Interaction of cationic surfactants with DNA: a single-molecule study

Impact of the Hydrocarbon Chain Length of Biodegradable Ester-Bonded Cationic Gemini Surfactants on Self-Assembly, In Vitro Gene Transfection, Cytotoxicity, and Antimicrobial Activity

Gemini surfactants, due to their unique structural features and enhanced properties compared to conventional surfactants, are becoming more popular in the domain of colloid and interface science, drug delivery, and gene delivery science. This distinct class of surfactants forms a wide range of self-assembled aggregates depending on their chemical structure and environmental conditions. The present work aims to develop Gemini with three distinct chain lengths linked through the ester group and quaternary nitrogen head groups that can bind DNA molecules and ultimately serve as vectors for DNA transfection. Thus, we synthesized three distinct cationic Gemini with 12, 14, and 16 carbons in their tails and studied the effect of the hydrocarbon chain length on their physicochemical properties and biological applications. The self-assembly of these Geminis in aqueous solution was investigated by a number of techniques, including surface tension, electrical conductivity, fluorescence probe, calorimetry, dynamic light scattering, and atomic force microscopy. All three Gemini were extremely surface active and self-assembled above a very low critical micelle concentration. Calorimetric studies suggested the formation of thermodynamically favorable aggregates in an aqueous medium. Chain length dependence was observed in the size as well as the morphology of the aggregates. These Gemini ions were found to bind DNA strongly, as indicated by the high binding constant values. In vitro gene transfection studies using the RAW 264.7 cell line suggested that all three cationic Gemini had transfection efficiencies comparable to that of commercial standard turbofectamine. MTT assay was also performed for concentration selection while using these Gemini as transfection vectors. Overall, it was observed that Gemini had very little cytotoxicity within the investigated concentration range, highlighting the significance of the ester link within the structure. When compared with known antimicrobials such as kanamycin and ampicillin, all three Gemini furnished excellent antimicrobial activity in both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) microorganisms.

Exploring the binding mode of ester-based cationic gemini surfactants with calf thymus DNA: A detailed physicochemical, spectroscopic and theoretical study

Gene therapy is a transfectant method for the treatment of hereditary disease, which transfers the gene mutation into the cells. In the view of the high prospects of utilization of cationic gemini surfactants as a non-viral vector for the gene transfection, we have made a comprehensive study on the interactions between a recently synthesized series of ester-functionalized cationic C_m-E2O-C_m gemini surfactants (m = 12, 14 and 16) with calf thymus deoxyribonucleic acid (ctDNA) utilizing various techniques. The micellization behavior of gemini surfactants has been altered in the presence of ctDNA. A series of measurements (fluorescence, UV-vis and time-resolved fluorescence) show that the quenching of ctDNA proceeds by a static mechanism. The competitive displacement studies (EB, AO and HO), KI quenching analysis, CD studies and viscosity measurements suggested intercalative binding mode in a stoichiometry ratio of 1:1 with the K_b (binding constant) order being: C₁₆-E2O-C₁₆ > C₁₄-E2O-C₁₄ > C₁₂-E2O-C₁₂. The thermodynamic parameters show that the geminis interacted with ctDNA spontaneously through ionic/electrostatic interactions. Furthermore, the theoretical approaches offer accurate insights about the binding of gemini surfactants with DNA, and are in consistence with the experimental results.

Effect of Alkyl Chain Length on the Photophysical, Photochemical, and Photobiological Properties of Ruthenium(II) Polypyridyl Complexes for Their Application as DNA-Targeting, Cellular-Imaging, and Light-Activated Therapeutic Agents

A family of six Ru(II) polypyridyl complexes (1-6) which contain phenanthroline-based ligands functionalized with alkyl chains of different lengths (one methyl group, 10 and 21 carbon alkyl chains) and either 1,10-phenanthroline (phen) or 1,4,5,8-tetraazaphenanthrene (TAP) as ancillary ligands have been synthesized and characterized. The influence of the alkyl chain length on their photophysical and photochemical properties as well as in their photobiological applications has been elucidated by monitoring the changes in their MLCT-centered absorption and emission bands. The presence of one methyl group or 10 carbon alkyl chains does not seem to significantly affect the photophysical and photochemical properties of the resulting Ru(II) complexes when compared to the well-known [Ru(phen)₃]²⁺ and [Ru(TAP)₂phen]²⁺. However, an effect on their emission properties and in their ability to photosensitize singlet oxygen is observed for the Ru(II) complexes containing 21 carbon alkyl chains. The binding of these complexes to salmon testes DNA (stDNA) was investigated by observing the changes in the photophysical properties. Complexes 1, 2, 4, and 5 all showed changes in their MLCT bands that could be analyzed using conventional fitting methods, such as the Bard equation. In contrast, complexes 3 and 6, possessing long aliphatic chains, gave rise to nonclassic behavior. In addition to these analyses, both thermal denaturation and circular dichroism studies of 1-6 were carried out in the presence of stDNA which confirmed that these complexes bind to DNA. Confocal microscopy and viability studies in HeLa cervical cancer cells reveal an alkyl chain-length dependence on the cellular uptake and cytotoxicity of the resulting Ru(II) complexes due to an enhancement of their lipophilicity with increasing alkyl chain length. Thus, complexes containing 10 and 21 carbon alkyl chains are rapidly taken up into HeLa cells and, in particular, those with 21 carbon alkyl chains show a significant phototoxicity against the same cell line. Therefore, this study provides further insight into the possible modulation of the photophysical, photochemical, and photobiological properties of Ru(II) polypyridyl complexes by varying the length of the alkyl chains attached to the polypyridyl ligands coordinated to the Ru(II) center and the nature of the auxiliary groups, which we show has a significant effect on photophysical and biological properties.

Cationic Single-Chained Surfactants with a Functional Group at the End of the Hydrophobic Tail DNA Compacting Efficiency

The interaction between calf-thymus DNA, ctDNA, and various single-chained surfactants with different functional groups at the end of hydrophobic tail was studied with the goal of investigating the influence of the functional group nature on surfactant DNA compacting efficiency. The surfactants investigated were dodecyltriethylammonium bromide (DTEABr), triethyl(1-phenoxydodecyl)ammonium bromide (12PhBr), triethyl(2-naphthoxydodecyl)ammonium bromide (12NBr) and 11-(isonicotinoyloxy)-N,N,N-triethyl-1-undecanaminium bromide (11PyBr). Results made evident that the surfactants' tendencies to self-aggregation is the key factor determining their efficiency to compact the nucleic acid. Subsequently, DOPE/12NBr/pEGFP-C1 lipoplexes, with different cationic surfactant molar fractions (α) and mass ratios (L/D), were prepared and characterized. DOPE is a zwitterionic phospholipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, and the plasmid pEGFP-C1 carries a GFP coding sequence with the necessary regulatory elements for constitutive expression of the gene in human cells. 12NBr was chosen because it was the most efficient DNA compacting agent among the surfactants investigated. Finally, the cytotoxicity and transfection efficiency (TE) of DOPE/12NBr/pDNA lipoplexes, with different compositions, were investigated.

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.

Kelvin probe force microscopy to study electrostatic interactions of DNA with lipid-gemini surfactant monolayers for gene delivery

In novel gene therapy mechanisms utilising gemini surfactants, electrostatic interactions of the surfactant molecules with the DNA strands is a primary mechanism by which the two components of the delivery vehicle bind. In this work, we show for the first time direct evidence of electrostatic interactions of these compounds visualised with Kelvin probe force microscopy (KPFM) and correlated to their topography from atomic force microscopy (AFM). We construct monolayers of lipids and gemini surfactant to simulate interactions on a cellular level, using lipids commonly found in cell membranes, and allow DNA to bind to the monolayer as it is formed on a Langmuir-Blodgett trough. The difference in topography and electrical surface potential between monolayers with and without DNA is striking. In fact, KPFM reveals a strongly positive relative electrical surface potential in between where we identify a background lipid and the DNA strands, evidenced by the height profiles of the domains. Such identification is not possible without KPFM. We conclude that it is likely we are seeing cationic surfactant molecules surrounding DNA strands within a sea of background lipid.

Ionic Liquid-Functionalized Multiwalled Carbon Nanotube-Based Hydrophobic Coatings for Robust Antibacterial Applications

In recent years, the biomimetic superhydrophobic coatings have received tremendous attention, owing to their potential in fabricating self-cleaning surfaces, in environmental applications. Consequently, extensive research has been devoted to create a superhydrophobic surface using the oxidized derivatives of CNTs and graphene. Thus, the design and development of a self-cleaning/superhydrophobic surface with good biocompatibility are an effective approach to deal with the bacterial infections related to biomedical devices used in hospitals. In this context, herein, we have developed the material based on ionic liquid (IL)-functionalized multiwalled carbon nanotubes (MWCNTs) for hydrophobic coatings, which was fully characterized with various techniques such as Fourier transform infrared, powder X-ray diffraction, energy-dispersive X-ray spectroscopy, and scanning electron microscopy. We have evaluated the synthesized ILs for their antibacterial potential against the pathogenic bacterial strains such as Gram-positive (Staphylococcus aureus and methicillin-resistant S. aureus) and Gram-negative (Escherichia coli) bacterial strains. Further, atomic force and scanning electron microscopic studies have been performed to investigate the morphological changes to unravel the mechanism of action, whereas DNA binding study indicates the binding of IL-1d@MWCNT with DNA (K_a = 2.390 × 10⁴ M^-1). Furthermore, the developed material (IL-1d@MWCNT) is coated onto the surface of polyvinyl chloride (PVC) and evaluated for hydrophobicity through water contact angle measurements and possesses long-term antibacterial efficiency against both under-investigating pathogenic strains. For the biocompatibility assay, the obtained coated PVC material has also been evaluated for its cytotoxicity, and results reveal no toxicity against viable cells. These all results are taken together, indicating that by coating with the developed material IL-1d@MWCNT, a robust self-sterilizing surface has achieved, which helps in maintaining a bacteria-free surface.

Dimension-reconfigurable bubble film nanochannel for wetting based sensing

Dimensions and surface properties are the predominant factors for the applications of nanofluidic devices. Here we use a thin liquid film as a nanochannel by inserting a gas bubble in a glass capillary, a technique we name bubble-based film nanofluidics. The height of the film nanochannel can be regulated by the Debye length and wettability, while the length independently changed by applied pressure. The film nanochannel behaves functionally identically to classical solid state nanochannels, as ion concentration polarizations. Furthermore, the film nanochannels can be used for label-free immunosensing, by principle of wettability change at the solid interface. The optimal sensitivity for the biotin-streptavidin reaction is two orders of magnitude higher than for the solid state nanochannel, suitable for a full range of electrolyte concentrations. We believe that the film nanochannel represents a class of nanofluidic devices that is of interest for fundamental studies and also can be widely applied, due to its reconfigurable dimensions, low cost, ease of fabrication and multiphase interfaces.

Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers

We report that trivalent cobalt hexammine cations decrease the persistence length, stretching modulus, helical density, and size of plectonemes formed under torque of DNA but increase those of RNA. Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of plectonemes while increasing the helical densities of both DNA and RNA. The experimental results are explained by different binding modes of the cations on DNA and RNA in our all-atom molecular dynamics simulations. The significant variations of the helical densities and structures of DNA and RNA duplexes induced by high-valent cations may affect interactions of the duplexes with proteins.

Label-Free Detecting of the Compaction and Decompaction of ctDNA Molecules Induced by Surfactants with SERS Based on a nanoPAA-ZnCl2-AuLs Solid Substrate

DNA molecular compaction/decompaction is of great significance for the exploration of basic life processes, the research of biomedical and genetic engineering, and so forth. However, the detailed mechanism of DNA compaction/decompaction caused by surfactants remains an open and challenging problem that has not been fully solved so far. In this paper, a sort of novel solid substrate, nanoPAA-ZnCl₂-AuLs, with good stability and high sensitivity, was prepared by a self-assembly method. Based on this substrate, the surface-enhanced Raman scattering (SERS) technology was employed to investigate characteristics of interactions between DNA molecules and surfactants at a single molecular level. SERS spectra of calf thymus DNA (ctDNA), cetyl trimethyl ammonium bromide (CTAB), and sodium dodecyl sulfate (SDS) with a concentration as low as 10^-9 M, and SERS spectra of ctDNA-CTAB and ctDNA-CTAB-SDS composites were collected, respectively. The interactions between ctDNA and surfactants were analyzed by changes in SERS spectra, for example, disappearances and appearances of SERS bands and relative changes of peak intensity, in which CTAB resulted in the compaction of the DNA molecule while SDS induced the decompaction of the ctDNA-CTAB complex. Moreover, UV-visible spectrophotometry was employed to demonstrate the compaction/decompaction of ctDNA molecules caused by surfactants. The local binding modes of ctDNA molecules and surfactant molecules were expounded. This work will be helpful for understanding biological processes such as DNA compaction and recombination within nucleus or/and cells and for the development of gene therapy technologies.

Lipoaminoacids Enzyme-Based Production and Application as Gene Delivery Vectors

Biosurfactant compounds have been studied in many applications, including biomedical, food, cosmetic, agriculture, and bioremediation areas, mainly due to their low toxicity, high biodegradability, and multifunctionality. Among biosurfactants, the lipoplexes of lipoaminoacids play a key role in medical and pharmaceutical fields. Lipoaminoacids (LAAs) are amino acid-based surfactants that are obtained from the condensation reaction of natural origin amino acids with fatty acids or fatty acid derivatives. LAA can be produced by biocatalysis as an alternative to chemical synthesis and thus become very attractive from both the biomedical and the environmental perspectives. Gemini LAAs, which are made of two hydrophobic chains and two amino acid head groups per molecule and linked by a spacer at the level of the amino acid residues, are promising candidates as both drug and gene delivery and protein disassembly agents. Gemini LAA usually show lower critical micelle concentration, interact more efficiently with proteins, and are better solubilising agents for hydrophobic drugs when compared to their monomeric counterparts due to their dimeric structure. A clinically relevant human gene therapy vector must overcome or avoid detect and silence foreign or misplaced DNA whilst delivering sustained levels of therapeutic gene product. Many non-viral DNA vectors trigger these defence mechanisms, being subsequently destroyed or rendered silent. The development of safe and persistently expressing DNA vectors is a crucial prerequisite for a successful clinical application, and it one of the main strategic tasks of non-viral gene therapy research.

Influence of the degree of oligomerization of surfactants on the DNA/surfactant interaction

The interaction between calf thymus DNA, ctDNA, and a series of oligomeric surfactants derived from N-benzyl-N,N-dimethyl-N-(1-dodecyl)ammonium chloride is investigated. The influence of the surfactants' degree of oligomerization (2, 3 and 4) on the ctDNA/surfactant interaction is studied, as well as the effect of the structure of the spacer group linking the individual surfactant fragments. In particular, the effect of the distance between the positive charges and the hydrophobic chains within the oligomers on these interactions was examined, by using the three positional isomers (i.e., ortho-, meta-, and para-) with the rigid xylidene moiety as spacer. Results show that the dimeric ("gemini") surfactants are much more efficient in the inversion of the nucleic acid charge than the single-chained (monomeric) surfactant. Whereas the ortho - isomer causes a partial condensation, the meta - and para - isomers can completely condense ctDNA. The meta - and para - isomers of the trimeric surfactants can also completely condense the polynucleotide. In contrast, the tetrameric surfactant investigated does not change the morphology of the nucleic acid from an elongated coil into a compacted form, in spite of effectively inverting the nucleic acid's charge in their complex. Accordingly, the capacity for ctDNA compaction of oligomeric surfactants is not simply correlated to their degree of oligomerization, but depends on a complex balance of the number and relative distance of cationic charges and/or hydrophobic tails in the surfactants for effectively interacting with the nucleic acid to form the appropriate complex. This information will help to design more effective cationic surfactants as non-viral vectors for gene therapy.

The Length of Hydrophobic Chain in Amphiphilic Polypeptides Regulates the Efficiency of Gene Delivery

The major challenges of non-viral carriers are low transfection efficiency and high toxicity. To overcome this bottleneck, it is very important to investigate the structure-property-function (transfection efficiency) relationships of polycations. Herein, different length hydrophobic poly(l-leucine) chains in amphiphilic polypeptides were precisely synthesized by α-amino acid N-carboxyanhydrides (NCA) ring-opening polymerization and these biocompatible polypeptides were chosen as a model to further examine the transfection in vitro. These polypeptides were characterized by nuclear magnetic resonance spectroscopy (NMR) and size exclusion chromatography (SEC). Agarose gel electrophoresis (AGE) was employed to validate the ability of DNA condensation and transmission electron microscopy (TEM) was used to observe the assemblies of polyplexes. Cytotoxicity was evaluated in COS-7 cell lines and transfection was performed in normal cell COS-7 and cancer cell Hep G2. The results showed that NCA monomers were prepared and the amphiphilic polypeptides, poly(lysine(CBZ))₅₀-block-poly(l-leucine)₁₀, poly(l-lysine(CBZ))₅₀-block-poly(l-leucine)₁₅, and poly(l-lysine(CBZ))₅₀-block-poly(l-leucine)₂₅, were successfully synthesized with controlled molecular weight and narrow distribution. After deprotection of CBZ, these materials can condense plasmid DNA into 100 nm nanoparticles and the cellular uptake of polyplexes was as fast as 30 min. The transfection data shown these materials had a good transfection efficiency comparing to polyethylenimine (Branched, 25 kDa) while they displayed ignored cytotoxicity. More importantly, we discovered the length of hydrophobic poly(l-leucine) in amphiphilic polypeptides steadily regulates gene delivery efficiency in two kinds of cells ranking poly(l-lysine)₅₀-block-poly(l-leucine)₂₅ > poly(l-lysine)₅₀-block-poly(l-leucine)₁₅ > poly(l-lysine)₅₀-block-poly(l-leucine)₁₀.

Clear distinction between CAC and CMC revealed by high-resolution NMR diffusometry for a series of bis-imidazolium gemini surfactants in aqueous solutions

The aggregation behavior in the transition region was studied for a series of dicationic surfactants 3,3′-[α,ω-(dioxaalkane)]bis(1-dodecylimidazolium)dichlorides with varied spacer length from two to twelve carbon atoms. We employed Nuclear Magnetic Resonance diffusometry and Bayesian DOSY analysis to obtain the aggregate size distribution in the transition region. The critical concentrations CC were independently obtained from surface tension, electric conductivity, UV-Vis and NMR methods. The micelle aggregation numbers were estimated from the self-diffusion coefficients and were independently confirmed using steady-state fluorescence quenching. The morphology of the aggregates was characterized by small-angle scattering of synchrotron radiation and molecular dynamics simulations. The obtained CC values are identified as critical aggregation concentrations CAC. A broad transition region was observed, and stable micelles were obtained at much higher concentrations than CAC. The accurate CMC values could not be identified for the systems in the study. We indicated that the distribution of aggregate size becomes small and the system becomes homogeneous at much larger concentrations than CAC (typically 15–20 mM). The existence of a slow exchange between two environments, an aggregate and aqueous environment, was confirmed by ¹H NMR and 2D HSQC NMR spectroscopy.

The aggregation behavior in the transition region was studied for a series of dicationic surfactants 3,3′-[α,ω-(dioxaalkane)]bis(1-dodecylimidazolium)dichlorides with varied spacer length from two to twelve carbon atoms.

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.

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.

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.

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.

Self-Assembly of Amphiphilic Dendrimers: The Role of Generation and Alkyl Chain Length in siRNA Interaction

An ideal nucleic-acid transfection system should combine the physical and chemical characteristics of cationic lipids and linear polymers to decrease cytotoxicity and uptake limitations. Previous research described new types of carriers termed amphiphilic dendrimers (ADs), which are based on polyamidoamine dendrimers (PAMAM). These ADs display the cell membrane affinity advantage of lipids and preserve the high affinity for DNA possessed by cationic dendrimers. These lipid/dendrimer hybrids consist of a low-generation, hydrophilic dendron (G2, G1, or G0) bonded to a hydrophobic tail. The G2-18C AD was reported to be an efficient siRNA vector with significant gene silencing. However, shorter tail ADs (G2-15C and G2-13C) and lower generation (G0 and G1) dendrimers failed as transfection carriers. To date, the self-assembly phenomenon of this class of amphiphilic dendrimers has not been molecularly explored using molecular simulation methods. To gain insight into these systems, the present study used coarse-grained molecular dynamics simulations to describe how ADs are able to self-assemble into an aggregate, and, specifically, how tail length and generation play a key role in this event. Finally, explanations are given for the better efficiency of G2/18-C as gene carrier in terms of binding of siRNA. This knowledge could be relevant for the design of novel, safer ADs with well-optimized affinity for siRNA.

Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts

Capillary electrophoresis has been used to characterize the interaction of monovalent cations with 26-basepair DNA oligomers containing A-tracts embedded in flanking sequences with different basepair compositions. A 26-basepair random-sequence oligomer was used as the reference; lithium and tetrabutylammonium (TBA(+)) ions were used as the probe ions. The free solution mobilities of the A-tract and random-sequence oligomers were identical in solutions containing <∼ 100 mM cation. At higher cation concentrations, the A-tract oligomers migrated faster than the reference oligomer in TBA(+) and slower than the reference in Li(+). Hence, cations of different sizes can interact very differently with DNA A-tracts. The increased mobilities observed in TBA(+) suggest that the large hydrophobic TBA(+) ions are preferentially excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the A-tract oligomers and increasing the mobility. By contrast, Li(+) ions decrease the mobility of A-tract oligomers because of the preferential localization of Li(+) ions in the narrow A-tract minor groove. Embedding the A-tracts in AT-rich flanking sequences markedly alters preferential interactions of monovalent cations with the B(∗) conformation. Hence, A-tracts embedded in genomic DNA may or may not interact preferentially with monovalent cations, depending on the relative number of A · T basepairs in the flanking sequences.

Stabilization of DNA liquid crystals on doping with gold nanorods

We report on the impact of doping with gold nanorods (NRs) on the formation and stability of DNA liquid crystals (LCs).

Spectroscopic study on interaction between three cationic surfactants with different alkyl chain lengths and DNA

In this study, the interaction between cationic surfactants with different alkyl chain lengths, such as hexyltrimethyl ammonium bromide (HTAB), dodecyltrimethyl ammonium bromide (DTAB) and cetyltrimethyl ammonium bromide (CTAB), and DNA was investigated by UV-vis spectroscopy, fluorescence spectroscopy and viscosity techniques. The results showed that these three cationic surfactants with different hydrocarbon chain lengths could all interact with DNA. Their binding modes were estimated and their interaction strength was compared. In addition, the effects of the surfactant, NaCl and phosphate ion concentrations on the interaction were reviewed. It is wished that this work would provide some valuable references to investigate the influence of cationic surfactants with different alkyl chain lengths on DNA.

Polyethylenimine coated plasmid DNA-surfactant complexes as potential gene delivery systems

Nanometer scaled particles have been prepared from strong association between plasmid DNA (pcDNA3-FLAG-p53) and oppositely charged surfactants. Although these particles present suitable properties for gene delivery purposes, their cytotoxicity could compromise their use in gene therapy applications. To ensure biocompatibility of this potential gene delivery system, the nanoparticles were coated with polyethylenimine (PEI) with various molar ratios of PEI nitrogen to plasmid DNA phosphate groups. This led to a drastic increase in the cell viability of the particles, and in addition particle characteristics such as size, surface charge and loading efficiency, have also been enhanced as a result of the PEI coating process. The dissolution or swelling/deswelling behaviour displayed by these particulate vehicles could be tailored and monitored in time, to promote the controlled and sustained release of plasmid DNA. Moreover, we show that both the surfactant alkyl chain length and the ratio of nitrogen to phosphate groups are important parameters for controlling the plasmid DNA release. Overall, the developed plasmid DNA carriers have the potential as a new nanoplatform to be further explored for advances in the gene therapy field.

Surfactants modify the torsion properties of proteins: a single molecule study

Surfactants are widely used in diagnostic assays to prevent protein aggregation and non-specific adsorption at surfaces. Here, a single molecule magnetic torque tweezers study is reported, aiming to quantify surfactant-induced changes in the torsional flexibility of a protein model system: protein-G-immunoglobulin G (IgG) attached to a glass surface. The influences of Sodium Dodecyl Sulphate (SDS) and Polysorbate 20 (Tween 20) on the protein pair have been investigated. The proteins were exposed to the surfactants at concentrations relative to the Critical Micelle Concentration (CMC), namely 0.1× CMC, 1× CMC and 10× CMC. Both surfactants increase the torsional flexibility of the protein-G-IgG complex. Tween 20 is most effective at increasing the torsional flexibility of the complex at the surface while SDS is more effective at dissociating the protein bonds. Tweezer data on the IgG-IgG protein pair show no influence of Tween 20 on the torsional flexibility. Furthermore, temperature dependent near-UV and far-UV Circular Dichroism (CD) data at 10× CMC show that Tween 20 does not significantly alter the secondary and tertiary structure of both protein-G and IgG while SDS does. These results provide evidence that both the mechanical properties of the protein structure and the interaction between proteins can alter the torsional rigidity measured with magnetic torque tweezers. This study shows for the first time the ability to use magnetic torque tweezers as a probe for surfactant-induced changes in proteins at a single molecule level.

Exploration of the binding interaction of a potential nervous system stimulant with calf-thymus DNA and dissociation of the drug–DNA complex by detergent sequestration

The binding interaction of a potential nervous system stimulant with calf-thymus DNA has been divulged and dissociation of the drug–DNA complex has been achieved by the detergent sequestration method.

On the effects of intercalators in DNA condensation: a force spectroscopy and gel electrophoresis study

In this work we have characterized the effects of the intercalator ethidium bromide (EtBr) on the DNA condensation process by using force spectroscopy and gel electrophoresis. We have tested two condensing agents: spermine (spm(4+)), a tetravalent cationic amine which promotes cation-induced DNA condensation, and poly(ethylene glycol) (PEG), a neutral polymer which promotes DNA ψ-condensation. Two different types of experiments were performed. In the first type, bare DNA molecules disperse in solution are first treated with EtBr for intercalation, and then the condensing agent is added to the sample with the purpose of verifying the effects of the intercalator in hindering DNA condensation. In the second experiment type, the bare DNA molecules are first condensed, and then the intercalator is added to the sample in order to verify its influence on the previously condensed DNA. The results obtained with the two different experimental techniques used agree very well, indicating that previously intercalated EtBr can hinder both cation-induced and ψ-condensation, being more efficient in the first case. On the other hand, EtBr has little effect on the previously formed cation-induced condensates, but is efficient in unfolding the ψ-condensates.

Conformational changes of DNA in the presence of 12-s-12 gemini surfactants (s=2 and 10). Role of the spacer's length in the interaction surfactant-polynucleotide

A multifaceted study on the interaction of calf-thymus DNA with two different cationic gemini surfactants alkanediyl-α-ω-bis(dodecyldimethyl-amonium)bromide, 12-s-12,2Br(-) (with s=2, G2, and 10, G10) was carried out. The measurements were done at different molar ratios X=[surfactant]/[DNA]. Results show two different conformational changes in DNA: a first compaction of the polynucleotide corresponding to a partial conformational (not total) change of DNA from an extended coil state to a globular state that happens at the lower molar ratio X. A second change corresponds to a breaking of the partial condensation, that is, the transition from the compacted state to a new more extended conformation (for the higher X values) different to the initial extension. According to circular dichroism spectra and dynamic light scattering measurements, this new state of DNA seems to be similar to a ψ-phase. Measurements confirm that interactions involved in the compaction are different to those previously obtained for the analog surfactant CTAB. X values at which the conformational changes happen depend on the length of the spacer in the surfactant along with the charge of the polar heads.

Interaction between DNA and trimethyl-ammonium bromides with different alkyl chain lengths

The interaction between λ--DNA and cationic surfactants with varying alkyl chain lengths was investigated. By dynamic light scattering method, the trimethyl-ammonium bromides-DNA complex formation was shown to be dependent on the length of the surfactant's alkyl chain. For surfactants with sufficient long alkyl chain (CTAB, TTAB, DTAB), the compacted particles exist with a size of ~60-110 nm at low surfactant concentrations. In contrast, high concentration of surfactants leads to aggregates with increased sizes. Atomic force microscope scanning also supports the above observation. Zeta potential measurements show that the potential of the particles decreases with the increase of surfactant concentration (CTAB, TTAB, DTAB), which contributes much to the coagulation of the particles. For OTAB, the surfactant with the shortest chain in this study, it cannot fully neutralize the charges of DNA molecules; consequently, the complex is looser than other surfactant-DNA structures.

Nanostructure-induced DNA condensation

The control of the DNA condensation process is essential for compaction of DNA in chromatin, as well as for biological applications such as nonviral gene therapy. This review endeavours to reflect the progress of investigations on DNA condensation effects of nanostructure-based condensing agents (such as nanoparticles, nanotubes, cationic polymer and peptide agents) observed by using atomic force microscopy (AFM) and other techniques. The environmental effects on structural characteristics of nanostructure-induced DNA condensates are also discussed.

New gluconamide-type cationic surfactants: Interactions with DNA and lipid membranes

New linear cationic surfactants - 2-(alkyldimethylammonio)ethylgluconamide bromides, denoted as CnGAB, n=10, 12, 14 and 16 - were synthesized from natural resources and characterized with respect to their potential as gene-delivery agents in gene therapy applications. Interactions with plasmid DNA and with model membranes were studied both experimentally and theoretically. The compounds with n=12, 14 and 16 show exponentially increasing ability to fully condense DNA. C16GAB condenses DNA at 1:1 surfactant to nucleotide molar ratio. Furthermore, CnGABs interact with model membrane, slightly lowering the temperature of the main phase transition Tm of the DPPC bilayer. C10GAB is found to interact only at the membrane surface. C16GAB reduces Tm less than C12GAB and C14GAB, and forms domains in the bilayer at the surfactant/DPPC molar ratio of 0.1 and higher. The results suggest that C16GAB can be a promising candidate for building gene-delivery carrier systems.

Parallel lipoplex folding pathways revealed using magnetic tweezers

Lipid-coated DNA nanoparticles (lipoplexes) are a powerful gene delivery tool with promising therapeutic applications. The mechanism of lipoplex assembly remains poorly understood. We explored DNA packing by a cationic lipid DSTAP (distearoyl trimethylammonium-propane) using magnetic tweezers. DSTAP-induced DNA condensation occurred as a series of bursts with the mean step size of 60-80 nm. The pause time preceding the steps could be approximated as a bimodal distribution, which reveals at least two distinct condensation pathways. The rapidly condensed DNA was more resilient to force-induced decondensation. The proportion of the stable, fast-formed complexes decreased at high salt concentrations. A similar trend was observed in bulk experiments. Lipoplexes assembled at low salt concentration more efficiently shielded DNA from fluorescent dyes and DNase even after transfer to the high salt conditions. These data reveal that lipoplex folding occurs via two parallel pathways even at the single molecule level. The progress through the two pathways can be monitored in real time using single DNA manipulations. The relative efficiency of the two pathways can be varied by external conditions.

Compaction and decompaction of DNA induced by the cationic surfactant CTAB

A multifaceted study on the interaction of the cationic surfactant CTAB with calf thymus DNA was carried out by using different techniques. The measurements were done at different molar ratios X = [CTAB]/[DNA]. Results show the conformational change that DNA suffers due to the interaction with surfactant molecules at low molar ratios: the condensation of the polynucleotide, from an extended coil state to a globular state. The effect observed at the higher molar ratios is worth noting: the decondensation of DNA, that is, the transition from a compact state to a more extended conformation. Experimental data obtained confirm that this latter state is not exactly the same as that found in the absence of the surfactant. Attractive interactions between different parts of the molecule by ion correlation effects are the driving force to produce both the compaction and decompaction events. Results also show the importance of choosing both a proper system for the study and the most seeming measuring technique to use. The study demonstrates that, in some cases, the use of several techniques is desirable in obtaining reliable and accurate results.

Detecting DNA targets through the formation of DNA/CTAB complex and its interactions with liquid crystals

In this paper, we report the formation of a DNA/cetyl trimethylammonium bromide (CTAB) complex on a solid surface and its interaction with a thin layer of liquid crystals (LC) supported on the surface. Our results show that when the surface is decorated with DNA only, the LC gives a bright image, but when the surface is decorated with the DNA/CTAB complex, the LC becomes dark when the surface density of CTAB is above 5.25 ± 0.13 × 10(13)/cm(2). To exploit this phenomenon for detecting DNA targets, we used a surface decorated with electroneutral PNA probes for capturing DNA targets, and then treated the surface with 0.1 mM of CTAB. In the presence of DNA targets, a PNA/DNA/CTAB complex is formed and that leads to a dark image on the thin layer of the LC supported on the surface. Moreover, DNA targets with a complementary, 1-base mismatch and non-complementary sequence can be differentiated by using this method. This study provides a new principle for the label-free detection of DNA targets without any fluorescent labels.

Tunable fractionation of nucleic acids

We developed a method for selective purification of DNA using the cationic detergent, cetyltrimethylammonium bromide (CTAB), accompanied with urea and controlled high-salt (NaCl) concentration. This method is effective for rapid separation of DNA fragments from artifacts such as PCR primer dimers or ligation adapters. The CTAB-associated purification completely removed the short PCR artifacts and primers, as well as enzymes and buffer, while recovering a sufficient quantity of amplicons for subsequent experiments such as preparation of libraries. This method could also be applied to the fractionation of nucleic acids generated by other types of reactions.

Conical diffraction of linearly polarised light controls the angular position of a microscopic object

Conical diffraction of linearly polarised light in a biaxial crystal produces a beam with a crescent-shaped intensity profile. Rotation of the plane of polarisation produces the unique effect of spatially moving the crescent-shaped beam around a ring. We use this effect to trap microspheres and white blood cells and to position them at any angular position on the ring. Continuous motion around the circle is also demonstrated. This crescent beam does not require an interferometeric arrangement to form it, nor does it carry optical angular momentum. The ability to spatially locate a beam and an associated trapped object simply by varying the polarisation of light suggests that this optical process should find application in the manipulation and actuation of micro- and nano-scale physical and biological objects.

Visualizing the formation and collapse of DNA toroids

In living organisms, DNA is generally confined into very small volumes. In most viruses, positively charged multivalent ions assist the condensation of DNA into tightly packed toroidal structures. Interestingly, such cations can also induce the spontaneous formation of DNA toroids in vitro. To resolve the condensation dynamics and stability of DNA toroids, we use a combination of optical tweezers and fluorescence imaging to visualize in real-time spermine-induced (de)condensation in single DNA molecules. By actively controlling the DNA extension, we are able to follow (de)condensation under tension with high temporal and spatial resolution. We show that both processes occur in a quantized manner, caused by individual DNA loops added onto or removed from a toroidal condensate that is much smaller than previously observed in similar experiments. Finally, we present an analytical model that qualitatively captures the experimentally observed features, including an apparent force plateau.

Unraveling DNA tori under tension

Motivated by recent experiments, we develop a model for DNA toroids under external tension. We find that tori are the equilibrium states for our model up to a critical tension, above which they become only metastable. Above this tension, we find a cascade of transitions between discrete toroid states that successively lower the winding number, until the ground state (rod) is reached. In this process, this model predicts a nearly constant force plateau as a function of extension, in agreement with experiment.