Compaction and decompaction of DNA induced by the cationic surfactant CTAB

Critical assessment of interactions between ct-DNA and choline-based magnetic ionic liquids: evidences of compaction

Ionic liquids (ILs) have become an alternative green solvent for storage and for stability of DNA. However, an in-depth understanding of binding and molecular interactions between ILs and DNA is needed. In this respect, magnetic ILs (MILs) are promising due to their tunable physicochemical properties. Various spectroscopic techniques and molecular simulations have been employed to unravel the critical factors of the strength and binding mechanism of MILs with DNA. UV-vis spectra unravel the multimodal binding of MILs with DNA, and the intrusion of IL molecules into the minor groove of DNA has been observed from dye displacement studies. Fluorescence correlation spectroscopic studies and scanning electron microscopy confirm the compaction of the DNA. ITC and molecular docking studies estimate the binding affinity of DNA with MILs, of ∼7 kcal mol-1. The 1 μs long-MD simulations give insight into the structural changes in the DNA in the MIL environment. Due to strong interaction with choline ions in the close vicinity, DNA helixes bend or squeeze in length and dilate in diameter (elliptical → spherical), leading to compaction. The post-MD parameters suggest a stronger interaction with [Ch]2[Mn] IL than with [Ch][Fe] IL; hence, the former induces DNA compaction to a more significant extent. Furthermore, decompaction is observed with the addition of sodium salts and is characterized using spectroscopic methods.

DNA induced CTAB-caped gold bipyramidal nanoparticles self-assembly using for Raman detection of DNA molecules

DNA is an indispensable part of metabolism, which affects many important processes in the body, including gene expression, protein synthesis, and drug delivery. Surface-enhanced Raman spectroscopy (SERS) is one of the most important methods used to study the structure and function of DNA and can obtain rich DNA molecular fingerprints. However, it is still a great challenge to use SERS to directly analyze the characteristic Raman signals of the DNA molecule and achieve rapid and simple detection. Hence, a detection platform based on gold bipyramidal nanoparticles (AuNBs) self-assembly that can be directly used for the detection of DNA molecules without the need for additional aggregators and cleaning agents was designed in this study. The original hexadecyltrimethylammonium bromide (CTAB) of AuNBs can be used as the internal standard for DNA quantification without an additional standard. This is the first time that the Raman signals of the analyte molecule can be obtained directly without labels by using the interaction between the molecule and the enhanced substrate. We used this method to capture the original DNA molecules in methylated DNA, serum, and cell metabolites and obtained spectral data processing results using linear discriminant analysis (LDA). This provides new ideas for the digitization of disease treatment and the study of the metabolic processes of life.

Role of Gemini Surfactants with Variable Spacers and SiO2 Nanoparticles in ct-DNA Compaction and Applications toward In Vitro/In Vivo Gene Delivery

Compaction of calf thymus DNA (ct-DNA) by two cationic gemini surfactants, 12-4-12 and 12-8-12, in the absence and presence of negatively charged SiO₂ nanoparticles (NPs) (∼100 nm) has been explored using various techniques. 12-8-12 having a longer hydrophobic spacer induces a greater extent of ct-DNA compaction than 12-4-12, which becomes more efficient with SiO₂ NPs. While 50% ct-DNA compaction in the presence of SiO₂ NPs occurs at ∼77 nM of 12-8-12 and ∼130 nM of 12-4-12, but a conventional counterpart surfactant, DTAB, does it at its concentration as high as ∼7 μM. Time-resolved fluorescence anisotropy measurements show changes in the rotational dynamics of a fluorescent probe, DAPI, and helix segments in the condensed DNA. Fluorescence lifetime data and ethidium bromide exclusion assays reveal the binding sites of surfactants to ct-DNA. 12-8-12 with SiO₂ NPs has shown the highest cell viability (≥90%) and least cell death in the human embryonic kidney (HEK) 293 cell lines in contrast to the cell viability of ≤80% for DTAB. These results show that 12-8-12 with SiO₂ NPs has the highest time and dose-dependent cytotoxicity compared to 12-8-12 and 12-4-12 in the murine breast cancer 4T1 cell line. Fluorescence microscopy and flow cytometry are performed for in vitro cellular uptake of YOYO-1-labeled ct-DNA with surfactants and SiO₂ NPs using 4T1 cells after 3 and 6 h incubations. The in vivo tumor accumulation studies are carried out using a real-time in vivo imaging system after intravenous injection of the samples into 4T1 tumor-bearing mice. 12-8-12 with SiO₂ has delivered the highest amount of ct-DNA in cells and tumors in a time-dependent manner. Thus, the application of a gemini surfactant with a hydrophobic spacer and SiO₂ NPs in compacting and delivering ct-DNA to the tumor is proven, warranting its further exploration in nucleic acid therapy for cancer treatment.

Chemico-Physical Properties of Some 1,1'-Bis-alkyl-2,2'-hexane-1,6-diyl-bispyridinium Chlorides Hydrogenated and Partially Fluorinated for Gene Delivery

The development of very efficient and safe non-viral vectors, constituted mainly by cationic lipids bearing multiple charges, is a landmark for in vivo gene-based medicine. To understand the effect of the hydrophobic chain's length, we here report the synthesis, and the chemico-physical and biological characterization, of a new term of the homologous series of hydrogenated gemini bispyridinium surfactants, the 1,1'-bis-dodecyl-2,2'-hexane-1,6-diyl-bispyridinium chloride (GP12_6). Moreover, we have collected and compared the thermodynamic micellization parameters (cmc, changes in enthalpy, free energy, and entropy of micellization) obtained by isothermal titration calorimetry (ITC) experiments for hydrogenated surfactants GP12_6 and GP16_6, and for the partially fluorinated ones, FGPn (where n is the spacer length). The data obtained for GP12_6 by EMSA, MTT, transient transfection assays, and AFM imaging show that in this class of compounds, the gene delivery ability strictly depends on the spacer length but barely on the hydrophobic tail length. CD spectra have been shown to be a useful tool to verify the formation of lipoplexes due to the presence of a "tail" in the 288-320 nm region attributed to a chiroptical feature named ψ-phase. Ellipsometric measurements suggest that FGP6 and FGP8 (showing a very interesting gene delivery activity, when formulated with DOPE) act in a very similar way, and dissimilar from FGP4, exactly as in the case of transfection, and confirm the hypothesis suggested by previously obtained thermodynamic data about the requirement of a proper length of the spacer to allow the molecule to form a sort of molecular tong able to intercalate DNA.

A novel biocompatible polymer derived from D-mannitol used as a vector in the field of genetic engineering of eukaryotic cells

The design and preparation of new vectors to transport genetic material and increase the transfection efficiency continue being an important research line. Here, a novel biocompatible sugar-based polymer derived from D-mannitol has been synthesized to be used as a gene material nanocarrier in human (gene transfection) and microalga cells (transformation process). Its low toxicity allows its use in processes with both medical and industrial applications. A multidisciplinary study about the formation of polymer/p-DNA polyplexes has been carried out using techniques such as gel electrophoresis, zeta potential, dynamic light scattering, atomic force microscopy, and circular dichroism spectroscopy. The nucleic acids used were the eukaryotic expression plasmid pEGFP-C1 and the microalgal expression plasmid Phyco69, which showed different behaviors. The importance of DNA supercoiling in both transfection and transformation processes was demonstrated. Better results were obtained in microalga cells nuclear transformation than in human cells gene transfection. This was related to the plasmid's conformational changes, in particular to their superhelical structure. It is noteworthy that the same nanocarrier has been used with eukaryotic cells from both human and microalga.

Gold Nanosystems Covered with Doxorubicin/DNA Complexes: A Therapeutic Target for Prostate and Liver Cancer

Different gold nanosystems covered with DNA and doxorubicin (Doxo) were designed and synthesized for cancer therapy, starting from Au@16-Ph-16 cationic nanoparticles and DNA-Doxo complexes prepared under saturation conditions. For the preparation of stable, biocompatible, and small-sized compacted Au@16-Ph-16/DNA-Doxo nanotransporters, the conditions for the DNA-Doxo compaction process induced by gold nanoparticles were first explored using fluorescence spectroscopy, circular dichroism and atomic force microscopy techniques. The reverse process, which is fundamental for Doxo liberation at the site of action, was found to occur at higher C_Au@16-Ph-16 concentrations using these techniques. Zeta potential, dynamic light scattering and UV-visible spectroscopy reveal that the prepared compacted nanosystems are stable, highly charged and of adequate size for the effective delivery of Doxo to the cell. This fact is verified by in vitro biocompatibility and internalization studies using two prostate cancer-derived cell lines (LNCaP and DU145) and one hepatocellular carcinoma-derived cell line (SNU-387), as well as a non-tumor prostate (PNT2) cell line and a non-hepatocarcinoma hepatoblastoma cell line (Hep-G2) model used as a control in liver cells. However, the most outstanding results of this work are derived from the use of the C_I+N_I combined treatments which present strong action in cancer-derived cell lines, while a protective effect is observed in non-tumor cell lines. Hence, novel therapeutic targets based on gold nanoparticles denote high selectivity compared to conventional treatment based on free Doxo at the same concentration. The results obtained show the viability of both the proposed methodology for internalization of compacted nanocomplexes inside the cell and the effectiveness of the possible treatment and minimization of side effects in prostate and liver cancer.

Assessing the Suitability of a Dicationic Ionic Liquid as a Stabilizing Material for the Storage of DNA in Aqueous Medium

The present study has been undertaken with an objective to find out a suitable medium for the long-term stability and storage of the ct-DNA structure in aqueous solution. For this purpose, the potential of a pyrrolidinium-based dicationic ionic liquid (DIL) in stabilizing ct-DNA structure has been investigated by following the DNA-DIL interaction. Additionally, in order to understand the fundamental aspects regarding the DNA-DIL interaction in a comprehensive manner, studies are also done by employing structurally similar monocationic ionic liquids (MILs). The investigations have been carried out both at ensemble-average and single molecular level by using various spectroscopic techniques. The molecular docking study has also been performed to throw more light into the experimental observations. The combined steady-state and time-resolved fluorescence, fluorescence correlation spectroscopy, and circular dichroism measurements have demonstrated that DILs can effectively be used as better storage media for ct-DNA as compared to MILs. Investigations have also shown that the extra electrostatic interaction between the cationic head group of DIL and the phosphate backbone of DNA is primarily responsible for providing better stabilization to ct-DNA, retaining its native structure in aqueous medium. The outcomes of the present study are also expected to provide valuable insights in designing new polycationic IL systems that can be used in nucleic acid-based applications.

Fluorescent Calixarene-Schiff as a Nanovehicle with Biomedical Purposes

Gene therapy is a technique that is currently under expansion and development. Recent advances in genetic medicine have paved the way for a broader range of therapies and laid the groundwork for next-generation technologies. A terminally substituted difluorene-diester Schiff Base calix[4]arene has been studied in this work as possible nanovector to be used in gene therapy. Changes to luminescent behavior of the calixarene macrocycle are reported in the presence of ct-DNA. The calixarene macrocycle interacts with calf thymus DNA (ct-DNA), generating changes in its conformation. Partial double-strand denaturation is induced at low concentrations of the calixarene, resulting in compaction of the ct-DNA. However, interaction between calixarene molecules themselves takes place at high calixarene concentrations, favoring the decompaction of the polynucleotide. Based on cytotoxicity studies, the calixarene macrocycle investigated has the potential to be used as a nanovehicle and improve the therapeutic efficacy of pharmacological agents against tumors.

Interaction of calf thymus DNA and glucose-based gemini cationic surfactants with different spacer length: A spectroscopy and DLS study

The interactions between calf thymus DNA and a series of glucose-based cationic gemini surfactants 1a-1c with different spacer length, n = 4, 6 and 8, were studied by UV absorption, fluorescence spectroscopy, circular dichroism, FT-IR, dynamic light scattering and zeta potential measurements. The results showed that all the surfactants could interact with DNA efficiently. On addition of increasing concentration of the surfactants, UV absorption hypochromicity with insignificant blue shift were observed, until the DNA signal disappeared. The surfactant 1c was more efficient in the reduction of absorption intensity of DNA. According to the fluorescence quenching experiments by ethidium bromide exclusion, 1c exhibited the highest binding properties, with the binding constant at 3.25 × 10⁸ L·mol^-1. The spectroscopy study indicated that the surfactants bound with the DNA by a non-intercalative mode, mainly electrostatic interaction between the positively charged headgroups of the surfactants and negatively charged phosphate groups of DNA at low concentration, and the hydrophobic interaction among the alkyl chains at high concentration. The conformation of DNA during the interaction process could be kept B-form of DNA. For 1c, the DNA molecules can be compacted to about 103 nm in hydrodynamic diameter at 0.2 mM, while the minimum sizes of DNA were 140 nm and 133 nm, respectively, in the presence of 1a and 1b. The impact of the cationic gemini surfactants on the DNA compaction and condensation would shed light on their potential applications in gene delivery.

Impact of cationic surfactant-induced DNA compaction on the characteristics of a minor groove bound flavonol

3-Hydroxyflavone (3-HF), which binds to the minor groove of DNA, is a strong antioxidant and hence a potent therapeutic and diagnostic agent. A special photo-property, called excited state intramolecular proton transfer (ESIPT), makes the 3-HF derivatives sensitive to the cellular hydrophobic microenvironment. The present study depicts the various changes in the ESIPT of 3-HF due to cationic surfactant-induced compaction of DNA.

Demonstration of pH-controlled DNA-surfactant manipulation for biomolecules

The understanding of DNA-surfactant interactions is important for fundamental physical biology and developing biomedical applications. In the present study, we demonstrated a DNA-surfactant nano-machine model by modulating the compaction of DNA in dodecyldimethylamine oxide (DDAO) solutions. By controlling DDAO concentration and pH of solution, we are able to adjust the compacting force of DNA so as to pull biomolecular subunits connected to it. The pulling force of the machine depends on DDAO concentration and pH of solution, ranging from near zero to about 4.6 pN for 10 mM DDAO concentration at pH = 4. The response time of the machine is about 3 minutes for contracting and 2 minutes for releasing in 5 mM DDAO solution. We found that DDAO has no significant influence on DNA under basic conditions, but compacts DNA under acidic conditions, which is enhanced with decreasing pH of solution. Meanwhile, we found the accompanying charge inversion of DNA in the process of DNA compaction by DDAO.

Site-specific facet protection of gold nanoparticles inside a 3D DNA origami box: a tool for molecular plasmonics

Bare gold nanocubes and nanospheres with different sizes are incorporated into a rationally designed 3D DNA origami box. The encaged particles expose a gold surface accessible for subsequent site-specific functionalization, for example, for applications in molecular plasmonics such as SERS or SEF.

Divalent metal ions and intermolecular interactions facilitate DNA network formation

The interactions between divalent metal ions and DNA are crucial for basic life processes. These interactions are also important in advanced technological products such as DNA-based ion sensors. Current polyelectrolyte theories cannot describe these interactions well and do not consider the corresponding dynamics. In this study, we report the single-molecule dynamics of the binding of divalent metal ions to a single DNA molecule and the morphology characterization of the complex. We found that most of the divalent metal ions (Mn²⁺, Zn²⁺, Co²⁺, Ni²⁺, and Cd²⁺), except Mg²⁺ and Ca²⁺, could cause monomolecular DNA condensation. For transition metal ions, different ionic strengths were required to induce the compaction, and different shortening speeds were displayed in the dynamics, indicating ionic specificity. Atomic force microscopy revealed that the morphologies of the metal ion-DNA complexes were affected by the ionic strength of the metal ion, DNA chain length, and DNA concentration. At low metal ion concentration, DNA tended to adopt a random coil conformation. Increasing the ionic strength led to network-like condensed structures, suggesting that divalent metal ions can induce attraction between DNA molecules. Furthermore, higher DNA concentration and longer chain length enhanced intermolecular interactions and consequently resulted in network structures with a higher degree of interconnectivity.

A new approach to construct and modulate G-quadruplex by cationic surfactant

HYPOTHESIS

G-quadruplex structure has raised increasing attention in supramolecular chemistry as an effective template for ordered functional materials. Thus, it is of practical significance to advance our understanding regarding G-quadruplex structures. Typically, G-quadruplex structures are formed in the presence of suitable metal ions. New methods to construct such structures need to be explored.

EXPERIMENTS

The supramolecular assembly between CTAB and a guanosine derivative at different molar ratios was systematically studied, including assembly mechanisms, morphology, and macroscopic properties. Cationic surfactants with different alkyl chains were studied as control experiments.

FINDINGS

A novel strategy to construct G-quadruplex with the promotion of the cationic surfactant CTAB is presented in this work. The structure-property relationships of G-quadruplex gels are characterized by rheology and shrinkage ratio experiments. MacKintosh's theory was used to rationalize the relationship between gel elasticity and water content. The transition of G-quadruplex structures could be easily enabled by modulating CTAB concentration, which promotes the phase transition from gel/sol biphase to homogeneous sol phase. This work will provide a new viewpoint for the construction and modulation of G-quadruplex structures.

Interactions with ctDNA of novel sugar-based gemini cationic surfactants

The interactions between calf thymus DNA, ctDNA, and a series of sugar-based gemini cationic surfactants with different hydrophobic chains were investigated. The surface properties of the cationic gemini surfactants were firstly examined, and then their interactions with DNA and induced condensation of DNA were studied by UV-vis, ethidium bromide exclusion assay, circular dichroism, dynamic light scattering, zeta potential and atomic force microscopy. With the increase of hydrophobic chains of the surfactants, critical micelle concentrations decreased significantly, and the interactions with DNA were remarkably strengthened, with the binding constant up to 1.95 × 10⁷ L·mol^-1 according to fluorescence quenching experiments by ethidium bromide exclusion. The gemini surfactant with hexadecyl hydrocarbon chain, 1c, exhibited the highest compaction capacity for DNA, accompanied with conformation changes, as confirmed by CD and DLS measurements. The DNA molecules could be compacted to about 140 nm in hydrodynamic diameter at 0.2 mM of 1c, and the overall shifts of the positive band and significant increase of negative molar ellipticity indicated the formation of a supramolecualr chiral order of ѱ phase in which DNA were supposed to be tightly packed.

Enzymatic degradation of extracellular DNA exposed to chlorpyrifos and chlorpyrifos-methyl in an aqueous system

The persistence of extracellular DNA (eDNA) is crucial for ensuring species diversity and ecological function in aquatic systems. However, scarce information exists about the impact of pesticides on eDNA, although they often co-exist in the aquatic environment. Using a variety of spectroscopic analyses, eDNA degradation and the associated alterations in DNA secondary structure was investigated by exposing DNase I to tested DNA in the presence of chlorpyrifos, a commonly used organophosphate pesticide. Molecular dynamics simulation was used to explore the weak interactions between the tested DNA and chlorpyrifos. The results indicated that chlorpyrifos significantly enhanced DNA degradation without affecting the enzyme activity of DNase I in an aqueous system. Spectroscopic experiments confirmed that chlorpyrifos and the analog chlorpyrifos-methyl could bind with DNA to cause the bases noncovalent stacking interaction. Molecular simulations further demonstrated that pesticide binding with DNA molecules caused widening of the DNA grooves and destruction of the hydrated layer, which enhanced DNA degradation. The findings presented herein provide novel insight into the genotoxicity and ecotoxicity of chlorpyrifos and chlorpyrifos-methyl, as well as their impacts on DNA persistence in aquatic environments.

Cyclobutane-Containing Scaffolds as Useful Intermediates in the Stereoselective Synthesis of Suitable Candidates for Biomedical Purposes: Surfactants, Gelators and Metal Cation Ligands

Efficient and versatile synthetic methodologies are reported for the preparation of products that are suitable candidates to be used as surfactants, gelators for hydroxylic solvents or metal cation ligands, with potential use in several fields including biomedical applications. The common structural feature of all the synthesized products is the presence of a cis or trans-1,2- or cis-1,3-difunctionalized cyclobutane ring. In the two first cases, the key intermediates including enantiomerically pure 1,3-diamines and 1,3-amino alcohols have been prepared from β-amino acid derivatives obtained, in turn, from a chiral half-ester. This compound is also precursor of γ-amino esters. Furthermore, two kind of polydentate ligands have also been synthesized from a symmetric 1,5-diamine obtained from norpinic acid, which was easily prepared from commercial verbenone.

Structural characterization of transfection nanosystems based on tricationic surfactants and short double stranded oligonucleotides

For several years cationic surfactants have been the subjects of extensive studies as potential transgene carriers to be used in gene therapy. We report the formation of stable complexes between 21 base pairs oligonucleotides - siRNA, enhancing DMPK gene, and dsDNA and two tricationic surfactants (1,2,3-propanetri[oxymethyl-3-(1-dodecylimidazolium)]chloride and 1,2,3-propanetri[(oxymethyl)dimethyldodecylammonium]chloride. Structural studies by SAXS and TEM have shown that the dominant structure of the obtained lipoplexes is based on hexagonal, lamellar and cubic phases, packed in highly ordered aggregates. It has been established that tricationic surfactants can be used as siRNA carriers in gene therapy.

What controls the unusual melting profiles of small AuNPs/DNA complexes

The effect of the addition of low concentrations of an inner electrolyte on ds-DNA CT-DNA (calf thymus DNA) and ss-DNA conformational changes induced by small N-(2-mercaptopropionyl)glycine gold nanoparticles (AuNPs) is here studied in detail by using different spectroscopic and structural techniques. The high affinity of ss-DNA to AuNPs compared with ds-DNA is easily demonstrated by the results of competitive binding with SYBR Green I (SG). Additionally, it is proven that at 25.0 °C, AuNPs/ds-DNA and AuNPs/ss-DNA complexes undergo a transition from extended-coil to more compact structures when the AuNPs concentration (C_AuNPs) is increased, which for the ds-DNA system is accompanied by partial denaturation. Particularly, for the AuNPs/ss-DNA system all of these techniques confirm that at a high C_AuNPs, the compaction process is followed by a discrete transition to aggregation and an increase in structure size. A thorough analysis of the conformational changes described indicates that these processes are larger in low salt concentration and at high temperature. However, the most striking feature of this work is the abnormal melting temperature profiles (T_m) registered at high R = C_AuNPs/C_DNA ratios, which are remarkable and of interest for chemical sensing. At a suitable R ratio, which varies depending on C_NaCl, a complex melting profile for the AuNPs/ds-DNA system was registered with two characteristic transitions: T_m,1 = 65.0 °C and T_m,2 = 95.0 °C. The highly sensitive atomic force microscopy technique performed at 25.0 °C and 65.0 °C also showed a different behaviour in both ss- and AuNPs/ds-DNA systems, which explains the characteristic melting curves. Specifically for the AuNPs/ss-DNA system, AFM at 25.0 °C revealed the formation of large-sized aggregates formed by AuNPs/ss-DNA compact structures linked by AuNPs. However, when both AuNPs/ds-DNA and AuNPs/ss-DNA complexes were incubated at 65.0 °C, the formation of highly stable ordered structures was always visualized at high R. Therefore, this shows that some key parameters for effective control of the formation of DNA/RNA-linked particles are: the selection of an optimal temperature below the ds-DNA melting point, an appropriate C_AuNPs, and the addition of low C_NaCl. The optimization of these parameters for each AuNPs/DNA system could improve biological sensing and DNA/RNA delivery.

Fluorescent hybrid nanospheres induced by single-stranded DNA and magnetic carbon quantum dots

Assembled DNA nanospheres were preparedviaself-assembly with magnetic CQDGd as the building blocks and negatively charged ssDNA as the assembly units.

Reversible DNA compaction induced by partial intercalation of 16-Ph-16 gemini surfactants: evidence of triple helix formation

The interaction between calf thymus DNA and the gemini surfactants N,N'-[α,ω-phenylenebis(methylene)bis [N,N'-dimethyl-N-(1-hexadecyl)]-ammonium dibromide], p-16-Ph-16 (α = 1, ω = 3) and m-16-Ph-16 (α = 1, ω = 2), has been investigated via circular dichroism, fluorescence and UV-vis spectroscopy, zeta potential, dynamic light scattering, and AFM microscopy. Measurements were carried out in aqueous media at different molar ratios, R = (C16-Ph-16)/CDNA and C16-Ph-16 always below the critical micellar concentration (CMC) of the surfactant. Under these conditions, DNA undergoes two reversible conformational changes, compaction and decompaction, due to interaction with the surfactant molecules at low and high molar ratios, respectively. The extent of such conformational changes is correlated with both the degree of surfactant partial intercalation, and the size and charge of the surfactant aggregates formed, in each case. Comparison of the results shows that the para-form of the surfactant intercalates into the DNA to a major extent; therefore, the compaction/decompaction processes are more effective. Among these, the structure of the resulting 16-Ph-16/DNA decompacted complex is worthy of note. For the first time it can be demonstrated that the partial intercalation of the 16-Ph-16 gemini surfactants induces the formation of triplex DNA-like structures at a high R ratio.

Importance of hydrophobic interactions in the single-chained cationic surfactant-DNA complexation

The goal of this work was to understand the key factors determining the DNA compacting capacity of single-chained cationic surfactants. Fluorescence, zeta potential, circular dichroism, gel electrophoresis and AFM measurements were carried out in order to study the condensation of the nucleic acid resulting from the formation of the surfactant-DNA complexes. The apparent equilibrium binding constant of the surfactants to the nucleic acid, K_app, estimated from the experimental results obtained in the ethidium bromide competitive binding experiments, can be considered directly related to the ability of a given surfactant as a DNA compacting agent. The plot of ln(K_app) vs. ln(cmc), cmc being the critical micelle concentration, for all the bromide and chloride surfactants studied, was found to be a reasonably good linear correlation. This result shows that hydrophobic interactions mainly control the surfactant DNA compaction efficiency.

Nanocapsules of Magnetic Au Self-Assembly for DNA Migration and Secondary Self-Assembly

To endow valuable responsiveness to self-assemblies of Au nanoparticles (Au NPs), the magnetic Au nanoparticles (Au NPs)/C₁₆H₃₃(CH₃)₃N⁺[CeCl₃Br]^- (CTACe) mixtures were first prepared by using an emulsion self-assembly of a magnetic surfactant, C₁₆H₃₃(CH₃)₃N⁺[CeCl₃Br]^-. A versatile morphology of self-assemblies of Au NPs could be controlled by the counterions in surfactants including [CeCl₃Br]^-, [FeCl₃Br]^-, and Br^- as well as solvent. In particular, the magnetic counterion, [CeCl₃Br]^-, can induce self-growth of Au NPs in an emulsion self-assembly process due to the oxidability of [CeCl₃Br]^-. It enhances the rigidity of Au NPs/CTACe scaffolds template compared with Au NPs/hexadecyltrimethylammonium bromide. [CeCl₃Br]^- engaged Au NPs/CTACe with fascinating capability of conglutination and targeted migration of DNA (150 μmol/L) under a magnet field. The conglutination capability of the DNA molecules can increase to 39.8% by adopting the magnetic strategy when using Au NPs/CTACe as a magnetic booster. Au NPs/CTACe mixtures can ideally self-assemble to be scaffolds, providing abundant conjugation sites of surface charges. Magnetic Au NPs/CTACe can serve as a template scaffold to secondary self-assemble with DNA (40 mmol/L) outside, producing smooth-faced and hollow DNA nanocapsules. We believe that the creative Au NPs/CTACe/DNA nanocapsules will extend the biological application field of Au NPs assemblies.

A new surfactant–copper(ii) complex based on 1,4-diazabicyclo[2.2.2]octane amphiphile. Crystal structure determination, self-assembly and functional activity

A new complex [Cu(L)Br₃] (where LBr is 1-cetyl-4-aza-1-azoniabicyclo[2.2.2]octane bromide) has been synthesized and characterized.

Studying compaction-decompaction of DNA molecules induced by surfactants

The mechanism and detailed processes of DNA compaction and decompaction are essential for the life activities, as well as for the researches in the molecular biology, genetics and biomedicine. The compaction of two kinds of DNA molecules caused by Cetyltrimethyl Ammonium Bromide (CTAB) and their decompaction induced with sodium dodecyl sulfate (SDS) or excessive amount of CTAB have been investigated with multiple perspectives such as the UV-VIS spectrophotometry, dynamic light scattering, and zeta potential. The compaction phenomenon of DNA can easily be observed when the CTAB combines with the DNA, not just when the molar ratio Q_CTAB/Q_DNA is approximately equal to 1 as the conventional recognition, but also when Q_CTAB/Q_DNA <1,DNA can be compacted; Molecular state of DNA is only changed in the conformational structure, but not in the chemical structure. Finally, a model is suggested to help catch on the biophysical mechanism of DNA chain conformational change.

Magnetic Fullerene-DNA/Hyaluronic Acid Nanovehicles with Magnetism/Reduction Dual-Responsive Triggered Release

We created the dual-responsive nanovehicle that can effectively combine and abundantly utilize magnetic and glutathione (GSH)-reductive triggers to control the drug delivery and achieve more intelligent and powerful targeting. In the nanovehicles, paramagnetic fullerene (C₆₀@CTAF) was prepared via one-step modification of fullerene with magnetic surfactant CTAF by hydrophobic interaction for the first time. The perfect conjugation of C₆₀ and CTAF increased the solubility or dispersity of fullerenes and qualified CTAF with more powerful assembly capability with DNA. DNA molecule in the nanovehicles acted as an electrostatic scaffold to load anticancer drug Dox as well as the important building block for assembly with C₆₀@CTAF into C₆₀@CTAF/DNA. The further combination of deshielding and targeting functions in reduction-responsive disulfide modified HA-SS-COOH coating on C₆₀@CTAF/DNA complexes could reduce the agglomeration and regulate the morphology of C₆₀@CTAF/DNA complexes from irregular microstructures to more uniform ones. More importantly, the introduction of HA-SS-COOH provided a response to a simulating reductive extra-tumoral environment by efficient cleavage of disulfide linkages by GSH and site-specific drug delivery to HepG2 cells. Amazingly, the final nanovehicles presented an increased magnetic susceptibility compared with paramagnetic CTAF, and they "walked" under an applied magnetic field. Because of their facile fabrication, rapid responsiveness to extra tumoral environment, and external automatic controllability by external magnet, the drug delivery nanovehicles constructed by magnetic fullerene-DNA/hyaluronic acid might be of great interest for making new functional nucleic-acid-based drug carriers.

Investigation on interaction of DNA and several cationic surfactants with different head groups by spectroscopy, gel electrophoresis and viscosity technologies

In this study, the interaction between DNA and several cationic surfactants with different head groups such as ethyl hexadecyl dimethyl ammonium bromide (EHDAB), hexadecyl dimethyl benzyl ammonium chloride (HDBAC), and cetyl pyridinium bromide (CPB) were investigated by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, gel electrophoresis, and viscosity technologies. The results show that these cationic surfactants can interact with DNA and major binding modes are electrostatic and hydrophobic. Also, CPB and HDBAC molecules interact with DNA by partial intercalation, and CPB has slightly stronger intercalation than HDBAC, while EHDAB interacts with DNA by non-intercalation. The different head groups of the surfactant molecules can influence the interaction strength. CPB has the stronger interaction with DNA than the others. Moreover, surfactant concentration, the ratio of DNA and fluorescence probe, ionic strength can influence the interaction. The surfactants may interact with DNA by the competition reactions with BR for DNA-BR. The increase of ionic strength may favor the surface binding between DNA and surfactants to some extent. This work provides deep mechanistic insight on the toxicity of cationic surfactants with different head groups to DNA molecules.

Specific Conformational Change in Giant DNA Caused by Anticancer Tetrazolato-Bridged Dinuclear Platinum(II) Complexes: Middle-Length Alkyl Substituents Exhibit Minimum Effect

Derivatives of the highly antitumor-active compound [{cis-Pt(NH₃)₂}₂(μ-OH)(μ-tetrazolato-N2,N3)]²⁺ (5-H-Y), which is a tetrazolato-bridged dinuclear platinum(II) complex, were prepared by substituting a linear alkyl chain moiety at C5 of the tetrazolate ring. The general formula for the derivatives is [{cis-Pt(NH₃)₂}₂(μ-OH)(μ-5-R-tetrazolato-N2,N3)]²⁺, where R is (CH₂)_nCH₃ and n = 0 to 8 (complexes 1-9). The cytotoxicity of complexes 1-4 in NCI-H460 human non-small-cell lung cancer cells decreased with increasing alkyl chain length, and those of complexes 5-9 increased with increasing alkyl chain length. That is, the in vitro cytotoxicity of complexes 1-9 was found to have a U-shaped association with alkyl chain length. This U-shaped association is attributable to the degree of intracellular accumulation. Although circular dichroism spectroscopic measurement indicated that complexes 1-9 induced comparable conformational changes in the secondary structure of DNA, the tetrazolato-bridged complexes induced different degrees of DNA compaction as revealed by a single DNA measurement with fluorescence microsopy, which also had a U-shaped association with alkyl chain length that matched the association observed for cytotoxicity. Complexes 7-9, which had alkyl chains long enough to confer surfactant-like properties to the complex, induced DNA compaction 20 or 1000 times more efficiently than 5-H-Y or spermidine. A single DNA measurement with transmission electron microscopy revealed that complex 8 formed large spherical self-assembled structures that induced DNA compaction with extremely high efficiency. This result suggests that these structures may play a role in the DNA compaction that was induced by the complexes with the longer alkyl chains. The derivatization with a linear alkyl chain produced a series of complexes with unique cellular accumulation and DNA conformational change profiles and a potentially useful means of developing next-generation platinum-based anticancer drugs. In addition, the markedly high ability of these complexes to induce DNA compaction and their high intracellular accumulation emphasized the difference in mechanism of action from platinum-based anticancer drugs.

Synergistic enhancement in the drug sequestration power and reduction in the cytotoxicity of surfactants

Surfactants in supramolecular assemblies show a significant increase in their drug sequestration power with a remarkably reduced cytotoxicity.

Phase Transitions in DNA/Surfactant Adsorption Layers

The adsorption layers of complexes between DNA and oppositely charged surfactants dodecyltrimethylammonium bromide (DTAB) and cetyltrimethylammonium bromide (CTAB) at the solution/air interface were studied with surface tensiometry, dilational surface rheology, atomic force microscopy, Brewster angle microscopy, infrared absorption-reflection spectroscopy, and ellipsometry. Measurements of the kinetic dependencies of the surface properties gave a possibility to discover the time intervals corresponding to the coexistence of two-dimensional phases. One can assume that the observed phase transition is of the first order, unlike the formation of microaggregates in the adsorption layers of mixed solutions of synthetic polyelectrolytes and surfactants. The multitechniques approach together with the calculations of the adsorption kinetics allowed the elucidation of the structure of coexisting surface phases and the distinguishing of four main steps of adsorption layer formation at the surface of DNA/surfactant solutions.

Thermo-reversible capture and release of DNA by zwitterionic surfactants

The thermo-reversible capture and release of DNA were studied by the protonation and deprotonation of alkyldimethylamine oxide (CnDMAO, n = 10, 12 and 14) in Tris-HCl buffer solution. DNA/C14DMAO in Tris-HCl buffer solution with pH = 7.2 is transparent at 25 °C, indicating that DNA molecules exist mainly in individuals and the binding of C14DMAO is weak. With the increase of temperature, the pH of the buffer solution continuously decreases, which leads to protonation of C14DMAO (C14DMAO + H(+)→ C14DMAOH(+)) and an obvious increase of the turbidity of the samples. This indicates a stronger binding of the protonated C14DMAOH(+) to DNA. Further investigations demonstrated the formation of DNA/C14DMAOH(+) complexes, in which the stretched DNA molecules are effectively compacted as evidenced from UV-vis absorptions, circular dichroism (CD) measurements, atomic force microscopy (AFM) observations, dynamic light scattering (DLS) measurements and agarose gel electrophoresis (AGE). Interestingly, when the temperature is turned back to 25 °C, the compacted DNA molecules can fully recover to the stretched conformation. This cycle can be repeated several times without obvious loss of efficiency. The effect of the chain length of CnDMAO has also been investigated. When C14DMAO was replaced by C12DMAO, similar phenomena can be observed with a slightly higher critical surfactant concentration for DNA compaction and a slightly lower pH of Tris-HCl buffer solution with pH = 6.8. For the DNA/C10DMAO system, however, no DNA compaction was observed even in Tris-HCl buffer solution with a much lower pH and a much higher C10DMAO concentration. The negative charges of DNA molecules can easily be neutralized by positive charges of cationic CnDMAOH(+) (n = 12 and 14) micelles. DNA was compacted and then insoluble DNA/CnDMAOH(+) complexes were formed. Because of the much higher critical micelle concentration (cmc) of the shorter chain length C10DMAOH(+), cationic C10DMAOH(+) micelles cannot form under the studied condition to compact DNA. The strategy may provide an efficient and alternative approach for stimuli-responsive gene therapy and drug release.

Compaction of DNA using C12EO4 cooperated with Fe(3.)

Nonionic surfactant, tetraethylene glycol monododecyl ether (C12EO4), cannot compact DNA because of its low efficiency in neutralizing the negative charges of the phosphate groups of DNA. It is also well-known that nonionic surfactants as a decompaction agent can help DNA be released from cationic surfactant aggregates. Herein, with the "bridge" Fe(3+) of C12EO4, we found that C12EO4 can efficiently compact DNA molecules into globular states with a narrow size distribution, indicating that the cooperative Fe(3+) can transform C12EO4 molecules from decompaction agents to compaction ones. The mechanism of the interaction of DNA and C12EO4 by "bridge" Fe(3+) is that the Fe(3+)-C12EO4 complexes act as multivalent ions by cooperative and hydrophobic interaction. The improved colloidal-stability and endosome escape effect induced by C12EO4 would provide the potential applications of nonionic surfactant in the physiological characteristics of DNA complexes. Cell viability assay demonstrates that Fe(3+)-C12EO4 complexes possess low cytotoxicity, ensuring good biocompatibility. Another advantage of this system is that the DNA complexes can be de-compacted by glutathione in cell without any other agents. This suggests the metal ion-nonionic surfactant complexes as compaction agent can act as the potential delivery tool of DNA in future nonviral gene delivery systems.

Binding of 12-s-12 dimeric surfactants to calf thymus DNA: Evaluation of the spacer length influence

Several cationic dimeric surfactants have shown high affinity towards DNA. Bis-quaternary ammonium salts (m-s-m) have been the most common type of dimeric surfactants investigated and it is generally admitted that those that posses a short spacer (s≤3) show better efficiency to bind or compact DNA. However, experimental results in this work show that 12-s-12 surfactants with long spacers make the surfactant/ctDNA complexation more favorable than those with short spacers. A larger contribution of the hydrophobic interactions, which control the binding Gibbs energy, as well as a higher average charge of the surfactant molecules bound to the nucleic acid, which favors the electrostatic attractions, could explain the experimental observations. Dimeric surfactants with intermediate spacer length seem to be the less efficient for DNA binding.

CTAB enhancement of FRET in DNA structures

The effect of cetyl-trimethylammonium bromide (CTAB) on enhancing the fluorescence resonance energy transfer (FRET) between two dye-conjugated DNA strands was studied using fluorescence emission spectroscopy and dynamic light scattering (DLS). For hybridized DNA where one strand is conjugated with a TAMRA donor and the other with a TexasRed acceptor, increasing the concentration of CTAB changes the fluorescence emission properties and improves the FRET transfer efficiency through changes in the polarity of the solvent, neutralization of the DNA backbone and micelle formation. For the DNA FRET system without CTAB, the DNA hybridization leads to contact quenching between TAMRA donor and TexasRed acceptor producing reduced donor emission and only a small increase in acceptor emission. At 50 µM CTAB, however, the sheathing and neutralization of the dye-conjugated dsDNA structure significantly reduces quenching by DNA bases and dye interactions, producing a large increase in FRET efficiency, which is almost four fold higher than without CTAB.

Structural, biocomplexation and gene delivery properties of hydroxyethylated gemini surfactants with varied spacer length

Gemini surfactants with hexadecyl tails and hydroxyethylated head groups bridged with tetramethylene (G4), hexamethylene (G6) and dodecamethylene (G12) spacers were shown to self-assemble at the lower critical micelle concentration compared to their conventional m-s-m analogs. The lipoplex formation and the plasmid DNA transfer into different kinds of host cells were studied. In the case of eukaryotic cells, high transfection efficacy has been demonstrated for DNA-gemini complexes, which increased as follows: G6<G4<G12. Different activity series, i.e., G6>G4>G12 has been obtained in the case of transformation of bacterial cells with plasmid DNA-gemini complexes, mediated by electroporation technique. Solely G6 shows transformation efficacy exceeding the control result (uncomplexed DNA), while the inhibitory effect occurs for G4 and G12. Analysis of physico-chemical features of single surfactants and lipoplexes shows that compaction and condensation effects change as follows: G6<G4 ≤ G12, i.e., agree with the order of transfection efficacy, which is supported by membrane tropic properties of G12. On the other hand, gel retardation assay and docking study testify low electrostatic affinity in G12/DNA pair, thereby indicating that hydrophobic effect probably plays important role in the lipoplex formation. Two factors are assumed to be responsible for the inhibition effect of gemini in the case of transformation of bacterial cells. They are (i) an unfavorable influence of cationic surfactants on the electroporation procedure due to depressing the electrophoretic effect; and (ii) antibacterial activity of cationic surfactants that may cause the disruption of integrity of cell membranes.

Gelatin-based nanoparticles as DNA delivery systems: Synthesis, physicochemical and biocompatible characterization

The rapidly rising demand for therapeutic grade DNA molecules requires associated improvements in encapsulation and delivery technologies. One of the challenges for the efficient intracellular delivery of therapeutic biomolecules after their cell internalization by endocytosis is to manipulate the non-productive trafficking from endosomes to lysosomes, where degradation may occur. The combination of the endosomal acidity with the endosomolytic capability of the nanocarrier can increase the intracellular delivery of many drugs, genes and proteins, which, therefore, might enhance their therapeutic efficacy. Among the suitable compounds, the gelification properties of gelatin as well as the strong dependence of gelatin ionization with pH makes this compound an interesting candidate to be used to the effective intracellular delivery of active biomacromolecules. In the present work, gelatin (either high or low gel strength) and protamine sulfate has been selected to form particles by interaction of oppositely charged compounds. Particles in the absence of DNA (binary system) and in the presence of DNA (ternary system) have been prepared. The physicochemical characterization (particle size, polydispersity index and degree of DNA entrapment) have been evaluated. Cytotoxicity experiments have shown that the isolated systems and the resulting gelatin-based nanoparticles are essentially non-toxic. The pH-dependent hemolysis assay and the response of the nanoparticles co-incubated in buffers at defined pHs that mimic extracellular, early endosomal and late endo-lysosomal environments demonstrated that the nanoparticles tend to destabilize and DNA can be successfully released. It was found that, in addition to the imposed compositions, the gel strength of gelatin is a controlling parameter of the final properties of these nanoparticles. The results indicate that these gelatin-based nanoparticles have excellent properties as highly potent and non-toxic intracellular delivery systems, rendering them promising DNA vehicles to be used as non-viral gene delivery systems.

Cooperative interaction between metallosurfactants, derived from the [Ru(2,2'-bpy)3](2+) complex, and DNA

With the idea of improving and advancing the design and preparation of new reagents based on cationic surfactants for gene therapy, two luminescent metallosurfactants derived from the [Ru(2,2'-bpy)3](2+) complex were synthesized. Their interaction with DNA and the effect they exert on the conformation of the polynucleotide were studied by using different techniques. The equilibrium binding constants, Kb, of the two surfactants to DNA were obtained at different molar ratios X=[surfactant]/[DNA]. The observed sigmoidal dependence of Kb on X confirms the cooperative character of the binding. After the addition of a determined surfactant concentration, the condensation of the polymer was observed. The amount of surfactant needed to produce this conformational change is lower for the double stranded surfactant than for the single chain surfactant due to a stronger hydrophobic interaction. The addition of α-cyclodextrin molecules to the metallosurfactant/DNA solutions results in polynucleotide decompaction, which confirms the importance of the hydrophobic interactions in the condensation of the polynucleotide. Results also show the importance of choosing both a proper system to study and the most seeming measuring technique to use. It is demonstrated that, in some cases, the use of several techniques is desirable to obtain reliable and accurate results.

Compaction and decompaction of DNA dominated by the competition between counterions and DNA associating with cationic aggregates

A systematic work concerning the DNA compaction and decompaction controlled by cationic surfactants, cetyltrimethylammonium with [FeCl3Br](-) (CTAFe), Br(-) (CTABr) and Cl(-) (CTACl) as counterions, respectively, was performed. We discovered that cationic surfactants with complex counterions, [FeCl3Br](-), cannot promote the decompaction of DNA like those with Br(-) and Cl(-) as counterions. The rod-like CTAFe micelles were found to remain free in supernatants and cannot directly promote any redissolution or decompaction of DNA. These interesting findings could provide a better understanding of the interaction behavior of DNA and cationic surfactants. We conclude that the fundamental reason of the DNA decompaction lies upon the electrostatic competition between the counterions and DNA for associating with the cationic aggregates. At a high concentration, the binding of counterions to cationic CTA(+) aggregates is promoted, which weakens and screens the electrostatic attraction between DNA and cationic aggregates. This could cause the decompaction of DNA as the cases of CTABr/DNA and CTACl/DNA mixtures. Our data revealed the fundamental reason of the compaction and decompaction behavior of DNA induced by cationic surfactants independently, a reasonable three-step model of the conformational changes of DNA controlled by different amounts of cationic surfactants was presented. The current work could provide a clear guidance in gene delivery, gene therapy and biomedicine fields.

A Green Solvent Induced DNA Package

Mechanistic details of DNA compaction is essential blue print for gene regulation in living organisms. Many in vitro studies have been implemented using several compaction agents. However, these compacting agents may have some kinds of cytotoxic effects to the cells. To minimize this aspect, several research works had been performed, but people have never focused green solvent, i.e. room temperature ionic liquid as DNA compaction agent. To the best of our knowledge, this is the first ever report where we have shown that guanidinium tris(pentafluoroethyl)trifluorophosphate (Gua-IL) acts as a DNA compacting agent. The compaction ability of Gua-IL has been verified by different spectroscopic techniques, like steady state emission, circular dichroism, dynamic light scattering and UV melting. Notably, we have extensively probed this compaction by Gua-IL through field emission scanning electron microscopy (FE-SEM) and fluorescence microscopy images. We also have discussed the plausible compaction mechanism process of DNA by Gua-IL. Our results suggest that Gua-IL forms a micellar kind of self aggregation above a certain concentration (≥1 mM), which instigates this compaction process. This study divulges the specific details of DNA compaction mechanism by a new class of compaction agent, which is highly biodegradable and eco friendly in nature.