Highly stable DNA triplexes formed with cationic phosphoramidate pyrimidine alpha-oligonucleotides

The ability of cationic phosphoramidate pyrimidine alpha-oligonucleotides (ONs) to form triplexes with DNA duplexes was investigated by UV melting experiments, circular dichroism spectroscopy and gel mobility shift experiments. Replacement of the phosphodiester linkages in alpha-ONs with positively charged phosphoramidate linkages results in more efficient triplex formation, the triplex stability increasing with the number of positive charges. At a neutral pH and in the absence of magnesium ions, it was found that a fully cationic phosphoramidate alpha-TFO (triplex-forming oligonucleotide) forms a highly stable triplex that melts at a higher temperature than the duplex target. No hysteresis between the annealing and melting curves was noticed; this indicates fast association. Moreover, the recognition of a DNA duplex with a cationic alpha-TFO through Hoogsteen base pairing is highly sequence-specific. To the best of our knowledge, this is the first report of stable triplexes in the pyrimidine motif formed by cationic alpha-oligonucleotides and duplex targets.     

Design and Hybridization Properties of Acyclic Xeno Nucleic Acid Oligomers

Xeno nucleic acids (XNAs) are analogues of DNA and RNA that have a non-ribose artificial scaffold. XNAs are possible prebiotic genetic carriers as well as alternative genetic systems in artificial life. In addition, XNA oligomers can be used as biological tools. Acyclic XNAs, which do not have cyclic scaffolds, are attractive due to facile their synthesis and remarkably high nuclease resistance. To maximize the performance of XNAs, a negatively charged backbone is preferable to provide sufficient water solubility; however, acyclic XNAs containing polyanionic backbones suffer from high entropy cost upon duplex formation, because of the high flexibility of the acyclic nature. Herein, we review the relationships between the structure and duplex hybridization properties of various acyclic XNA oligomers with polyanion backbones.     

Synthesis and transfection activity of new cationic phosphoramidate lipids: high efficiency of an imidazolium derivative

In an effort to enhance the gene-transfer efficiencies of cationic lipids and to decrease their toxicities, a series of new phosphoramidate lipids with chemical similarity to cell membrane phospholipids was synthesised. These lipids contained various cationic headgroups, such as arginine methyl ester, lysine methyl ester, homoarginine methyl ester, ethylenediamine, diaminopropane, guanidinium and imidazolium. Their transfection abilities, either alone or with the co-lipid DOPE, were evaluated in HEK293-T7 cells. We found that imidazolium lipophosphoramidate 7 a/DOPE lipoplexes gave the most efficient transfection with low toxicity (15 %). The luciferase activity was 100 times higher than that obtained with DOTAP/DOPE lipoplexes. The size, zeta potential, pDNA-liposome interactions and cellular uptakes of the lipoplexes were determined. No definitive correlation between the zeta potential values and the transfection efficiencies could be established, but the uptake of lipoplexes by the cells was correlated with their final transfection efficiencies. Our results show that imidazolium phosphoramidate lipids constitute a potential new class of cationic lipids for gene transfer.     

Towards Zwitterionic Oligonucleotides with Improved Properties: the NAA/LNA-Gapmer Approach

Oligonucleotides (ON) are promising therapeutic candidates, for instance by blocking endogenous mRNA (antisense mechanism). However, ON usually require structural modifications of the native nucleic acid backbone to ensure satisfying pharmacokinetic properties. One such strategy to design novel antisense oligonucleotides is to replace native phosphate diester units by positively charged artificial linkages, thus leading to (partially) zwitterionic backbone structures. Herein, we report a “gapmer” architecture comprised of one zwitterionic central segment (“gap”) containing nucleosyl amino acid (NAA) modifications and two outer segments of locked nucleic acid (LNA). This NAA/LNA-gapmer approach furnished a partially zwitterionic ON with optimised properties: i) the formation of stable ON-RNA duplexes with base-pairing fidelity and superior target selectivity at 37 °C; and ii) excellent stability in complex biological media. Overall, the NAA/LNA-gapmer approach is thus established as a strategy to design partially zwitterionic ON for the future development of novel antisense agents.     

合成型两性水凝胶研究进展

两性水凝胶因其良好的环境响应特性,而成为吸水保水材料领域的研究热点。以阴离子单体与阳离子单体共聚制备两性聚电解质水凝胶和内盐型两性离子单体聚合制备聚甜菜碱型水凝胶为重点,介绍了两性水凝胶的制备、溶胀特性以及性能改进等方面的国内外研究现状及发展趋势。     

A Dynamic Combinatorial Approach for Identifying Side Groups that Stabilize DNA-Templated Supramolecular Self-Assemblies

DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.     

Mixtures of anionic and cationic surfactants with single and twin head groups: Solubilization and adsolubilization of styrene and ethylcyclohexane

Mixtures of anionic and cationic surfactants with single and twin head groups were used to solubilized styrene and ethylcyclohexane into mixed micelles and adsolubilize them into mixed admicelles on silica and alumina surfaces. Two combinations of anionic and cationic surfactants were studied: (i) a single-head anionic surfactant, sodium dodecyl sulfate (SDS), with a twin-head cationic surfactant, pentamethyl-octadecyl-1,3-propane diammonium dichloride (PODD), and (ii) a twin-head anionic surfactant, sodium hexadecyl-diphenyloxide disulfonate (SHDPDS), with a single-head cationic surfactant, dodecylpyridinium chloride (DPCl). Mixtures of SDS/PODD showed solubilization synergism (increased oil solubilization capacity) when mixed at a molar ratio of 1∶3; however, the SHD-PDS/DPCl mixture at a ratio of 3∶1 did not show solubilization enhancement over SHDPDS alone. Adsolubilization studies of SDS/PODD (enriched in PODD) adsorbed on negatively charged silica and SHDPDS/DPCl adsorbed on positively charged alumina showed that while mixtures of anionic and cationic surfactants had little effect on the adsolubilization of styrene, the adsolubilization of ethylcyclohexane was greater in mixed SHPDS/DPCl systems than for SHDPDS alone. Finally, it was concluded that whereas mixing anionic and cationic surfactants with single and double head groups can improve the solubilization capacity of micelles or admicelles, the magnitude of the solubilization enhancement depends on the molecular structure of the surfactant and the ratio of anionic surfactant to cationic surfactant in the micelle or admicelle.     

Dissociation of hydrophobic and charged nano particles in aqueous guanidinium chloride and urea solutions: a molecular dynamics study

It has been a long history that urea and guanidinium chloride (GdmCl) are used as agents for denaturing proteins. The underlying mechanism has been extensively studied in the past several decades. However, the question regarding why GdmCl is much stronger than urea has seldom been touched. Here, through molecular dynamics simulations, we show that a 4 M GdmCl solution is more able than 7 M urea solution to dissociate both hydrophobic and charged nano-particles (NP). Both urea and GdmCl affect the NPs' aggregation through direct binding to the NP surface. The advantages of GdmCl originate from the net charge of bound guanidinium ions which can generate a local positively charged environment around hydrophobic and negatively charged NPs. This effective coating can introduce Coulombic repulsion between all the NPs. Urea shows certain ability to dissociate hydrophobic NPs. However, in the case of charged NPs, urea molecules located between two opposite-charged NPs will form ordered hydrogen bonds, acting like "glue" which prevents separation of the NPs. Although urea can form hydrogen bonds with either hydrophilic amino acids or the protein backbone, which are believed to contribute to protein denaturation, our findings strongly suggest that this property does not always contribute positively to urea's denaturation power.     

Mixtures of anionic and cationic surfactants with single and twin head groups: Adsorption and precipitation studies

This research reports on the adsorption and precipitation of mixtures of anionic and cationic surfactants having single and twin head groups. The surfactant mixtures investigated were: (i) a single-head anionic surfactant, sodium dodecyl sulfate (SDS), in a mixture with the twin-head cationic surfactant pentamethyl-octadecyl-1,3-propane diammonium dichloride (PODD)—adsorption was studied on negatively charged silica; and (ii) a twin-head anionic surfactant, sodium hexadecyl-diphenyloxide disulfonate (SHDPDS), and the single-head cationic surfactant dodecylpyridinium chloride (DPCI)—adsorption was studied on positively charged alumina. Whereas the mixed surfactant system of SHDPDS/DPCI showed adsorption on alumina that was comparable to the of SHDPDS alone, the mixed surfactant system of SDS/PODD showed increased adsorption on silica as compared with PODD alone. The adsorption of the SDS/PODD mixture increased as the anionic and cationic system approached an equimolar ratio. Precipitation diagrams for mixtures of single- and twin-head surfactant systems showed smaller precipitation areas than for single-head-only surfactant mixtures. Thus, the combination of single- and double-head surfactants helps reduce the precipitation region and can increase the adsorption levels, although the magnitude of the effect is a function of the specific surfactants used.     

Tailoring Chitosan/LTA Zeolite Hybrid Aerogels for Anionic and Cationic Dye Adsorption

Chitosan (CS) is largely employed in environmental applications as an adsorbent of anionic dyes, due to the presence in its chemical structure of amine groups that, if protonated, act as adsorbing sites for negatively charged molecules. Efficient adsorption of both cationic and anionic dyes is thus not achievable with a pristine chitosan adsorbent, but it requires the combination of two or more components. Here, we show that simultaneous adsorption of cationic and anionic dyes can be obtained by embedding Linde Type A (LTA) zeolite particles in a crosslinked CS-based aerogel. In order to optimize dye removal ability of the hybrid aerogel, we target the crosslinker concentration so that crosslinking is mainly activated during the thermal treatment after the fast freezing of the CS/LTA mixture. The adsorption of isotherms is obtained for different CS/LTA weight ratios and for different types of anionic and cationic dyes. Irrespective of the formulation, the Langmuir model was found to accurately describe the adsorption isotherms. The optimal tradeoff in the adsorption behavior was obtained with the CS/LTA aerogel (1:1 weight ratio), for which the maximum uptake of indigo carmine (anionic dye) and rhodamine 6G (cationic dye) is 103 and 43 mg g⁻¹, respectively. The behavior observed for the adsorption capacity and energy cannot be rationalized as a pure superposition of the two components, but suggests that reciprocal steric effects, chemical heterogeneity, and molecular interactions between CS and LTA zeolite particles play an important role.     

Duplex formation of the simplified nucleic acid GNA

Glycol nucleic acid (GNA) has an acyclic backbone of propylene glycol nucleosides that are connected by phosphodiester bonds. This paper characterizes the duplex-formation properties of this simplified nucleic acid. Although single and multiple GNA nucleotides are highly destabilizing if incorporated into DNA duplexes, the two enantiomeric oligomers (S)-GNA and (R)-GNA form antiparallel homoduplexes that are thermally and thermodynamically significantly more stable than analogous duplexes of DNA and RNA. The salt-dependence and Watson-Crick-pairing fidelity of GNA duplexes are similar to those of DNA duplexes, but, apparently, the 2'-deoxyribonucleotide and the propylene glycol backbones are not compatible with each other. This conclusion is further supported by cross-pairing experiments. Accordingly, both (S)- and (R)-GNA strands do not generally pair with DNA. However, (S)-GNA, but not (R)-GNA, forms stable heteroduplexes with RNA in sequences that are low in G:C content. Altogether, the high stability and fidelity of GNA duplex formation in combination with the economical accessibility of propylene glycol building blocks for oligonucleotide synthesis render GNA an attractive candidate for the design of self-assembling materials. They further suggest that GNA could be considered as a potential candidate for a predecessor of RNA during the evolution of life on Earth.     

Triplex-Forming Peptide Nucleic Acids with Extended Backbones

Peptide nucleic acid (PNA) forms a triple helix with double-stranded RNA (dsRNA) stabilized by a hydrogen-bonding zipper formed by PNA's backbone amides (N−H) interacting with RNA phosphate oxygens. This hydrogen-bonding pattern is enabled by the matching ∼5.7 Å spacing (typical for A-form dsRNA) between PNA's backbone amides and RNA phosphate oxygens. We hypothesized that extending the PNA's backbone by one −CH₂− group might bring the distance between PNA amide groups closer to 7 Å, which is favourable for hydrogen bonding to the B-form dsDNA phosphate oxygens. Extension of the PNA backbone was expected to selectively stabilize PNA-DNA triplexes compared to PNA-RNA. To test this hypothesis, we synthesized triplex-forming PNAs that had the pseudopeptide backbones extended by an additional −CH₂− group in three different positions. Isothermal titration calorimetry measurements of the binding affinity of these extended PNA analogues for the matched dsDNA and dsRNA showed that, contrary to our structural reasoning, extending the PNA backbone at any position had a strong negative effect on triplex stability. Our results suggest that PNAs might have an inherent preference for A-form-like conformations when binding double-stranded nucleic acids. It appears that the original six-atom-long PNA backbone is an almost perfect fit for binding to A-form nucleic acids.     

Acetyl‐α‐d‐mannopyranose‐based cationic polymer via RAFT polymerization for lectin and nucleic acid bindings

Functional cationic polymers carrying mannose moieties were synthesized in a facile manner by employing RAFT polymerization. Initially, a protected carbohydrate based monomer, [2‐(2,3,4,6‐tetra‐O‐acetyl‐α‐d ‐mannopyranosyloxy)ethyl methacrylate (AcManEMA)], was prepared by the O‐glycosylation of 2‐hydroxyethyl methacrylate (HEMA). Subsequently, a macroRAFT agent of poly[2‐(dimethyl)amino ethyl methacrylate] (PDMAEMA) was generated, and a further chain extension polymerization with AcManEMA was carried out in dioxane to form a acetylated mannose cationic diblock copolymer, PDMAEMA‐b‐PAcManEMA. It was attained in high yields and displayed low dispersity (Ð). Acetylated mannose moieties on the polymer were deprotected with sodium methoxide and the amines from the DMAEMA block were protonated to yield a cationic diblock glycopolymer, PDMAEMA‐b‐PManEMA. The cationic property of polymers were characterized by mixing with a negatively charged siRNA duplex and a pDNA, and aggregates of 102 and 233 nm were obtained, respectively. Agarose gel shift assay revealed that the polymers were able to retain the nucleic acids as large polymer complexes. Lectin binding assay proved that the mannose residue on the polymers were only able to bind specifically with ConA. PNA lectin was employed as a control and did not show specific binding. The cationic glycopolymer could be advantageous in targeted nucleic acids delivery in specific cells. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134, 44947.     

Adsorption, Desorption and Adsolubilization Properties of Mixed Anionic Extended Surfactants and a Cationic Surfactant

Anionic and cationic surfactant mixtures exhibit desirable synergism, but are limited by their tendency to form precipitates. This research evaluates the adsorption, adsolubilization and desorption of mixtures of carboxylate-based anionic extended surfactants and a pyridinium-based cationic surfactant. The mixture of cetylpyridinium chloride (CPC), selected as the cationic surfactant, with four anionic extended surfactants were studied. The anionic surfactants studied were alkyl propoxylated ethoxylated carboxylate with average number of carbon chain length of 16 and 17 or 16 and 18 with 4?mol of propylene oxide groups and either 2 or 5?mol of ethylene oxide groups. The adsorption of anionic extended and cationic surfactant mixtures onto a negatively charged metal oxide surface (silica dioxide) was evaluated. The adsolubilization of phenylethanol, styrene and ethylcyclohexane were evaluated for these mixed surfactant systems. The desorption potential of individual and mixed surfactant systems was also evaluated by varying the number of washing (desorption) steps. It was found that the plateau adsorption of mixed anionic extended surfactant and cationic surfactant occurred at lower surfactant concentration than that of the CPC alone, although the maximum adsorption capacity of CPC was not enhanced in our mixed surfactant systems. Adsolubilization capacities of these mixed surfactant systems are higher than that of the individual surfactant system. For desorption studies, these mixed surfactant systems showed lower stability than the individual surfactant system.     

油水界面上阴/阳离子型复配表面活性剂体系的分子动力学模拟

采油过程中阴/阳离子型表面活性剂复配使用可显著增强驱油效果,对其微观机理的深入研究有助于驱油用表面活性剂的结构优化设计及使用。采用分子动力学方法研究了不同摩尔比的阴离子表面活性剂聚醚羧酸钠(PECNa)和阳离子表面活性剂十八烷基三甲基氯化铵(OTAC)复配体系在油水界面上的分子行为和物理性质。结果表明,复配体系比单种表面活性剂体系更有利于降低油水界面张力。不同复配比体系中,两种表面活性剂头基相反电荷间的吸引作用使表面活性剂之间对各自反离子的静电吸引作用减弱,且等摩尔比体系尤为明显。阴离子表面活性剂的亲水头基对阳离子表面活性剂亲水头基形成的水化层内水分子的结构取向无显著影响,反之亦然。通过调节两种离子型表面活性剂的复配比例,可调整油水界面吸附层微观结构,有望降低油水界面张力,提高采收率。     

Water-soluble PPV and C60 nanocomposite with enhanced miscibility and enhanced photo-induced charge transfer through ground state electrostatic interactions

We report the preparation of highly charged nanocomposites comprised of water-soluble, anionic fullerene and cationic poly-phenylenevinylene (PPV) derivatives. The nanocomposites display high fluorescence quenching efficiency (99%) presumably due to enhanced miscibility between cationic PPV and anionic C₆₀ via electrostatic interactions. We show that complexation between the cationic PPV and anionic C₆₀ derivatives leads to formation of nanocomposites with optical and electronic properties distinct from individual components without preferential electrostatic interactions. Photo-induced charge transfer quenches fluorescence from the PPV component is consistent with the frontier energy offsets of PPV and C₆₀, and cyclic voltammetry and UV–Vis spectroscopy measurements. This result confirms high miscibility between donor and acceptor and resonance Raman spectra indicate a conformational changes of the PPV backbone upon complex formation.     

Intracellular Delivery of Molecular Cargo Using Cell-Penetrating Peptides and the Combination Strategies

Cell-penetrating peptides (CPPs) can cross cellular membranes in a non-toxic fashion, improving the intracellular delivery of various molecular cargos such as nanoparticles, small molecules and plasmid DNA. Because CPPs provide a safe, efficient, and non-invasive mode of transport for various cargos into cells, they have been developed as vectors for the delivery of genetic and biologic products in recent years. Most common CPPs are positively charged peptides. While delivering negatively charged molecules (e.g., nucleic acids) to target cells, the internalization efficiency of CPPs is reduced and inhibited because the cationic charges on the CPPs are neutralized through the covering of CPPs by cargos on the structure. Even under these circumstances, the CPPs can still be non-covalently complexed with the negatively charged molecules. To address this issue, combination strategies of CPPs with other typical carriers provide a promising and novel delivery system. This review summarizes the latest research work in using CPPs combined with molecular cargos including liposomes, polymers, cationic peptides, nanoparticles, adeno-associated virus (AAV) and calcium for the delivery of genetic products, especially for small interfering RNA (siRNA). This combination strategy remedies the reduced internalization efficiency caused by neutralization.     

Preparation of anionic ion exchange latex particles via heteroaggregation

To prepare relatively large negatively charged polymer particles in a size range from 0.3 μm to 0.5 μm, having high surface charge densities, the heteroaggregation of small (50–100 nm), highly charged (185 and 421 μeq/g) anionic polystyrene particles onto the surface of larger (317–466 nm) poly(vinylbenzyl choride)‐based cationic (10, 614, and 830 μeq/g) particles was carried out. As a result, particles with different surface charges, having a core‐shell structure, were successfully prepared. First, aggregated particles were formed via heteroaggregation of the lowest surface charge density anionic particles (185 μeq/g) with the lowest surface charge density cationic particles (10 μeq/g). However, the anionic particles in the shell layer desorbed with time owing to the relatively weak interaction between the two particles. Second, aggregated particles comprised of the highest surface charge density cationic (830 μeq/g) and anionic latex particles (421 μeq/g) were formed. However, to prepare a stable system, an excess of the small anionic particles was required, leaving a large number of small particles present in the aqueous phase, which proved difficult to remove. Finally, aggregated particles were formed by heteroaggregation of cationic particles with an intermediate surface charge density (614 μeq/g) with the highest surface charge anionic particles (421 μeq/g). As a result, not only were core‐shell particles formed, but few free small anionic particles remained in the aqueous phase. In this article, the preparation and characterization of each of these aggregates are discussed in terms of particle size, morphology, and extent of incorporation of the functional groups. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013