Acid Oligomers Research Articles

Thermal degradation of poly(lactic acid) oligomer: Reaction mechanism and multistep kinetic behavior

This study was aimed to reveal the kinetic and mechanistic features of the thermal degradation of linear poly(lactic acid) oligomer (PLAO) by analyzing the evolved gases and overall rate behavior during mass-loss processes. The thermal degradation reaction involved two partially overlapping mass-loss steps. The first mass-loss step started right after the reactant melted and was accompanied with the release of lactides as the main gaseous products while maintaining the microscopic appearance of molten PLAO. The mass-loss rate behavior was controlled by a diffusion process with an apparent activation energy (Ea) of approximately 90 kJ mol–1, with the diffusional transfer of lactides from the reaction sites to the top surface of the molten PLAO being considered as the rate-limiting step. The second mass-loss step became noticeable at reacting system temperatures above the boiling point of lactides. During this dramatically accelerated mass-loss step, carbon oxides, aldehydes, lactides, and cyclic PLAO with large molecular weights were simultaneously evolved with frequent formation and disappearance of gaseous bubbles in the molten reacting system. In this step, the overall rate behavior was largely influenced by the bubbling phenomena for which the Ea value was determined to be approximately 155 kJ mol–1. The changes in the chemical mechanism and the physico-geometrical reaction behavior midway through the thermal degradation reaction were both illustrated by the change in the molten reacting system in view of degradation-polymerization equilibrium via the boiling points of lactides.

Improved Cell Adhesion and Osteogenesis of op-HA/PLGA Composite by Poly(dopamine)-Assisted Immobilization of Collagen Mimetic Peptide and Osteogenic Growth Peptide.

A nanocomposite of poly(lactide-co-glycolide) (PLGA) and hydroxyapatite (HA) with a different grafting ratio of l-lactic acid oligomer (op-HA) showed better interface compatibility, mineralization, and osteogenetic abilities. However, surface modification of the composite is crucial to improve the osteointegration for bone regeneration. In this study, a biomimetic process via poly(dopamine) coating was utilized to prepare functional substrate surfaces with immobilized bioactive peptides that efficiently regulate the osteogenic differentiation of preosteoblasts (MC3T3-E1). Our study demonstrated that incorporation of collagen mimetic peptide significantly enhanced cell adhesion and proliferation. The immobilization of osteogenic growth peptide induced the osteodifferentiation of cells, as indicated by the alkaline phosphate activity test, quantitative real-time polymerase chain reaction analysis, and immunofluorescence staining. The mineralization on the peptide-modified substrates was also enhanced greatly. Findings from this study revealed that this biofunctionalized layer on op-HA/PLGA substrate improved mineralization and osteogenic differentiation. In conclusion, the surface modification strategy with bioactive peptides shows potential to enhance the osteointegration of bone implants.

Detection of KRAS mutations of colorectal cancer with peptide-nucleic-acid-mediated real-time PCR clamping

ABSTRACTColorectal cancer (CRC) is the third most common cancer in the world and its disease-specific mortality is estimated to be approximately 33% in the developed world. KRAS mutations have been shown to predict response to anti-EGFR (epidermal growth factor receptor) targeted monoclonal antibody therapy. Therefore, KRAS mutation testing of metastatic CRC patients is mandatory in the clinical setting to aid in the choice of appropriate therapy. Currently, the most common strategy for KRAS mutation detection consists of conventional polymerase chain reaction (PCR) and direct sequencing. However, it is a time-consuming and complicated procedure, not suitable for routine clinical test. The objective of this study is to develop and evaluate a highly sensitive and rapid method using peptide nucleic acid (PNA) oligomers mediated real-time PCR clamping for detection of KRAS mutations. The PNA-mediated PCR clamping assay can real-time detect a mutation in a sample containing 1% of the mutant allele in a mixture of wild-type genomic DNA, which also enables the accurate and rapid detection of all KRAS codon 12 and 13 mutations in a single reaction. The total assay time is short as it requires only 1.5 hours after the samples preparation. Thus, the present method offers a potential alternative to be applied in clinical samples of CRC for detection of DNA carrying KRAS mutations.

Kinetics of polymerization of N,N′-bismaleimide-4,4′-diphenylmethane, barbituric acid and aminopropyl phenylsiloxane oligomer

Kinetics of polymerizations of N,N′-bismaleimide-4,4′-diphenylmethane (BMI)/barbituric acid (BTA) [2/1 (mol/mol)] in the presence and absence of 20 wt% aminopropyl phenylsiloxane oligomer (APSi) was investigated. Microgel particles (MPs) of BMI/BTA/APSi and BMI/BTA formed during polymerizations at 100 or 130 °C. The initial particle growth rate of BMI/BTA/APSi MPs is faster than that of pristine BMI/BTA MPs due to the presence of APSi nuclei. The residual CC of BMI in BMI/BTA/APSi MPs is 53mol%, which is comparable to that of BMI in BMI/BTA MPs. The same kinetic model, characterized by reaction-controlled overall, could be used to describe both polymerization systems. The value of activation energy (54 kJmol−1) for the polymerization of BMI/BTA/APSi is higher than that (43 kJmol−1) for the polymerization of BMI/BTA. The thermal stability of the cured BMI/BTA/APSi polymer is better than that of the cured BMI/BTA polymer.

A Biodegradable and Amphiphilic Linear‐Dendritic Copolymer as a Drug Carrier Platform for Intracellular Drug Delivery

In this work, a biodegradable linear‐dendritic copolymer composed of methoxypolyethylene glycols (mPEG) and a third generation glycolic acid oligomer based dendron is synthesized. The amphiphilic copolymer can self‐assemble into polymeric micelles in aqueous solution with a low critical micelle concentration (CMC). Hydrophobic doxorubicin (DOX) is incorporated into the micellar core via the dialysis method with a high drug loading content of 21.2%. The drug release result implies that the encapsulated drug can be released rapidly at pH 5.0, due to the hydrolysis of the ester bond resulting in quick disassembly of drug‐loaded micelles. Moreover, the results of fluorescence microscopy imaging and flow cytometry measurements demonstrate that the drug carriers can be internalized and DOX released rapidly from them upon endocytosis. Importantly, this drug delivery system exhibits excellent performance to inhibit cancer cell proliferation. image

Periodic vs. molecular cluster approaches to resolving glass structure and properties: Anorthite a case study

Periodic and molecular cluster models are presented for anorthite (CaAl2Si2O8), a cement forming glass with desirable thermal and mechanical properties also tested in dental applications. Both the crystalline and amorphous structures were characterised by ab initio molecular dynamics and found to be in good agreement with experiment. Additional investigations of the elongation and fracture of the glass were also made. The recovery of material properties signaled the failure of the periodic method to generate acceptable fracture surfaces to model cement forming-sites. Isolated molecular cluster models of anorthite were therefore investigated with electronic structure methods and showed sound structural matches with the traditional periodic structures. The equilibrated glass clusters were used to develop cement models, through binding of short acid oligomers to selected Al-centres, simulating the glass-polymer interface. Overall, the anorthite glass structures emerging from periodic and cluster models were in close agreement. Results suggest that bare molecular cluster models represent an alternative avenue for accurately investigating amorphous systems, providing more realistic descriptions of edge and corner sites, as well as interfaces.

The suitable itaconic acid content in polyacrylonitrile copolymers used for PAN‐based carbon fibers

ABSTRACTThis article was to provide some new insights into the influences of itaconic acid (IA) content in polyacrylonitrile (PAN) copolymers on polymerization, structural evolution, thermal behaviors and carbon yield relatively comprehensively. High IA containing poly(acrylonitrile‐co‐itaconic acid) (PAI) oligomers were successfully extracted from PAI copolymers with 2.0 and 3.0 mol % IA. PAI copolymers with 0.5 mol % and 1.0 mol % IA possessed more cyclized structures, conjugated carbonyl group, conjugated nitrile group, and less β‐amino nitrile group as well as faster structural evolution rate than those of the other three PAI copolymers. Kinetic parameters indicated that excessive IA content in PAI copolymer did not have advantages in promoting cyclization reaction. The PAI copolymers with 0.5 wt % to 1.0 mol % IA possessed better crystalline parameters as well as higher carbon yield than those of the other two PAI copolymers after carbonization at 1350 ºC. In summary, PAI copolymers with 0.5 mol % to 1.0 mol % IA will be more suitable for fabricating of high performance PAN‐based carbon fibers. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43919.

Isolation and structure elucidation of pectic polysaccharide from rose hip fruits (Rosa canina L.)

A pectic polysaccharide from rose hip (RH) fruits has been obtained by extraction with 1% aqueous citric acid. It was found that the polysaccharide fraction mainly consisted of galacturonic acid (45.5%) next to galactose (5.5%) and arabinose (4.7%). RH pectin is having a relatively high degree of methylesterification (62%) and acetylation (10%) and consists of different molecular weight populations in the range of 10–100kDa. Enzymatic fingerprinting was performed using a combination of pectin lyase (PL) and endo-polygalacturonase. Detailed information about the structure and level of galacturonic acid oligomers released was obtained using LC-HILIC-MS/ELSD and HPAEC. Predominantly, unsaturated and methyl-esterified oligomers (DP 3–5) were released indicating that high proportions of methylesterified ‘PL degradable’ areas were present within the pectin. The data revealed that homogalacturonan is the main building block of the extracted pectin and consists of long methylesterified/acetylated GalA sequences interspersed with small blocks of non-methyl-esterified GalA units.

Green One-Pot Synthesis of Surface Hydrophobized Cellulose Nanocrystals in Aqueous Medium

The surface hydrophobization of cellulose nanocrystals (CNCs) by fatty acids (FAs), biodiesel, or plant oils was conducted via a green process using an organic solvent less one-pot method. In the process, an aqueous lactic acid syrup served as a reactive solvent to provide a stable and well-dispersed water suspension of CNC and participate in esterification reactions, producing an intermediate product of polylactic acid (PLA) oligomer grafted CNCs (CNC-g-PLA). This reactive solvent and intermediate product system allows for an in situ solvent exchange from water to lactic acid without prior drying of the CNC and a subsequent efficient esterification reaction of CNC with carboxylic acids or esters having a long hydrocarbon chain (FAs). Another advantage of the proposed process is the possibility to reuse the reagents in the subsequent reaction in order to reduce the production cost. The grafting efficiency of the CNC-g-PLA-FA samples covalently grafted with PLA and FAs were characterized by Fourier transfo...

Fingerprinting of oligosaccharide-hydrolyzing enzymes that catalyze branched reaction schemes

We present three case studies, based on literature data, in which the “fingerprinting” method of determining the relative specificities of an enzyme is applied to branched reaction schemes. The first case study involves the hydrolysis of maltoheptaose by a β-amylase and shows that the fingerprinting method can be applied to schemes involving processivity. The analysis reveals that the native β-amylase has a 1.26-fold preference for attacking maltoheptaose by the processive route over the non-processive route, but that for a mutant enzyme this preference is 0.18-fold. The second case study involves the hydrolysis of β-1,6-N-acetylglucosamine oligomers by DispersinB. Our set of relative specificity constants is more consistent with the results of initial rate experiments than is the set that the authors obtained by fitting a pseudo-first order model to their data. The third case study involves the hydrolysis of galacturonic acid oligomers by an endopolygalacturonase. This enzyme can catalyze a total of 11 different reactions with a mixture of tri-, tetra-, penta-, hexa- and heptagalacturonates. We determined the relative specificity constants for these 11 reactions. The fingerprinting method has advantages over the methods that have been previously used to determine specificity constants for branched reaction schemes, being able to use a single experimental reaction profile for determination of all relative specificity constants.

Assessing the Delivery of Molecules to the Mitochondrial Matrix Using Click Chemistry.

Mitochondria are central to health and disease, hence there is considerable interest in developing mitochondria‐targeted therapies that require the delivery of peptides or nucleic acid oligomers. However, progress has been impeded by the lack of a measure of mitochondrial import of these molecules. Here, we address this need by quantitatively detecting molecules within the mitochondrial matrix. We used a mitochondria‐ targeted cyclooctyne (MitoOct) that accumulates several‐ hundredfold in the matrix, driven by the membrane potential. There, MitoOct reacts through click chemistry with an azide on the target molecule to form a diagnostic product that can be quantified by mass spectrometry. Because the membrane potential‐dependent MitoOct concentration in the matrix is essential for conjugation, we can now determine definitively whether a putative mitochondrion‐targeted molecule reaches the matrix. This “ClickIn” approach will facilitate development of mitochondria‐targeted therapies.

The influence of liposomal formulation on the incorporation and retention of PNA oligomers

Liposomal formulations composed of phospholipids with different unsaturation degrees, head groups and at different cholesterol content have been tested for the encapsulation of Peptide Nucleic Acid (PNA) oligomers. The best loading capability (177μg, ER%=87.2) was obtained for pure liposomes of phosphatidylglycerol (DOPG) with negatively charged head group. The insertion of a 10–20% of cholesterol in DOPG based liposomes provides a slight decrease (∼160μg) of the PNA loading. On the other hand, the cholesterol addition (20–30%) slows down the PNA’s release (∼27%) in fetal bovine serum from the liposomal formulation. Based on the encapsulation and the release properties, PEGylated DOPG liposomes with a percentage of cholesterol of 10–20% are the optimal formulation for the loading of PNA-a210.

Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets.

We have designed a protocol and server to aid in the search for putative binding sites in 16S rRNA that could be targeted by peptide nucleic acid oligomers. Various features of 16S rRNA were considered to score its regions as potential targets for sequence-specific binding that could result in inhibition of ribosome function. Specifically, apart from the functional importance of a particular rRNA region, we calculated its accessibility, flexibility, energetics of strand invasion by an oligomer, as well as similarity to human rRNA. To determine 16S rRNA flexibility in the ribosome context, we performed all-atom molecular dynamics simulations of the 30S subunit in explicit solvent. We proposed a few 16S RNA target sites, and one of them was tested experimentally to verify inhibition of bacterial growth by a peptide nucleic acid oligomer.

Poly(lactic acid)‐based nanocomposites filled with cellulose nanocrystals with modified surface: all‐atom molecular dynamics simulations

AbstractPolymer bio‐nanocomposites are widely used nowadays in various applications. One of the most promising polymers for producing such materials is poly(lactic acid) (PLA) filled with cellulose nanocrystals (CNCs). To increase the compatibility of hydrophobic PLA and hydrophilic cellulose, the surface of the latter can be chemically modified. Among the various surface modifications, the grafting of lactic acid oligomers (OLAs) is of special interest. In this paper, the first all‐atom molecular dynamics simulation of nanocomposites of PLA filled with CNCs with surface‐grafted OLAs is presented. The influence of the degree of modification of the CNCs with OLA chains on the PLA structure near the CNC surface and on the grafted OLA, as well as on the thermal and mechanical properties of the nanocomposites is studied. It is demonstrated that a 50% modification of CNCs with OLA chains leads to PLA expulsion from the CNC surface. © 2016 Society of Chemical Industry

Homologous PNA Hybridization to Noncanonical DNA G-Quadruplexes.

Potential guanine (G) quadruplex-forming sequences (QFSs) found throughout the genomes and transcriptomes of organisms have emerged as biologically relevant structures. These G-quadruplexes represent novel opportunities for gene regulation at the DNA and RNA levels. Recently, the definition of functional QFSs has been expanding to include a variety of unconventional motifs, including relatively long loop sequences (i.e., >7 nucleotides) separating adjacent G-tracts. We have identified a QFS within the 25S rDNA gene from Saccharomyces cerevisae that features a long loop separating the two 3'-most G-tracts. An oligonucleotide based on this sequence, QFS3, folds into a stable G-quadruplex in vitro. We have studied the interaction between QFS3 and several loop mutants with a small, homologous (G-rich) peptide nucleic acid (PNA) oligomer that is designed to form a DNA/PNA heteroquadruplex. The PNA successfully invades the DNA quadruplex target to form a stable heteroquadruplex, but with surprisingly high PNA:DNA ratios based on surface plasmon resonance and mass spectrometric results. A model for high stoichiometry PNA-DNA heteroquadruplexes is proposed, and the implications for quadruplex targeting by G-rich PNA are discussed.

Antibacterial Peptide Nucleic Acid-Antimicrobial Peptide (PNA-AMP) Conjugates: Antisense Targeting of Fatty Acid Biosynthesis.

Antisense peptide nucleic acid (PNA) oligomers constitute a novel class of potential antibiotics that inhibit bacterial growth via specific knockdown of essential gene expression. However, discovery of efficient, nontoxic delivery vehicles for such PNA oligomers has remained a challenge. In the present study we show that antimicrobial peptides (AMPs) with an intracellular mode of action can be efficient vehicles for bacterial delivery of an antibacterial PNA targeting the essential acpP gene. The results demonstrate that buforin 2-A (BF2-A), drosocin, oncocin 10, Pep-1-K, KLW-9,13-a, (P59→W59)-Tat48-60, BF-2A-RXR, and drosocin-RXR are capable of transporting PNA effectively into E. coli (MICs of 1-4 μM). Importantly, presence of the inner-membrane peptide transporter SbmA was not required for antibacterial activity of PNA-AMP conjugates containing Pep-1-K, KLW-9,13-a, or drosocin-RXR (MICs of 2-4 μM).

Biodegradable polyesters based on star-shaped lactic acid oligomers

Catalytic polymerization of ε-caprolactone and copolymerization of maleic anhydride and propylene or ethylene oxide carried out in the presence of star-shaped L-lactic acid oligomers were studied. The analysis of the reaction products by means of GPC, MALDI ToF and 1H NMR show that the applied processes allowed to combine oligomers with polyesters produced by ring opening polymerization and obtain a new type of lactic acid copolymers of relative molar masses in the range 15–60 kg/mol. DSC studies revealed that the formed polyesters segments were fully or partially miscible with poly(lactic acid) core causing the reduction of its glass transition temperature. Selected copolymers were subjected to enzymatic degradation, which indicated that all of these compounds underwent partial decomposition. An analysis of weight loss showed, however, that the degradation occurred more slowly than in the case of poly(lactic acid) of similar molar masses and chain architecture.

Oligosaccharide formation during commercial pear juice processing

The effect of enzyme treatment and processing on the oligosaccharide profile of commercial pear juice samples was examined by high performance anion exchange chromatography with pulsed amperometric detection and capillary gas chromatography with flame ionization detection. Industrial samples representing the major stages of processing produced with various commercial enzyme preparations were studied. Through the use of commercially available standards and laboratory scale enzymatic hydrolysis of pectin, starch and xyloglucan; galacturonic acid oligomers, glucose oligomers (e.g., maltose and cellotriose) and isoprimeverose were identified as being formed during pear juice production. It was found that the majority of polysaccharide hydrolysis and oligosaccharide formation occurred during enzymatic treatment at the pear mashing stage and that the remaining processing steps had minimal impact on the carbohydrate-based chromatographic profile of pear juice. Also, all commercial enzyme preparations and conditions (time and temperature) studied produced similar carbohydrate-based chromatographic profiles.

Enhanced in Vitro Mineralization and in Vivo Osteogenesis of Composite Scaffolds through Controlled Surface Grafting of L-Lactic Acid Oligomer on Nanohydroxyapatite.

Nanocomposite of hydroxyapatite (HA) surface grafted with L-lactic acid oligomer (LAc oligomer) (op-HA) showed improved interface compatibility, mechanical property, and biocompatibility in our previous study. In this paper, composite scaffolds of op-HA with controlled grafting different amounts of LAc oligomer (1.1, 5.2, and 9.1 wt %) were fabricated and implanted to repair rabbit radius defects. The dispersion of op-HA nanoparticles was more uniform than n-HA in chloroform and nanocomposites scaffold. Calcium and phosphorus exposure, in vitro biomineralization ability, and cell proliferation were much higher in the op-HA1.1 wt %/PLGA scaffolds than the other groups. The osteodifferentiation and bone fusion in animal tests were significantly enhanced for op-HA5.2 wt %/PLGA scaffolds. The results indicated that the grafted LAc oligomer of 5.2 or 9.1 wt %, which formed a barrier layer on the HA surface, prevented the exposure of nucleation sites. The shielded nucleation sites of op-HA particles (5.2 wt %) might be easily exposed as the grafted LAc oligomer was decomposed easily by enzyme systems in vivo. Findings from this study have revealed that grafting 1.1 wt % amount of LAc oligomer on hydroxyapatite could improve in vitro mineralization, and 5.2 wt % could promote in vivo osteogenesis capacity of composite scaffolds.

Generation and characterization of novel DNA aptamers against coat protein of grouper nervous necrosis virus (GNNV) with antiviral activities and delivery potential in grouper cells

Nervous necrosis virus (NNV) infected larvae and juveniles of more than 50 fish species, resulting in mortality rates of greater than 95%. However, there is no efficient method to control NNV infections. Aptamers generated by selective evolution of ligands by exponential enrichment (SELEX) are short, single-stranded nucleic acid oligomers. They display a high degree of affinity and specificity for many targets, such as viruses and viral proteins. In this study, three novel DNA aptamers (A5, A10, and B11) that specifically target the coat protein (CP) of grouper nervous necrosis virus (GNNV) were selected using SELEX. Secondary structures and minimum free energy (ΔG) predictions indicated that these aptamers could form stable, secondary stem-loop structures. Electrophoretic mobility shift assays, enzyme-linked immunosorbent assays, Kd measurements, the co-localization of tetramethylrhodamine (TAMRA) labeled-aptamers with the CP and flow cytometry analysis revealed that these aptamers could specifically bind the CP with high (nanomolar) affinities. In addition, competition analysis suggested the aptamers shared some common CP binding sites with the anti-CP antibody. Moreover, all three aptamers did not show any cytotoxic effects in vitro or in vivo, and anti-viral analysis indicated the selected aptamers could inhibit NNV infection in vitro and in vivo. Compared with controls, mortality of GNNV-infected fish decreased by 40% and 80% after 10 days infection, when the GNNV was pre-incubated with the 1000 nM A10 and B11, respectively. TAMRA-labeled aptamers could bind to NNV virions and directly enter NNV-infected cells, suggesting they could be used as tracers to study the mechanism of viral infection, as well as for targeted therapy. This is the first time that aptamers targeting a viral protein of marine fish have been generated and characterized. These aptamers hold promise as diagnostic, therapeutic, and targeted drug delivery agents for controlling NNV infections.