Efficient synthesis of functionalized oligodeoxyribonucleotides with base-labile groups using a new silyl linker

In this study, we developed new 3′-terminal deoxyribonucleoside-loading reagents 1 with a new silyl-type linker. These reagents could increase the efficiency of introduction of 3′-terminal deoxyribonucleoside components into polymer supports to a level of 17–29 μmol/g. The efficiency was higher than that of previous T-loading reagents because reagents 1 contain a 4-aminobutyryl residue as a spacer. Moreover, we could synthesize not only unmodified DNA oligomers but also a base-labile modified DNA oligomer using resins 9a–d in the activated phosphite method without base protection.     

Biodegradation of poly(epsilon-caprolactone)/starch blends and composites in composting and culture environments: the effect of compatibilization on the inherent biodegradability of the host polymer

The biodegradability of poly(epsilon-caprolactone) (PCL) was studied in blends and composites of modified and granular starch. Four types of PCL-starch compositions were prepared: (i) PCL-granular starch blends; (ii) hydrophobic coating of starch particles by n-butylisocyanate (C(4) starch) and octadecyltrichlorosilane (C(18) starch), followed by melt blending with PCL; (iii) PCL-starch blends compatibilized by PCL-g-dextran grafted copolymer (PGD); and (iv) PCL-grafted starch particles (PGS) as obtained by in situ ring-opening polymerization of caprolactone (CL) initiated directly from hydroxyl functions at the granular starch surface. Biodegradability of these materials was measured by monitoring the percentage of weight loss in composting and the rate of fungal colonization when samples were used as a sole carbon source for fungus (A. niger). Intrinsic viscosity [eta] of host PCL chains was measured after extraction of composted samples in boiled chloroform. SEM was used to study the surface morphology after compost incubation of the samples. The inherent biodegradability of host polymer was enhanced with surface compatibilization during composting for longer incubation. It was observed that the weight loss during composting increased with the decrease in interfacial tension between filler and polymer. In general, it was concluded that inherent biodegradability does not depend very significantly on the concentration of starch in the polyester matrix, but on the compatibilization efficiency. The effect of the PCL fraction in the graft copolymer, when used as compatibilizer, was also studied on the biodegradability of the host polymer.     

Preparation of poly(acrylamide-co-acrylic acid)-grafted gum and its flocculation and biodegradation studies

Biodegradation studies of Gum ghatti (Gg) and acrylamide-co-acrylic acid based flocculants [Gg-cl-poly(AAm-co-AA)] have been reported using the soil composting method. Gg-cl-poly(AAm-co-AA) was found to degrade 89.76% within 60 days. The progress of biodegradation at each stage was monitored through FT-IR and SEM. Polymer was synthesized under pressure using potassium persulphate-ascorbic acid as a redox initiator and N,N′-methylene-bis-acrylamide as a crosslinker. Synthesized polymer was found to show pH, temperature and ionic strength of the cations dependent swelling behavior. Gg-cl-poly(AAm-co-AA) was utilized for the selective absorption of saline from different petroleum fraction-saline emulsions. The flocculation efficiency of the polymer was studied as a function of polymer dose, temperature and pH of the solution. Gg-cl-poly(AAm-co-AA) showed maximum flocculation efficiency with 20 mol L⁻¹ polymer dose in acidic medium at 50 °C.     

Polymer–Magnesium Aluminum Silicate Composite Dispersions for Improved Physical Stability of Acetaminophen Suspensions

The aims of this study were to characterize the morphology and size of flocculates and the zeta potential and rheological properties of polymer–magnesium aluminum silicate (MAS) composite dispersions and to investigate the physical properties of acetaminophen (ACT) suspensions prepared using the composite dispersions as a flocculating/suspending agent. The polymers used were sodium alginate (SA), sodium carboxymethylcellulose (SCMC), and methylcellulose (MC). The results showed that SA, SCMC, and MC could induce flocculation of MAS by a polymer-bridging mechanism, leading to the changes in the zeta potential of MAS and the flow properties of the polymer dispersions. The microscopic morphology and size of the flocculates was dependent on the molecular structure of the polymer, especially ether groups on the polymer side chain. The residual MAS from the flocculation could create a three-dimensional structure in the SA–MAS and SCMC–MAS dispersions, which brought about not only an enhancement of viscosity and thixotropic properties but also an improvement in the ACT flocculating efficiency of polymers. The use of polymer–MAS dispersions provided a higher degree of flocculation and a lower redispersibility value of ACT suspensions compared with the pure polymer dispersions. This led to a low tendency for caking of the suspensions. The SCMC–MAS dispersions provided the highest ACT flocculating efficiency, whereas the lowest ACT flocculating efficiency was found in the MC–MAS dispersions. Moreover, the added MAS did not affect ACT dissolution from the suspensions in an acidic medium. These findings suggest that the polymer–MAS dispersions show good potential for use as a flocculating/suspending agent for improving the rheological properties and physical stability of the suspensions.     

Circular dichroism of poly(dG-dC) modified by the carcinogens N-methyl-4-aminoazobenzene or 4-aminobiphenyl.

Poly(dG-dC) was modified to different extents by the carcinogens 4-aminobiphenyl (ABP) or N-methyl-4-aminoazobenzene (MAB). HPLC analysis of the enzymatically hydrolyzed modified polymers indicates that more than 90% of the ABP and 81% of the MAB modification occurs at the C8 position of guanine. The conformational changes of the unmodified and modified polymers were studied as a function of ethanol and magnesium ion concentrations by the use of circular dichroism (CD). The modified polymers show a CD inversion pattern similar to that of the salt-induced B to Z transition of poly(dG-dC). Both of the modified polymers require less salt or ethanol than the unmodified polymer for the inversion of the spectra. The amount of ethanol or magnesium needed to induce the inverted CD spectrum is inversely proportional to the percentage of bound ABP or MAB. These data indicate that ABP and MAB can enhance conversion from B to Z conformation in alternating purine-pyrimidine sequences.     

Development of a novel and efficient cell culture flocculation process using a stimulus responsive polymer to streamline antibody purification processes

Recent advances in mammalian cell culture processes have significantly increased product titers, but have also resulted in substantial increases in cell density and cellular debris as well as process and product related impurities. As such, with improvements in titer, corresponding improvements in downstream processing are essential. In this study we have developed an alternative antibody harvest process that incorporates flocculation using a novel stimulus responsive polymer, benzylated poly(allylamine), followed by depth filtration. As tested on multiple antibodies, this process demonstrates high process yield, improved clearance of cells and cell debris, and efficient reduction of aggregates, host cell proteins (HCP) and DNA. A wide operating window was established for this novel flocculation process through design of experiments condition screening and optimization. Residual levels of impurities in the Protein A eluate were achieved that potentially meet requirements of drug substance and thus alleviate the burden for further impurities removal in subsequent chromatography steps. In addition, efficient clearance of residual polymer was demonstrated using a fluorescence tagged polymer in the presence of a stimulus reagent. The mechanism of HCP and aggregates removal during flocculation was also explored. This novel and efficient process can be easily integrated into current mAb purification platforms, and may overcome downstream processing challenges. Biotechnol. Bioeng. 2013;110: 2928–2937. © 2013 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.     

The conversion of tubulin carboxyl groups to amides has a stabilizing effect on microtubules.

In a recent study, we demonstrated that the conversion of carboxyl residues in the C-termini of tubulin to neutral amides with glycine ethyl ester enhanced the ability of the protein to assemble into microtubules and decreased its interaction with microtubule-associated proteins (MAPs). In this work, we investigated the effects of carboxyl modification on the dynamic behavior of microtubules at polymer mass steady state. After steady state, microtubules assembled from unmodified tubulin were sheared, and the mean polymer lengths decreased to 5 microns and then increased to 29 microns within 130 min. In contrast, lengths of sheared microtubules polymerized from tubulin containing 23 modified carboxyl groups increased by only 2-fold. Stabilization of polymer lengths was also observed directly by video-enhanced light microscopy of microtubules grown off of axonemes. Rapid shortening was seen in microtubules composed of unmodified but not modified tubulin. Further evidence for the less dynamic behavior of microtubules as a result of carboxyl modification was obtained from kinetic studies of the elongation phase during assembly which showed a 3-fold lower off-rate constant, k-, for modified microtubules. Another effect of the modification was a 12-fold reduction in the steady-state rate constant for GTP hydrolysis (165 s-1 for unmodified and 14 s-1 for modified). These results suggest that reduction of the negative charges in the C-termini by modification of the acidic residues stabilizes microtubules against depolymerization. MAPs may stabilize microtubules in an analogous manner.     

Surface modification of cellulose with triazine derivative to improve printability with reactive dyes

Chemical modification of cellulose with triazine derivative, 2,4,6-tri-[(2-hydroxy-3-trimethyl-ammonium)propyl]-1,3,5-triazine chloride (Tri-HTAC), was investigated. Micro-FT-IR and nitrogen element analysis were applied to characterize molecular structure of the modified cellulose. The printing properties of the modified cellulose fabric with Tri-HTAC were discussed. Tri-HTAC was able to form covalent bonds with cellulose fibers. The apparent color strength of printed samples with three reactive dyes on the modified cellulose was higher than the corresponding color yields on the unmodified cellulose fabric. Compared with unmodified cellulose, the increases of the color yield were about 6–13%. The fixation rate was accelerated by the modification with Tri-HTAC. The wet rubbing and washing fastnesses of the printed cellulose fabrics modified with Tri-HTAC were better than those of the printed unmodified cellulose fabric. The modified cellulose with Tri-HTAC imparted good printing properties.     

Simple modifications of branched PEI lead to highly efficient siRNA carriers with low toxicity

Polymer carriers like PEI which proved their efficiency in DNA delivery were found to be far less effective for the applications with siRNA. In the current study, we generated a number of nontoxic derivates of branched PEI through modification of amines by ethyl acrylate, acetylation of primary amines, or introduction of negatively charged propionic acid or succinic acid groups to the polymer structure. The resulting products showed high efficiency in siRNA-mediated knockdown of target gene. In particular, succinylation of branched PEI resulted in up to 10-fold lower polymer toxicity in comparison to unmodified PEI. Formulations of siRNA with succinylated PEI were able to induce remarkable knockdown (80% relative to untreated cells) of target luciferase gene at the lowest tested siRNA concentration of 50 nM in Neuro2ALuc cells. The polyplex stability assay revealed that the efficiency of formulations which are stable in physiological saline is independent of the affinity of siRNA to the polymer chain. The improved properties of modified PEI as siRNA carrier are largely a consequence of the lower polymer toxicity. In order to achieve significant knockdown of target gene, the PEI-based polymer has to be applied at higher concentrations, required most probably for sufficient accumulation and proton sponge effects in endosomes. Unmodified PEI is highly toxic at such polymer concentrations. In contrast, the far less toxic modified analogues can be applied in concentrations required for the knockdown of target genes without side effects.     

Synthesis and properties of triple helix-forming oligodeoxyribonucleotides containing 7-chloro-7-deaza-2'-deoxyguanosine.

Multiple incorporations of 7-chloro-7-deaza-2'-deoxyguanosine in place of 2'-deoxyguanosine have been performed into a triple helix-forming oligodeoxyribonucleotide involving a run of six contiguous guanines designed to bind in a parallel orientation relative to the purine strand of the DNA target. The ability of these modified oligodeoxyribonucleotides to form triple helices in a buffer containing monovalent cations was studied by UV--melting curves analysis, gel shift assay and restriction enzyme protection assay. In the presence of Na(+), the incorporation of two, three or five modified nucleosides in the third strand has improved the efficacy of formation of the triplex as compared to that formed with the unmodified oligonucleotide. The stabilities of the three modified triplexes were similar. The coupling of 6-chloro-2-methoxy-9-(omega-hexylamino)-acridine to the 5'-end of the oligonucleotides containing modified nucleosides led to an increase in triplex stability similar to that observed when the acridine was added to the 5'-end of the unmodified oligonucleotide. In the presence of K(+), only the oligodeoxyribonucleotides containing modified G retained the ability to form triple helices with the same efficiency. The incorporation of the modified nucleoside has two effects: (i) it decreases TFO self-association, and (ii) it slightly increases triplex stability. The enhanced ability of the modified oligonucleotides containing 7-chloro-7-deaza-2'-deoxyguanosine over the parent oligomer to form triple helices was confirmed by inhibition of restriction enzyme cleavage using a circular plasmid containing the target sequence.     

Characterization and evaluation of hydrophobically modified chitosan scaffolds: Towards design of enzyme immobilized flow-through electrodes

Chitosan scaffolds were fabricated by application of thermally induced phase separation from aqueous solutions of unmodified chitosan and hydrophobically modified chitosan polymer. The final pore structure, in terms of diameter and geometry, were correlated to freezing temperature and freezing time for both the unmodified and hydrophobically modified chitosan polymer. Results showed that the resulting pore structure is strongly dependent upon the freezing temperature and less dependant upon the freezing time. For scaffolds produced from unmodified chitosan, the pore size decreased as expected with decreasing freezing temperature from ?5 °C to ?10 °C. However, an inconsistency in this trend was observed as the freezing temperature was decreased to ?20 °C. Combined analysis of pore size distribution and average pore diameter suggested that the freezing process was mainly mass transfer dominated at ?5 °C and ?10 °C, but principally heat transfer dominated at ?20 °C. In comparison, the scaffolds produced from hydrophobically modified chitosan (butyl-chitosan) followed the expected trend of decreasing mean pore diameter with decreased freezing temperatures throughout the entire temperature range. The scaffolds produced from the unmodified chitosan were more stable and rigid, and possessed average pore diameters that were generally smaller than those fabricated from the hydrophobically modified chitosan. The generally larger pores in the butyl-modified chitosan scaffolds might be explained by increased phase separation rates due to the introduced hydrophobicity of the chitosan polymer. Among the scaffolds fabricated from the butyl-modified chitosan, those produced at ?20 °C yielded the most uniform pore structure, the smallest average pore diameters, and the least temporal broadening of pore size distribution.     

Application of an HIV gp41-derived peptide for enhanced intracellular trafficking of synthetic gene and siRNA delivery vehicles

Endosomal release is an efficiency-limiting step for many nonviral gene delivery vehicles. In this work, nonviral gene delivery vehicles were modified with a membrane-lytic peptide taken from the endodomain of HIV gp41. Peptide was covalently linked to polyethylenimine (PEI) and the peptide-modified polymer was complexed with DNA. The resulting nanoparticles were shown to have similar physicochemical properties as complexes formed with unmodified PEI. The gp41-derived peptide demonstrated significant lytic activity both as free peptide and when conjugated to PEI. Significant increases in transgene expression were achieved in HeLa cells when compared to unmodified polyplexes at low polymer to DNA ratios. Additionally, peptide-modified polyplexes mediated significantly enhanced siRNA delivery compared to unmodified polyplexes. Despite increases in transgene expression and siRNA knockdown, there was no increase in internalization or binding of modified carriers as determined by flow cytometry. The hypothesis that the gp41-derived peptide increases the endosomal escape of vehicles is supported by confocal microscopy imaging of DNA distributions in transfected cells. This work demonstrates the use of a lytic peptide for improved trafficking of nonviral gene delivery vehicles.     

Effect of conductive polymers coated anode on the performance of microbial fuel cells (MFCs) and its biodiversity analysis

Conductive polymer, one of the most attractive electrode materials, has been applied to coat anode of MFC to improve its performance recently. In this paper, two conductive polymer materials, polyaniline (PANI) and poly(aniline-co-o-aminophenol) (PAOA) were used to modify carbon felt anode and physical and chemical properties of the modified anodes were studied. The power output and biodiversity of modified anodes, along with unmodified carbon anode were compared in two-chamber MFCs. Results showed that the maximum power density of PANI and PAOA MFC could reach 27.4 mW/m(2) and 23.8 mW/m(2), comparing with unmodified MFC, increased by 35% and 18% separately. Low temperature caused greatly decrease of the maximum voltage by 70% and reduced the sorts of bacteria on anodes in the three MFCs. Anode biofilm analysis showed different bacteria enrichment: a larger mount of bacteria and higher biodiversity were found on the two modified anodes than on the unmodified one. For PANI anode, the two predominant bacteria were phylogenetically closely related to Hippea maritima and an uncultured clone MEC_Bicarb_Ac-008; for PAOA, Clostridiales showed more enrichment. Compare PAOA with PANI, the former introduced phenolic hydroxyl group by copolymerization o-aminophenol with aniline, which led to a different microbial community and the mechanism of group effect was proposed.     

Photocrosslinkable biodegradable responsive hydrogels as drug delivery systems

Recently, controlled release from biocompatible materials has received much attention for biomedical applications. Due to their biocompatibility and biodegradability, glucopyranosides such as dextran appear as promising polymeric materials if one is able to regulate their rheological properties and the encapsulation/release efficiency. In this work graft polymer hydrogels from dextran and N-isopropylacrylamide (NIPAAm) were prepared and characterized.Dextran molecules were modified with 2-isocyanatoethylmethacrylate (IEMA) in order to obtain a polymer with carbon double bonds. Urethane linkages resulted from the reaction between hydroxyl groups (OH) of the dextran and isocyanate groups (NCO) of the IEMA. The obtained polymer was then crosslinked by UV irradiation in the presence of the photoinitiating agent Irgacure 2959 by CIBA^®. The drug Ondansetron^® was entrapped in the final system and its release profile was determined at 25 and 37 °C.The characterization of the materials was accomplished by: ATR-FTIR (Attenuated Total Reflectance-Fourier Transform Infrared) spectroscopy, elemental analysis, lower critical solution temperature (LCST) determination, swelling behaviour evaluation, determination of surface energy by contact angle measurement and drug delivery profile studies.     

Improving Cathodes with a Polymer Interlayer in Reversed Organic Solar Cells

The effects of cathode modification by a conjugated polymer interlayer PFPA1 on the performance of reversed organic solar cells (substrate/cathode/active layer/transparent anode) based on different active material systems and different substrate electrodes are systematically investigated. A reduction of the work function irrespective of the substrate cathode used is observed upon the deposition of the PFPA1 interlayer, which is further related to an improved built‐in electric field and open‐circuit voltage. The amphiphilic character of the PFPA1 interlayer alters the surface energy of the substrate cathode, leading to the formation of a better active layer morphology aiding efficient exciton dissociation and photocurrent extraction in the modified solar cells. Hence, internal quantum efficiency is found to be significantly higher than that of their unmodified counterparts, while optically, the modified and unmodified solar cells are identical. Moreover, the deep highest occupied molecular orbital (HOMO) of the PFPA1 interlayer improves the selectivity for all investigated substrate cathodes, thus enhancing the fill factor.     

Improved efficiency and robustness in qPCR and multiplex end-point PCR by twisted intercalating nucleic acid modified primers

We introduce quantitative polymerase chain reaction (qPCR) primers and multiplex end-point PCR primers modified by the addition of a single ortho-Twisted Intercalating Nucleic Acid (o-TINA) molecule at the 5'-end. In qPCR, the 5'-o-TINA modified primers allow for a qPCR efficiency of 100% at significantly stressed reaction conditions, increasing the robustness of qPCR assays compared to unmodified primers. In samples spiked with genomic DNA, 5'-o-TINA modified primers improve the robustness by increased sensitivity and specificity compared to unmodified DNA primers. In unspiked samples, replacement of unmodified DNA primers with 5'-o-TINA modified primers permits an increased qPCR stringency. Compared to unmodified DNA primers, this allows for a qPCR efficiency of 100% at lowered primer concentrations and at increased annealing temperatures with unaltered cross-reactivity for primers with single nucleobase mismatches. In a previously published octaplex end-point PCR targeting diarrheagenic Escherichia coli, application of 5'-o-TINA modified primers allows for a further reduction (>45% or approximately one hour) in overall PCR program length, while sustaining the amplification and analytical sensitivity for all targets in crude bacterial lysates. For all crude bacterial lysates, 5'-o-TINA modified primers permit a substantial increase in PCR stringency in terms of lower primer concentrations and higher annealing temperatures for all eight targets. Additionally, crude bacterial lysates spiked with human genomic DNA show lesser formation of non-target amplicons implying increased robustness. Thus, 5'-o-TINA modified primers are advantageous in PCR assays, where one or more primer pairs are required to perform at stressed reaction conditions.     

Interaction of a spin-labeled adenine-acridine conjugate with a DNA duplex containing an abasic site model

The abasic site is a common lesion in DNA that is also formed as an intermediate in the base excision repair of damaged bases. We have previously reported the adenine-acridine conjugate 1 that was designed to bind to the abasic site and interfere with the repair process. High-field NMR had shown that 1 forms specific complexes with a DNA duplex containing an apurinic abasic site model. We report here the dynamics of the interaction of the nitroxide-labeled analogue 3 of the conjugate 1 with the same apurinic oligonucleotide and with the parent unmodified duplex. Identical study of the labeled acridine subunit 5 used as a reference is also reported. In the presence of the apurinic duplex and depending on the concentrations and drug ratios, three species are observed: the radical "free in solution", the "intercalation" complex characterized by its similarity to that observed in the presence of the parent unmodified duplex, and the "abasic-site-specific" complex which is the sole species visible at low drug ratios. The experimental data reinforced by molecular modeling of the complex and theoretical calculation of correlation times suggest (i) the most immobilized form corresponds to that observed by NMR and (ii) complexation of the drug is little or not modified by the spin-label. We also show that the abasic site constitutes a binding site for the propylaminoacridine intercalator 5.     

Harvesting of Chlorella vulgaris using a bioflocculant from Paenibacillus sp. AM49

Microbial flocculants for harvesting mass cultured Chlorella vulgaris were screened and that from Paenibacillussp. AM49 was identified as the best. The flocculation efficiency of this bioflocculant increased with the pH within a range of pH 5–11 and was 83%, which was higher than the 72% and 78% produced by aluminum sulfate and polyacrylamide, respectively. The highest flocculation efficiency was with 6.8 mm CaCl₂ as co-flocculant. The bioflocculant from Paenibacillussp. AM49 can be used effectively to harvest C. vulgaris from large-scale cultures.     

Zeta potential as a measure of polyelectrolyte flocculation and the effect of polymer dosing conditions on cell removal from fermentation broth

Characterization of flocculation for cell removal from fermentation broth via polyelectrolyte addition is commonly based on qualitative methods such as physical appearance of the floc. The use of zeta potential as a quantitative measure of floc character was evaluated as an indicator of optimal polymer addition. Zeta potential was found to increase with increasing cationic polyelectrolyte dosage, but never reached zero regardless of the total amount of polymer added, indicating flocculation occurs at least partially through a bridging type mechanism. Experiments were conducted using various polymer concentrations (25-75 g/L) and dosing methods (batch, incremental and continuous addition) that resulted in variable overall polymer requirements to achieve optimum flocculation. Zeta potential was found to be constant at optimal floc character regardless of the total amount of polymer added, polymer concentration, or method of polymer addition. Experiments with two additional types of fermentation broth also showed characteristic zeta potentials at optimal flocculation. Polymer requirements to achieve a particular floc character can vary greatly, depending on polymer dosing conditions and fermentation batch. The effect of polymer dosing conditions on the polymer requirement to obtain optimal floc character was evaluated. Polymer dosing method and calcium concentration were both found to have a significant effect (P < 0.0001) with continuous polymer addition and high calcium concentration requiring less polymer than did batch polymer addition and low calcium concentration, respectively. Polymer dosing concentration did not significantly affect polymer requirement for optimal flocculation.