Triple Helical Poly(U)·Poly(A)·Poly(U) Studied by Raman Spectroscopy

Abstract

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.     

Formation of Inhalable Rifampicin–Poly(l-lactide) Microparticles by Supercritical Anti-solvent Process

Formation of inhalable microparticles containing rifampicin and poly(l-lactide) (L-PLA) by using supercritical anti-solvent process (SAS) was investigated. The solutions of drug and polymer in methylene chloride were sprayed into supercritical carbon dioxide. The effect of polymer content and operating conditions, temperature, pressure, carbon dioxide molar fraction, and concentration of solution, on product characteristics were studied. The prepared microparticles were characterized with respect to their morphology, particle size and size distribution, drug content, drug loading efficiency, and drug release characteristic. Discrete, spherical microparticles were obtained at high polymer:drug ratios of 7:3, 8:2, and 9:1. The shape of L-PLA microparticles became more irregular and agglomerated with decreasing polymer content. Microparticles with polymer content higher than 60% exhibited volumetric mean diameter less than 5 μm, but percent drug loading efficiency was relatively low. Drug-loaded microparticles containing 70% and 80% L-PLA showed a sustainable drug release property without initial burst release. Operating temperature level influenced on mean size and size distribution of microparticles. The operating pressure and carbon dioxide molar fraction in the range investigated were unlikely to have an effect on microparticle formation. An increasing concentration of feed solution provided larger size microparticles. Rifampicin-loaded L-PLA microparticles could be produced by SAS in a size range suitable for dry powder inhaler formulation.     

Poly(vinylferrocene)–poly(ethylene glycol) glutamate oxidase electrode for determination of L-glutamate in commercial soy sauces

An amperometric L-glutamate oxidase (GLOD) electrode based on a multilayer of polymer films was developed for the high selective determination of L-glutamate. The multilayer film consisted of three layers as the following configuration i.e., inner membrane of electropolymerized 1,3-diaminobenzene, middle layer of L-GLOD entrapped in photopolymerized poly(vinylferrocene)–poly(ethylene glycol) hydrogel polymer, and outer dialysis membrane. In this manner, the sensor could eliminate interferences and was able to work at a low potential poised at +0.085 V vs. Ag/AgCl. When used in a flow injection system, the sensor responded to L-glutamate in the range 0.5–8.0 mM, with a sensitivity of 9.48 nA mM^–1. The sensor was stable for 5 days of continuous uses (250 assays) and retained 60% activity after 16 days. When used to analyse the L-glutamate contents of a number of different off-the-shelf soy sauces, the sensor gave results in good agreement with the standard colorimetric method.     

Structure of Poly(dA)·Poly(dT) is not Identical to the AT Rich Regions of the Single Crystal Structure of CGCGAATTBrCGCG. The Consequence of this to Netropsin Binding to Poly(dA)·Poly(dT)

Abstract

The basic assumption of Dickerson and Kopka (J. Biomole. Str. Dyns. 2, 423, 1985) that the conformation of poly(dA)·poly(dT) in solution is identical to the AT rich region of the single crystal structure of the Dickerson dodecamer is not supported by any experimental data. In poly(dA)·poly(dT), NOE and Raman studies indicate that the dA and dT units are conformationally equivalent and display the (anti-S-type sugar)-conformation; incorporation of this nucleotide geometry into a double helix leads to a conventional regular B-helix in which the width of the minor groove is 8A. The derived structure is consistent with all available experimental data on poly(dA)·poly(dT) obtained under solution conditions. In the crystal structure of the dodecamer, the dA and dT units have distinctly different conformations—dA residues adopt (anti, S-type sugar pucker), while dT residues belong to (low anti, N-type sugar pucker). These different conformations of the dA and dT units along with the large propeller twist can be accommodated in a double helix in which the minor groove is shrunk from 8A to less than 4A. In the conventional right handed B-form of poly(dA)·poly(dT) with the 8A wide minor groove, netropsin has to bind asymmetrically along the dA strand to account for the NOE and chemical shift data and to generate a stereochemically sound structure (Sarma et al, J. Biomole. Str. Dyns. 2, 1085, 1985).     

Development of Push–Pull Osmotic Tablets Using Chitosan–Poly(Acrylic Acid) Interpolymer Complex as an Osmopolymer

The objectives of this study were to prepare push–pull osmotic tablets (PPOT) of felodipine using an interpolymer complex of chitosan (CS) and poly(acrylic acid) (PAA) as an osmopolymer, and to study the mechanisms of drug release from these tablets. The interpolymer complexes were prepared with different weight ratios of CS to PAA. Preparation of PPOT involved the fabrication of bilayered tablets with the drug layer, containing felodipine, polyethylene oxide, and the polymeric expansion layer, containing the CS–PAA complex. The effects of polymer ratios, type of plasticizers, and compression forces on release characteristics were investigated. It was found that drug release from PPOT exhibited zero-order kinetics and could be prolonged up to 12 or 24 h depending on the plasticizer used. PPOT using dibutyl sebacate showed a longer lag time and slower drug release than that using polyethylene glycol 400. In the case of polyethylene glycol 400, an increase in the CS proportion resulted in an increase in the drug release rate. The compression force had no effect on drug release from PPOT. Drug release was controlled by two consecutive mechanisms: an osmotic pump effect resulting in the extrusion of the drug layer from the tablet and subsequent erosion and dissolution of the extruded drug layer in the dissolution medium. The mathematical model (zero-order) related to extrusion and erosion rates for describing the mechanism of drug release showed a good correlation between predicted and observed values.     

The Z-Conformation of Poly(dA-dT) · Poly(dA-dT) in Solution as Studied by Ultraviolet Resonance Raman Spectroscopy

Abstract

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″^?1coupled 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 adenien 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.     

Poly(3-mercaptopropionate): a nonbiodegradable biopolymer?

Polythioesters (PTEs) represent a novel class of biopolymers, which basically can be synthesized with polyhydroxyalkanoate (PHA) biosynthesis systems. Albeit technical applications of PTEs have not been elucidated yet, biodegradability might be an important property of this new thermoplastic material. In this study, extensive approaches were employed to isolate microorganisms capable of degrading poly(3-mercaptopropionate), poly(3MP), as a model compound of PTEs. Screening of 74 different environmental samples using various enrichment techniques were applied, but neither bacteria nor fungi could be isolated hydrolyzing poly(3MP). Furthermore, microcosms such as soil, compost, or activated sludge were applied to search for poly(3MP) degrading microorganisms, considering microbial communities and/or nonculturable bacteria, and the poly(3MP) material was exposed for more than half a year. However, no poly(3MP) degrading organisms were found, indicating an unexpected persistence of this biologically produced polymer.     

Influence of Surfactant Type and Concentration on Electrospinning of Chitosan–Poly(Ethylene Oxide) Blend Nanofibers

Electrospun blend nanofibers were fabricated from chitosan (1,000 kDa, 80% DDA) and poly(ethylene oxide) (PEO; 900 kDa) at a ratio of 3:1 dispersed in 50% and 90% acetic acid. The influence of surfactants on the production of electrospun nanofibers was investigated by adding nonionic polyoxyethylene glycol dodecyl ether (Brij 35), anionic sodium dodecyl sulfate, or cationic dodecyl trimethyl ammonium bromide below, at, and above their specific critical micellar concentration to the polymer blend solution. Viscosity, conductivity, and surface tension of polymer solutions, as well as morphology and composition, of nanofibers containing surfactants were determined. Pure chitosan did not form fibers and was instead deposited as beads. Addition of PEO and an increasing concentration of surfactants induced spinnability and yielded larger fibers with diameters ranging from 10 to 240 nm. Surfactants affected morphology yielding needle-like, smooth, or beaded fibers. Compositional analysis revealed that nanofibers consisted of both polymers and surfactants with concentration of the constituents in nanofibers differing from that in polymer solutions. Results suggest that surfactants may modulate polymer–polymer interactions thus influencing the morphology and composition of deposited nanostructures.     

Conformational Variability of Poly(dA-dT)·Poly(dA-dT) and Some Other Deoxyribonucleic Acids Includes a Novel Type of Double Helix

Abstract

The article reviews data indicating that poly(dA-dT)?poly (dA-dT) is able of adopting three distinct double helical structures in solution, of which only the A form conforms to classical notions. The other two structures have dinucleotides as double helical repeats. At low salt concentrations poly(dA-dT)?poly(dA-dT) adopts a B-type alternating conformation which is exceptionally variable. Its architecture can gradually move in the limits demarcated by the CD spectra with inverted long wavelength CD bands and the ³¹P NMR spectra with a very low and a 0.6 ppm separation of two resonances. Contrary to Z-DNA, the ³¹P NMR spectrum of the limiting alternating B conformation of poly(dA-dT)?poly(dA-dT) is characterized by an upfield shift of one resonance. We attribute the exceptional conformational flexibility of the alternating B conformation to the unequal tendency of bases in the dA-dT and dT-dA steps to stack.

However, by assuming the limiting alternating B conformation, the variability of the synthetic DNA is not exhausted. Specific agents make it isomerize into another conformation by a fast, two-state mechanism, which is reflected by a further deepening of the negative long wavelength CD band and a downfield shift of the ³¹P NMR resonance of poly (dA-dT)?poly(dA-dT) that was constant in the course of the gradual alterations of the alternating B conformation. These changes are, however, qualitatively different from the way poly(dG-dC)?poly(dG-dC) behaves in the course of the B-Z isomerization. Poly(dG-dC) ?poly(dG-dC) displays purine-pyrimidine (dGpdC) resonance in the characteristic downfield position, while the downfield resonance of poly(dA-dT)?poly(dA-dT) belongs to the pyrimidine-purine (dTpdA) phosphodiester linkages. Consequently, phosphodiester linkages in the purine-pyrimidine steps play a similar role in the appearance of the Z form to the pyrimidine-purine phosphodiesters in the course of the isomerization of poly(dA-dT)?poly(dA-dT). This excludes that the high-salt structures of poly(dA-dT)?poly(dA-dT) and poly(dG-dC)?poly(dG-dC) are members of the same conformational family. We call the high-salt conformation of poly(dA-dT)?poly(dA-dT) X-DNA.

It furthermore follows from the review that synthetic molecules of DNA with alternating purine-pyrimidine sequences of bases can adopt either the Z form or the X form, or even both, depending on the environmental conditions. This introduces a new dimension into the DNA double helix conformational variability. The possible biological relevance of the X form is suggested by experiments with linear molecules of natural DNA. These indicate that Arich regions in natural DNAs can isomerize into the X form while the bulk of the molecule remains in the B form. The coexistence of both structures in a single DNA molecule may be understood in view of the favourable kinetic and thermodynamic properties with which the X form appears.     

Poly(rA) • Poly(rU) with Ni2+ Ions at Different Temperatures: Infrared Absorption and Vibrational Circular Dichroism Spectroscopy

Abstract

Phase transitions were studied of the sodium salt of poly(rA) ?poly(rU) induced by elevated temperature without Ni²⁺ and with Ni²⁺ in 0.07 M concentration in D₂O (～0.4 [Ni]/[P]). The temperature was varied from 20° C to 90° C. The double-stranded conformation of poly(rA)?poly(rU) was observed at room temperature (20° C—23° C) with and without Ni²⁺ ions. In the absence of Ni²⁺ ions, partial double- to triple-strand transition of poly(rA) ?poly(rU) occurred at 58° C, whereas only single-stranded molecules existed at 70° C. While poly(rU) did not display significant helical structure, poly(rA) still maintained some helicity at this temperature. Ni²⁺ ions significantly stabilized the triple-helical structure. The temperature range of the stable triple-helix was between 45° C and 70° C with maximum stability around 53° C. Triple-to single-stranded transition of poly(rA) ?poly(rU) occurred around 72° C with loss of base stacking in single-stranded molecules. Stacked or aggregated structures of poly(rA) formed around 86° C. Hysteresis took place in the presence of Ni²⁺ during the reverse transition from the triple-stranded to the double-stranded form upon cooling. Reverse Hoogsteen type of hydrogen-bonding of the third strand in the triplex was suggested to be the most probable model for the triple-helical structure. VCD spectroscopy demonstrated significant advantages over infrared absorption or the related electronic CD spectroscopy.     

Poly(ADP-Ribose) Polymerase 1–Sirtuin 1 Functional Interplay Regulates LPS-Mediated High Mobility Group Box 1 Secretion

Pathophysiological conditions that lead to the release of the prototypic damage-associated molecular pattern molecule high mobility group box 1 (HMGB1) also result in activation of poly(ADP-ribose) polymerase 1 (PARP1; now known as ADP-ribosyl transferase 1 [ARTD1]). Persistent activation of PARP1 promotes energy failure and cell death. The role of poly(ADP-ribosyl)ation in HMGB1 release has been explored previously; however, PARP1 is a versatile enzyme and performs several other functions including cross-talk with another nicotinamide adenine dinucleotide- (NAD⁺) dependent member of the Class III histone deacetylases (HDACs), sirtuin-1 (SIRT1). Previously, it has been shown that the hyperacetylation of HMGB1 is a seminal event prior to its secretion, a process that also is dependent on HDACs. Therefore, in this study, we seek to determine if PARP1 inhibition alters LPS-mediated HMGB1 hyperacetylation and subsequent secretion due to its effect on SIRT1. We demonstrate in an in vitro model that LPS treatment leads to hyperacetylated HMGB1 with concomitant reduction in nuclear HDAC activity. Treatment with PARP1 inhibitors mitigates the LPS-mediated reduction in nuclear HDAC activity and decreases HMGB1 acetylation. By utilizing an NAD⁺-based mechanism, PARP1 inhibition increases the activity of SIRT1. Consequently, there is an increased nuclear retention and decreased extracellular secretion of HMGB1. We also demonstrate that PARP1 physically interacts with SIRT1. Further confirmation of this data was obtained in a murine model of sepsis, that is, administration of PJ-34, a specific PARP1 inhibitor, led to decreased serum HMGB1 concentrations in mice subjected to cecal ligation and puncture (CLP) as compared with untreated mice. In conclusion, our study provides new insights in understanding the molecular mechanisms of HMGB1 secretion in sepsis.     

Near-Infrared Metal-Enhanced Fluorescence Using a Liquid–Liquid Droplet Micromixer in a Disposable Poly(Methyl Methacrylate) Microchip

Solution-based metal-enhanced fluorescence of near-infrared fluorophores in a poly(methyl methacrylate) microchip is studied. A liquid–liquid droplet micromixer is used for rapid mixing of fluorophores with silver nanoparticles while maintaining discrete packets of known analytes for reproducible quantitative analysis. Nanoparticle aggregation within the microchip is controlled by individually adjusting salt concentration, colloid concentration, and mixing efficiency. Results identify an optimal salt concentration for aggregate formation and enhanced fluorescence, while the impacts of colloid concentration and mixing efficiency increase linearly, suggesting the possibility of further enhancement. Fluorescence enhancements of 35-fold were achieved on a microfluidics device using metal-enhanced fluorescence in a discrete solution-based system with exposure times of only 50 ms.     

The Complex of Poly(dG) · Poly(dC) with Arginine: Stabilization of the B Form and Transition to Multistranded Structures

Abstract

We have studied by X-ray diffraction fibers of complexes of poly(dG)·poly(dC) with N-α-acetyl-L-arginine ethylamide. Although these polynucleotides favour the A form of DNA, in this complex it is never found, thus confirming that arginine prevents the appearance of this form of DNA At high relative humidity the B form is present. Upon dehydration two new structures appear. One of them is a triple helix, most likely formed by poly(dC⁺) · poly(dG) · poly(dC). The other structure found also has features which indicate a multistranded conformation.     

Electrospun Poly(L-lactide)/Poly(ε-caprolactone) Blend Nanofibrous Scaffold: Characterization and Biocompatibility with Human Adipose-Derived Stem Cells

The essence of tissue engineering is the fabrication of autologous cells or induced stem cells in naturally derived or synthetic scaffolds to form specific tissues. Polymer is thought as an appealing source of cell-seeded scaffold owing to the diversity of its physicochemical property and can be electrospun into nano-size to mimic natural structure. Poly (L-lactic acid) (PLLA) and poly (ε-caprolactone) (PCL) are both excellent aliphatic polyester with almost “opposite” characteristics. The controlling combination of PLLA and PCL provides varying properties and makes diverse applications. Compared with the copolymers of the same components, PLLA/PCL blend demonstrates its potential in regenerative medicine as a simple, efficient and scalable alternative. In this study, we electrospun PLLA/PCL blends of different weight ratios into nanofibrous scaffolds (NFS) and their properties were detected including morphology, porosity, degradation, ATR-FTIR analysis, stress-stain assay, and inflammatory reaction. To explore the biocompatibility of the NFS we synthesized, human adipose-derived stem cells (hASCs) were used to evaluate proliferation, attachment, viability and multi-lineage differentiation. In conclusion, the electrospun PLLA/PCL blend nanofibrous scaffold with the indicated weight ratios all supported hASCs well. However, the NFS of 1/1 weight ratio showed better properties and cellular responses in all assessments, implying it a biocompatible scaffold for tissue engineering.     

Monte-Carlo Simulation of DNA Duplex Hydration. B and B′ Conformations of Poly(dA) · Poly(dT) Have Different Hydration Shells

Abstract

Monte-Carlo simulation of poly(dA) · poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36° helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(dA) · poly(dT) B′ form with a narrowed minor groove. The mean energies and the mean numbers of water-water and water-DNA hydrogen bonds are close for the two conformations. Nevertheless, the hydration shell of the B' form differs drastically from that of the standard B form. The water arrangement in the minor groove of the B′ form resembles the spine of hydration in the central part of Dickerson's dodecamer d(CGCGAATTCGCG). No such spine is formed in the hydration shell of the usual B form with a wider minor groove. In this conformation water bridges between adenine N3 or thymine O2 and oxygen of the sugar ring of the neighbouring nucleotide along the chain can be formed (“strings” in Dickerson's decamer d(CCAAGATTGG)).     

Poly(A) polymerase (PAP) diversity in gene expression – Star-PAP vs canonical PAP

Almost all eukaryotic mRNAs acquire a poly(A) tail at the 3′-end by a concerted RNA processing event: cleavage and polyadenylation. The canonical PAP, PAPα, was considered the only nuclear PAP involved in general polyadenylation of mRNAs. A phosphoinositide-modulated nuclear PAP, Star-PAP, was then reported to regulate a select set of mRNAs in the cell. In addition, several non-canonical PAPs have been identified with diverse cellular functions. Further, canonical PAP itself exists in multiple isoforms thus illustrating the diversity of PAPs. In this review, we compare two nuclear PAPs, Star-PAP and PAPα with a general overview of PAP diversity in the cell. Emerging evidence suggests distinct niches of target pre-mRNAs for the two PAPs and that modulation of these PAPs regulates distinct cellular functions.