Acid Oligomers Research Articles

Bile Acid Oligomers and Their Combination with Antibiotics To Combat Bacterial Infections

The ever-growing risk of bacterial resistance is a critical concern. Among the various antimicrobial resistant bacterial strains, methicillin and vancomycin resistant Staphylococcus aureus are among the most dreadful, causing serious complications. On the basis of the hypothesis that microbes have reduced ability to develop resistance against membrane targeting antibiotics, bile acid oligomers having unique facially amphiphilic topologies were designed and synthesized. The oligomers with specific linkers exhibited potent and selective antibacterial activity against Gram-positive bacteria. The lead compounds also improved the efficacy of a range of known antibiotics belonging to different classes when tested in combination. The active dimers were found to be effective against antibiotic-resistant clinical isolates of S. aureus, including multidrug resistant isolates. A significant inhibitory activity against S. aureus biofilm, a highly drug-resistant bacterial phenotype often unresponsive to antibiotic therapy, was also noticed. No adverse effects were observed by these dimers in a cell viability assay against HEK293 cells.

Kinetics of radical telomerization of acrylic acid in the presence of 1-octadecanethiol

Abstract The oligomer of acrylic acid with a thiooctadecyl end-group was obtained by using octadecyl mercaptan as the chain-transfer agent. The resulting oligomer was characterized by 1H NMR and 13C NMR spectroscopy and critical micelle concentration was determined in aqueous solution. The order with respect to the initiator concentration was 0.5 and 1.6 with respect to the monomer concentration. The abnormal reaction order with respect to the monomer concentration was explained by participation in the chain propagation of unassociated and associated forms of acrylic acid, which were stabilized by formation of hydrogen bonds. The kinetic parameters of telomerization were determined. Telomerization with acrylic acid in the non-associated form had lower activation energy and lower pre-exponential factor than in the case of associated forms. The synthesis of the acrylic acid oligomer with a thiooctadecyl end-group having a low critical micelle concentration in water was carried out in one stage and corresponds to the concept of atom economy.

Prebiotic Evolution and Self-Assembly of Nucleic Acids.

Prebiotic evolution is the stage that is assumed to have taken place prior to the emergence of the first living entities, during which time the abiotic synthesis of monomers, oligomers, and supramolecular systems that led to the hypothesized RNA world occurred. In this Perspective, the success of one-pot Miller-Urey type synthesis of organic compounds is compared with the multipot syntheses developed within the framework of systems chemistry, which attempts to demonstrate that RNA could have been formed directly in the primitive environment. The prebiotic significance of liquid-crystal ordering of nucleic acid oligomers and self-organizing assemblages of RNA and DNA that are formed in the absence of membranes or mineral matrices is also addressed.

Handedness switch of synthesized helical polyaniline nanofibers featuring the use of a single enantiomeric acid and aniline oligomers

The polymerization of aniline (AN) was assisted with an oligomer that possessed two amino end groups (2AO) in the presence of a single enantiomeric acid, (1S)-(+)-10-camphorsulfonic acid ((S)CSA). The reaction produced helical polyaniline (PANI) nanofibers with the opposite helical sense due to the concentration changes of (S)CSA in the polymerization system. The similar dependence of the circular dichroism (CD) signal on the (S)CSA concentration was also observed in the oxidization of the oligomer 2AO by ammonium persulfate (APS) in the presence of (S)CSA. In addition, under a certain (S)CSA concentration, the 2AO-assisted polymerization at low and high temperatures also produced the PANI fibers with the opposite helical sense. It is likely that these result from the different interaction modes of (S)CSA with the 2AO at different (S)CSA concentration. As a consequence, the oxidized 2AO (oligomer seeds) with different chirality in the early stage of the polymerization control the helicity of the resulting PANI nanofibers.

Synthesis of Amphiphilic Oligomers of Acrylic Acid

Synthesis of amphiphilic oligomers of acrylic acid via radical polymerization in the presence of thiols as molecular mass regulators is described. The effect of the length of the introduced hydrophobic terminal group on the critical micellization concentration of the acrylic acid oligomers has been elucidated. It has been shown that the incorporation of an antituberculous drug (prothionamide) in the micelles of acrylic acid oligomers is enhanced with the increase in the length of the hydrophobic moiety. The preparation of hydroxyapatite-filled calcium-polycarboxylate bone cements containing prothionamide (promising for the sealing of postoperative cavities) is described.

A new instrument with high mass and high ion mobility resolution

A new instrument combining a two meter long ion mobility drift tube fabricated of resistive glass with a high-resolution time-of-flight (TOF) mass spectrometer is presented and new features are discussed in detail. Ions are formed by electrospray ionization. An ion gate positioned at the exit of the drift tube allows analysis of mobility-selected ions. A quadrupole mass filter and a collision cell are located between the drift tube and the TOF analyzer, an arrangement which allows collision-induced dissociation experiments of mass-selected and/or mobility-selected ions. The ability of the TOF spectrometer to resolve isotopologues differing by 1 Da in mass even for multiply charged ions opens up exceptional possibilities for ion selection and mobility analysis. The unique combination of instrument attributes including gentle ion production and analysis, the first principles measurement of cross sections, and high mobility (R∼100) and mass (R>20k) resolving powers allows for the analysis of a broad range of analytes including amino acid oligomer clusters (e.g. Phe97), peptides, and proteins.

Transesterification of Lactic Acid Oligomers with Ethanol, a Way to Anhydrous Ethyl Lactate: A Kinetic Study.

A new method for the preparation of anhydrous ethyl ester of lactic acid was studied. The selected method is based on catalytic transesterification of lactic acid oligomers, which were prepared for this purpose by autocatalytic oligomerization of lactic acid. In this work, a kinetic model for the case of catalytic alcoholysis of oligoesters was derived assuming a first-order reaction and equimolar content of reactants in the reaction mixture. The model makes it possible to obtain the values of the reaction rate and equilibrium constants and the equilibrium alcohol concentration by regression analysis at one time. The model was verified by measuring the rate of consumption of ethanol over the time at various reaction temperatures with anhydrous FeCl3 as the catalyst. The reaction was studied at overpressure under autogenous conditions in the temperature range of 100–180 °C. For the catalyst concentration of 1 mol %, the activation energy value was 64.35 kJ·mol−1. The dependence of equilibrium composition and rate constant on the temperature was obtained. The derived model is generally applicable to all first-order equilibrium reactions. The presumption is that the forward and reverse reactions are of the same order and have the same stoichiometry and equivalent amounts of reactants at the beginning of the reaction.

Lactic acid oligomer (OLLA) grafted gum arabic based green adhesive for structural applications

L-Lactic acid (LA)-grafted-gum arabic (GA) graft copolymer [OLLA-g-GA] was prepared by using microwave heating in which the hydrophilic GA was grafted with insitu grown lactic acid oligomer. The grafting at OH and NH groups in GA backbone with oligo-(l-lactic acid) (OLLA) chains proved with the help of FTIR and NMR analyses. The grafted GA was dispersed uniformly in OLLA due to the formation of amphiphile GA backbone grafted with OLLA chains, which is supported by XRD, SEM and TEM analyses. This synthesized OLLA-g-GA graft copolymer showed adhesive characteristics with various substrates such as glass and granite. The single lap shear joint of two glass and two granite substrates were fabricated and the adhesive properties of these laminated substrates were tested using Universal Testing Machine. The synthesized biobased adhesive showed excellent shear strength with respect to the present biobased adhesives and substrate failure was observed at optimized conditions during the shear test.

Abstract 3900: Plasma ctDNA multigene mutation analysis for the diagnosis and treatment monitoring of colorectal cancer patients

Abstract Introduction Colorectal cancer is a highly preventable disease as early detection increases rates of patient survival to near 100%. Also during therapy colorectal tumors can develop resistance due to mutations in cellular growth factor receptor signaling pathway genes such as KRAS and BRAF. Herein we report new validation studies of a novel multigene mutation biomarker real-time PCR based assay for qualitative detection of colorectal cancer associated mutations including the tumor suppressor APC, growth factor signaling pathway genes KRAS and BRAF and the essential WNT pathway signaling gene Beta- catenin (CTNNB1) called ColoScapeTM .The assay allows the sensitive detection of the presence or absence of mutations in the targeted regions of the genes interrogated. While tumor-tissue remains the ‘gold standard' for genetic analysis in cancer patients, it is challenged with the advent of circulating cell-free tumor DNA (ctDNA) analysis from blood samples; so called 'liquid biopsy'. Here we broaden our previous study on the initial validation of FFPE samples to include plasma DNA in colorectal cancer patients and by evaluating its clinical utility as a method for monitoring tumor ctDNA mutations during and after therapy as well as a potential screening test for early diagnosis of colorectal cancer. Methodology he high sensitivity of this multigene biomarker assay is achieved due to xenonucleic acid (XNA) probe technology. XNA probes are novel backbone modified oligomers having natural nucleoside bases (A,T,C and G) that hybridize by Watson-Crick base pairing to natural DNA and RNA with much higher binding affinity than natural deoxyribonucleic acid oligomers of the same sequence. XNA probes are designed that bind to the selected wild-type sequences at the respective genetic loci in the target genes. These XNA probes have a much higher Tm than the primer annealing temperature and suppress amplification of WT DNA templates and only allow amplification of the target mutant DNA templates in the sample. Both single nucleotide polymorphisms (SNP's) and insertion/deletions (indels) mutations can be detected. Performance parameters of the assay were established on DNA of colorectal cancer patients extracted from FFPE as well as reference DNA materials (synthetic and cell line derived DNA). This study presents further validation of the test as a potential landmark clinical test for colorectal cancer initial detection in FIT posiive patients and for recurrence and therapy monitoring Conclusion: The ColoScapeTM Colorectal Cancer Mutation Detection assay is shown to be a sensitive tool intended to facilitate research in Colon Cancer development, early detection, disease monitoring and therapeutic interventions. Citation Format: Michael J. Powell, Elena Peletskaya, Qing Sun, Jinwei Du, Larry Pastor, Jyoti Phatak, Jenny Wilding, Walter F. Bodmer, Aiguo Zhang. Plasma ctDNA multigene mutation analysis for the diagnosis and treatment monitoring of colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3900.

Enzymatic Synthesis of 6'-Sialyllactose, a Dominant Sialylated Human Milk Oligosaccharide, by a Novel exo-α-Sialidase from Bacteroides fragilis NCTC9343.

Gut bacteria provide a rich source of glycosidases that can recognize and/or hydrolyze glycans for nutrition. Interestingly, some glycosidases have also been found to catalyze transglycosylation reactions in vitro and thus can be used for oligosaccharide synthesis. In this work, six putative and one known exo-α-sialidase genes-three from Bacteroides fragilis NCTC9343, three from Clostridium perfringens ATCC 13124, and one known from Bifidobacterium bifidum JCM1254-were subjected to gene cloning and heterogeneous expression in Escherichia coli The recombinant enzymes were purified, characterized for substrate specificity, and screened for transglycosylation activity. A sialidase, named BfGH33C, from B. fragilis NCTC9343 was found to possess excellent transglycosylation activity for the synthesis of sialylated human milk oligosaccharide. The native BfGH33C was a homodimer with a molecular weight of 113.6 kDa. The Km and kcat values for 4-methylumbelliferyl N-acetyl-α-d-neuraminic acid and sialic acid dimer were determined to be 0.06 mM and 283.2 s-1, and 0.75 mM and 329.6 s-1, respectively. The enzyme was able to transfer sialyl from sialic acid dimer or oligomer to lactose with high efficiency and strict α2-6 regioselectivity. The influences of the initial substrate concentration, pH, temperature, and reaction time on transglycosylation were investigated in detail. Using 40 mM sialic acid dimer (or 40 mg/ml oligomer) and 1 M lactose (pH 6.5) at 50°C for 10 min, BfGH33C could specifically produce 6'-sialyllactose, a dominant sialylated human milk oligosaccharide, at a maximal conversion ratio above 20%. It provides a promising alternative to the current chemical and enzymatic methods for obtaining sialylated oligosaccharides.IMPORTANCE Sialylated human milk oligosaccharides are significantly beneficial to the neonate, as they play important roles in supporting resistance to pathogens, gut maturation, immune function, and brain and cognitive development. Therefore, access to the sialylated oligosaccharides has attracted increasing attention both for the study of saccharide functions and for the development of infant formulas that could mimic the nutritional value of human milk. Nevertheless, nine-carbon sialic acids are rather complicated for the traditional chemical modifications, which require multiple protection and deprotection steps to achieve a specific glycosidic bond. Here, the exo-α-sialidase BfGH33C synthesized 6'-sialyllactose in a simple step with high transglycosylation activity and strict regioselectivity. Additionally, it could utilize oligosialic acid, which was newly prepared in an easy, economical way to reduce the substrate cost, as a glycosyl donor. All the studies laid a foundation for the practical use of BfGH33C in large-scale synthesis of sialylated oligosaccharides in the future.

How to fold back grafted chains in dipolar brushes

Recent fully atomistic molecular dynamics (MD) simulation of polymer nanocomposites based on polylactic acid (PLA) filled with cellulose nanocrystals (CNC) covalently modified by grafting of lactic acid oligomers (OLA) [A.D. Glova et al. Soft Matter 13 (2017) 6627] have revealed a non-trivial structure of the OLA brush. It was found that a segregation of grafted OLA chains into two groups, or populations, occurs due to the presence of partial charges so that a fraction of chains folds back to the surface and acquires a hairpin-like conformation. Motivated by these results, we study the structure of a brush made of polymers with dipole moments oriented along the main chain (dipolar chains of A type) by using the numerical self-consistent field method for lattice models. In full agreement with the results of MD simulation study, the segregation of brush chains in two populations is observed as the strength of dipole-dipole interactions increases: A part of the brush chains folds back to form hairpin-like conformation while the remaining chains are extended and directed towards the brush periphery. An increase of the strength of dipole-dipole interactions and/or grafting density leads to the increase in the fraction of backfolded chains. We develop an analytical mean-field theory for the brush in the “dry” state which demonstrates the thermodynamic advantage of backfolding for a fraction of the brush chains. We find that the key factor leading to the observed non-trivial brush structure is the grafting of the chains in the brush via the same end. In contrast, in the case of the brush with the equal amount of chains grafted via each of the two ends, the dipole-dipole interactions do not result in the backfolding. This prediction for the lattice model is confirmed by additional fully atomistic molecular dynamics simulations of the corresponding OLA brush grafted onto CNC surface and immersed in the PLA melt.

Active pectin fragments of high in vitro antiproliferation activities toward human colon adenocarcinoma cells: Rhamnogalacturonan II

This study was to identify active pectin fragments of high in vitro anti-proliferation activities against human colon adenocarcinoma Caco-2 cells, using various pectin fragment preparations dominant with rhamnogalacturonan I (RG-I), rhamnogalacturonan II (RG-II), and galacturonic acid oligomers (GAOS). The samples were prepared from citrus high and low methoxy pectins (HPE and LPE) by endo-α-D-(1,4)-polygalacturonase action coupling with a green process as ultrafiltration (membrane molecular weight cut off > 10k, 1k-10k, and < 1k, giving fragment preparations I, II, and III, respectively). It is indicated that, in the fragment preparations HPE-I, II, and III, the molecular fractions HPE-F1 (RG-I), HPE-F2 (RG-II), and HPE-F3 (GAOS) showed an averaged Mw = 26.7k, 3.4k, and 0.3k, respectively, notably higher than their LPE counterparts. All fragment preparations exhibited concentration-dependent, inhibition effects on Caco-2 cells, where HPE-II (RG-II-domain) revealed an interesting inhibition effect, significantly higher than those did HPE-I (RG-I domain) and HPE-III (GAOS). The HPE-F2 (RG-II) was elucidated and found of IR = 88% at 1.0 mg/mL and half-inhibition concentration (IC50) = 0.12 mg/mL, doubling the effect of HPE-F1 (RG-I) (IR = 45% at 1.0 mg/mL). Conclusively, citrus RG-II fragment showed a promisingly high anti-Caco-2 activity, significantly higher than did RG-I and GAOS, possibly attributed to its special branched structure and low molecular size.

Molecular Insights into the Effects of Media-Drug and Carrier-Drug Interactions on pH-Responsive Drug Carriers.

We have performed two sets of all atom molecular dynamics (MD) simulations of poly(acrylic acid) (PAA) oligomers, considered as a model pH-responsive drug carrier. In the first set, multiple oligomers of PAA are simulated in model gastric and intestinal fluids, where the degree of deprotonation of PAA oligomers is varied with the medium pH. Since the gastric fluid has a pH substantially lower than that of intestinal fluid, PAA is relatively lesser ionized in gastric fluid and forms aggregates. In the second set, we simulated multiple oligomers of PAA with multiple molecules of a cationic anticancer drug, doxorubicin (DOX), for a range of pH values representative of various physiological conditions. The diffusion coefficient of DOX decreases with an increase in pH due to an increase in the ionic complexation of PAA with DOX, despite a decrease in PAA aggregation. Our findings are in agreement with recent experimental reports on pH-triggered targeting of tumor cells by the PAA-DOX system. Results of these two sets of studies establish that both carrier aggregation and carrier-drug interactions are competing influences that together determine the drug release from pH-responsive polymers.

Facile dispersion of exfoliated graphene/PLA nanocomposites via in situ polycondensation with a melt extrusion process and its rheological studies

This work attempted to improve the dispersion of graphene by coating poly(lactic acid) pellets with a masterbatch before melt processing. An in situ polycondensation reaction of lactic acid oligomer was utilized to prepare the masterbatch (MB) of exfoliated graphene (GR). MB dispersed composites of poly(lactic acid) (PLA) were fabricated by melt extrusion of MB‐coated PLA. One normal coated composite without MB coating (PLA‐M‐0.2GR) was fabricated for comparing properties. X‐ray diffraction, Raman spectroscopy, and morphological studies revealed better compatibility, dispersion, and interaction of GR for the diluted‐MB composite compared to the normal coated composite. The thermal stability, crystallization properties, and mechanical properties of the composites were examined, and the effect of short PLA chains in diluted‐MB composites was observed. The melt rheology nature of the composites was examined. Cole–Cole plots and Han plots suggested a uniform distribution of graphene. The sample PLA‐MB‐0.05GR showed improved modulus and elongation at break. It also showed better dispersion of GR, comparable thermal stability, good miscibility, good chain mobility, and high activation energy. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018, 135, 46476.

Cytocompatibility and Cellular Internalization of PEGylated "Clickable" Nucleic Acid Oligomers.

The recently developed synthetic oligonucleotides referred to as "click" nucleic acids (CNAs) are promising due to their relatively simple synthesis based on thiol-X reactions with numerous potential applications in biotechnology, biodetection, gene silencing, and drug delivery. Here, the cytocompatibility and cellular uptake of rhodamine tagged, PEGylated CNA copolymers (PEG-CNA-RHO) were evaluated. NIH 3T3 fibroblast cells treated for 1 h with 1, 10, or 100 μg/mL PEG-CNA-RHO maintained an average cell viability of 86%, which was not significantly different from the untreated control. Cellular uptake of PEG-CNA-RHO was detected within 30 s, and the amount internalized increased over the course of 1 h. Moreover, these copolymers were internalized within cells to a higher degree than controls consisting of either rhodamine tagged PEG or the rhodamine alone. Uptake was not affected by temperature (i.e., 4 or 37 °C), suggesting a passive uptake mechanism. Subcellular colocalization analysis failed to indicate significant correlations between the internalized PEG-CNA-RHO and the organelles examined (mitochondria, endoplasmic reticulum, endosomes and lysosomes). These results indicate that CNA copolymers are cytocompatible and are readily internalized by cells, supporting the idea that CNAs are a promising alternative to DNA in antisense therapy applications.

Engineering star-shaped lactic acid oligomers to develop novel functional adhesives

Abstract

Cationic nucleopeptides as novel non-covalent carriers for the delivery of peptide nucleic acid (PNA) and RNA oligomers

Cationic nucleopeptides belong to a family of synthetic oligomers composed by amino acids and nucleobases. Their capability to recognize nucleic acid targets and to cross cellular membranes provided the basis for considering them as novel non-covalent delivery agents for nucleic acid pharmaceuticals. Herein, starting from a 12-mer nucleopeptide model, the number of cationic residues was modulated in order to obtain new nucleopeptides endowed with high solubility in acqueous medium, acceptable bio-stability, low cytotoxicity and good capability to bind nucleic acid. Two candidates were selected to further investigate their potential as nucleic acid carriers, showing higher efficiency to deliver PNA in comparison with RNA. Noteworthy, this study encourages the development of nucleopeptides as new carriers to extend the known strategies for those nucleic acid analogues, especially PNA, that still remain difficult to drive into the cells.

Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides

BackgroundShort nucleic acid oligomers have found a wide range of applications in experimental physics, biology and medicine, and show potential for the treatment of acquired and genetic diseases. These applications rely heavily on the predictability of hybridization through Watson–Crick base pairing to allow positioning on a nanometer scale, as well as binding to the target transcripts, but also off-target binding to transcripts with partial homology. These effects are of particular importance in the development of therapeutic oligonucleotides, where off-target effects caused by the binding of mismatched sequences need to be avoided.ResultsWe employ a novel method of probing DNA hybridization using optically active DNA-stabilized silver clusters (Ag-DNA) to measure binding efficiencies through a change in fluorescence intensity. In this way we can determine their location-specific sensitivity to individual mismatches in the sequence. The results reveal a strong dependence of the hybridization on the location of the mismatch, whereby mismatches close to the edges and center show a relatively minor impact. In parallel, we propose a simple model for calculating the annealing ratios of mismatched DNA sequences, which supports our experimental results.ConclusionThe primary result shown in this work is a demonstration of a novel technique to measure DNA hybridization using fluorescent Ag-DNA. With this technique, we investigated the effect of mismatches on the hybridization efficiency, and found a significant dependence on the location of individual mismatches. These effects are strongly influenced by the length of the used oligonucleotides. The novel probe method based on fluorescent Ag-DNA functions as a reliable tool in measuring this behavior. As a secondary result, we formulated a simple model that is consistent with the experimental data.

Synthesis of luminescent 2,3-diphenylmaleimide-labelled peptide nucleic acid oligomers

A lys-GTAGATCACT-lys peptide nucleic acid (PNA) decamer labelled with the luminescent 2,3-diphenyl maleimido (DPM) group on the ε-position of the terminal lysine residue was prepared through an automated solid phase synthesis. Fluorescence emission of the DPM-labelled PNA thus obtained was found to be significant and promising for the potential application in DNA recognition.

Selection and Characterization of Single-Stranded DNA Aptamers Binding Human B-Cell Surface Protein CD20 by Cell-SELEX.

The B-lymphocyte antigen (CD20) is a suitable target for single-stranded (ss) nucleic acid oligomer (aptamers). The aim of study was selection and characterization of a ssDNA aptamer against CD20 using Cell-Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX). The cDNA clone of CD20 (pcDNA-CD20) was transfected to human embryonic kidney (HEK293T) cells. Ten rounds of Cell-SELEX was performed on recombinant HEK-CD20 cells. The final eluted ssDNA pool was amplified and ligated in T/A vector for cloning. The plasmids of positive clones were extracted, sequenced and the secondary structures of the aptamers predicted using DNAMAN® software. The sequencing results revealed 10 different types; three of them had the highest thermodynamic stability, named AP-1, AP-2 and AP-3. The AP-1 aptamer was the most thermodynamically stable one (ΔGAP-1 = −10.87 kcal/mol) with the highest binding affinity to CD20 (96.91 ± 4.5 nM). Since, the CD20 is a suitable target for recognition of B-Cell. The selected aptamers could be comparable to antibodies with many advantages. The AP-1, AP-2 and AP-3 could be candidate instead of antibodies for diagnostic and therapeutic applications in immune deficiency, autoimmune diseases, leukemia and lymphoma.