Molecular mechanism and thermodynamics study of plasmid DNA and cationic surfactants interactions

The molecular mechanism and thermodynamics of the interactions between plasmid DNA and cationic surfactants were investigated by isothermal titration calorimetry (ITC), dynamic light scattering, surface tension measurements, and UV spectroscopy. The cationic surfactants studied include benzyldimethyldodecylammonium chloride, benzyldimethyltetradecylammonium chloride, cetylpyridinium chloride, and cetyltrimethylammonium chloride. The results indicate a critical aggregation concentration (cac) of a surfactant: above the cac the surfactant forms aggregates with plasmid DNA; below the cac, however, there is no detectable interaction between DNA and surfactant. Surfactants with longer hydrocarbon chains have smaller cac, indicating that hydrophobic interaction plays a key role in DNA-surfactant complexation. Moreover, an increase in ionic strength (I) increases the cac but decreases the critical micellization concentration (cmc). These opposite effects lead to a critical ionic strength (I(c)) at which cac = cmc; when I < I(c), cac < cmc; when I > I(c), DNA does not form complexes with surfactant micelles. In the interaction DNA exhibits a pseudophase property as the cac is a constant over a wide range of DNA concentrations. ITC data showed that the reaction is solely driven by entropy because both deltaH(o) (approximately 2-6 kJ mol(-1)) and deltaS(o) (approximately 70-110 J K(-1) mol(-1)) have positive values. In the complex, the molar ratio of DNA phosphate to surfactant is in the range of 0.63-1.05. The reaction forms sub-micrometer-sized primary particles; those aggregate at high surfactant concentrations. Taken together, the results led to an inference that there is no interaction between surfactant monomers and DNA molecules and demonstrated that DNA-cationic surfactant interactions are mediated by the hydrophobic interactions of surfactant molecules and counterion binding of DNA phosphates to the cationic surfactant aggregates.     

DNA gel particles: particle preparation and release characteristics

Aqueous mixtures of oppositely charged polyelectrolytes undergo associative phase separation, resulting in coacervation, gelation, or precipitation. This phenomenon has been exploited here to form DNA gel particles by interfacial diffusion. We report the formation of DNA gel particles by mixing solutions of DNA (either single-stranded (ssDNA) or double-stranded (dsDNA)) with solutions of cationic surfactant CTAB and solutions of the protein lysozyme. Swelling, surface morphology, and DNA release determinations indicate different interaction of ssDNA and dsDNA with both the surfactant and the protein. By using CTAB and lysozyme as the base material, the formation of a DNA reservoir hydrogel, without adding any kind of cross-linker or organic solvent, was demostrated.     

Effect of headgroup on DNA-cationic surfactant interactions

The interaction behavior of DNA with different types of hydroxylated cationic surfactants has been studied. Attention was directed to how the introduction of hydroxyl substituents at the headgroup of the cationic surfactants affects the compaction of DNA. The DNA-cationic surfactant interaction was investigated at different charge ratios by several methods like UV melting, ethidium bromide exclusion, and gel electrophoresis. Studies show that there is a discrete transition in the DNA chain from extended coils (free chain) to a compact form and that this transition does not depend substantially on the architecture of the headgroup. However, the accessibility of DNA to ethidium bromide is preserved to a significantly larger extent for the more hydrophilic surfactants. This was discussed in terms of surfactant packing. Observations are interpreted to reflect that the surfactants with more substituents have a larger headgroup and therefore form smaller micellar aggregates; these higher curvature aggregates lead to a less efficient, "patch-like" coverage of DNA. The more hydrophilic surfactants also presented a significantly lower cytotoxicity, which is important for biotechnological applications.     

Are hydrotropes distinct from surfactants?

The physicochemical properties of a homologous series of sodium p-n-alkylbenzoates have been investigated. The objective was to determine whether there is a clear transition point from hydrotropic to surfactant-like behavior with increasing alkyl chain length n, so as to shed clear light on the aggregation mechanism of so-called "hydrotropes". Electrical conductivity measurements were used for a first estimation of the critical aggregation concentrations (cac). As for classical surfactants, log(cac) depends on alkyl chain length n, but two branches of behavior were observed: one having a gradient typical of long chain fatty acid salts and the other with a more shallow dependence. Surface tension (γ) measurements of high purity aqueous solutions were used to generate limiting headgroup areas A(cac), which were in the range (40-50 ?(2)) being consistent with monolayer formation. Small-angle neutron scattering conclusively shows that the lower chain length homologues (classed as hydrotropes) exhibit sharp transitions in aggregation as a function of bulk concentration, typical of regular surfactants. As such, there is little to suggest from this study that hydrotropes differ in association behavior from regular surfactants.     

Effect of additives on swelling of covalent DNA gels

The volumetric response of polymer gels on cosolute addition depends on the interaction of the polymer with the cosolute and can be used as a simple and sensitive way of elucidating these interactions. Here we report on DNA networks, prepared by crosslinking double-stranded DNA with ethylene glycol diglycidyl ether (EGDE); these have been investigated with respect to their swelling in aqueous solution containing different additives, such as metal ions, polyamines, charged proteins, and surfactants. The deswelling on addition of metal ions occurs at lower concentrations with increasing valency of the counterion. The collapse of the gels in the presence of trivalent ions seems to follow the same kind of mechanism as the interaction in solution, but addition of these ions leads to DNA denaturation and formation of single-stranded DNA. Striking features were found in the deswelling of DNA gels by chitosan, spermine, spermidine, lysozyme, poly-l-lysine and poly-l-arginine. Chitosan is the most efficient cosolute of those investigated with respect to DNA gel collapse. The effect of the cationic surfactant tail length on the volume phase transition of DNA gels was studied as a function of surfactant concentration. Cationic surfactants effectively collapsed the gel from the critical aggregation concentration (cac), decreasing with increasing length of the hydrophobic tail. In several cases, the deswelling as a function of cosolute concentration shows a pronounced two-step behavior, which is interpreted in terms of a combination of DNA chain condensation and general osmotic deswelling. The studies included investigations on the state of the DNA chain after deswelling, on the reversibility of the deswelling as well as on the kinetics. With the exception for the trivalent lanthanide ions, it appears that the DNA chain always retains a double-helix conformation; with these metal ions, single-stranded DNA is found. The deswelling appears to be reversible as exemplified by addition of anionic surfactant subsequent to gel collapsed by cationic surfactant and addition of sodium bromide to gels collapsed by a polycation. An investigation of the kinetics shows that an increase in the surfactant tail length gives a pronouncedly slower deswelling kinetics.     

Enhancement of DNA compaction by negatively charged nanoparticles: effect of nanoparticle size and surfactant chain length

We study the compaction of genomic DNA by a series of alkyltrimethylammonium bromide surfactants having different hydrocarbon chain lengths n: dodecyl-(DTAB, n=12), tetradecyl-(TTAB, n=14) and hexadecyl-(CTAB, n=16), in the absence and in the presence of negatively charged silica nanoparticles (NPs) with a diameter in the range 15-100 nm. We show that NPs greatly enhance the ability of all cationic surfactants to induce DNA compaction and that this enhancement increases with an increase in NP diameter. In the absence of NP, the ability of cationic surfactants to induce DNA compaction increases with an increase in n. Conversely, in the presence of NPs, the enhancement of DNA compaction increases with a decrease in n. Therefore, although CTAB is the most efficient surfactant to compact DNA, maximal enhancement by NPs is obtained for the largest NP diameter (here, 100 nm) and the smallest surfactant chain length (here, DTAB). We suggest a mechanism where the preaggregation of surfactants on NP surface mediated by electrostatic interactions promotes cooperative binding to DNA and thus enhances the ability of surfactants to compact DNA. We show that the amplitude of enhancement is correlated with the difference between the surfactant concentration corresponding to aggregation on DNA alone and that corresponding to the onset of adsorption on nanoparticles.     

DNA and surfactants in bulk and at interfaces

Recent investigations of the DNA interactions with cationic surfactants and catanionic mixtures are reviewed. Several techniques have been used such as fluorescence microscopy, dynamic light scattering, electron microscopy, and Monte Carlo simulations.

The conformational behaviour of large DNA molecules in the presence of cationic surfactant was followed by fluorescence microscopy and also by dynamic light scattering. These techniques were in good agreement and it was possible to observe a discrete transition from extended coils to collapsed globules and their coexistence for intermediate amphiphile concentrations. The dependence on the surfactant alkyl chain was also monitored by fluorescence microscopy and, as expected, lower concentrations of the more hydrophobic surfactant were required to induce DNA compaction, although an excess of positive charges was still required.

Monte Carlo simulations on the compaction of a medium size polyanion with shorter polycations were performed. The polyanion chain suffers a sudden collapse as a function of the concentration of condensing agent, and of the number of charges on the polycation molecules. Further increase in the concentration increases the degree of compaction. The compaction was found to be associated with the polycations promoting bridging between different sites of the polyanion. When the total charge of the polycations was lower than that of the polyanion, a significant translational motion of the compacting agent along the polyanion was observed, producing only a small-degree of intrachain segregation, which can explain the excess of positive charges necessary to compact DNA.

Dissociation of the DNA–cationic surfactant complexes and a concomitant release of DNA was achieved by addition of anionic surfactants. The unfolding of DNA molecules, previously compacted with cationic surfactant, was shown to be strongly dependent on the anionic surfactant chain length; lower amounts of a longer chain surfactant were needed to release DNA into solution. On the other hand, no dependence on the hydrophobicity of the compacting agent was observed. The structures of the aggregates formed by the two surfactants, after the interaction with DNA, were imaged by cryogenic transmission electron microscopy. It is possible to predict the structure of the aggregates formed by the surfactants, like vesicles, from the phase behaviour of the mixed surfactant systems.

Studies on the interactions between DNA and catanionic mixtures were also performed. It was observed that DNA does not interact with negatively charged vesicles, even though they carry positive amphiphiles; however, in the presence of positively charged vesicles, DNA molecules compact and adsorb on their surface.

Finally Monte Carlo simulations were performed on the adsorption of a polyelectrolyte on catanionic surfaces. It was observed that the mobile charges in the surface react to the presence of the polyelectrolyte enabling a strong degree of adsorption even though the membrane was globally neutral. Our observations indicate that the adsorption behaviour of the polyelectrolyte is influenced by the response given by the membrane to its presence and that the number of adsorbed beads increases drastically with the increase of flexibility of the polymer. Calculations involving polymers with three different intrinsic stiffnesses showed that the variation is non-monotonic. It was observed also that a smaller polyanion typically adsorbs more completely than the larger one, which indicates that the polarisation of the membrane becomes less facilitated as the degree of disruption increases.     

Surfactant polymer interactions between strongly interacting cationic surfactants and anionic polyelectrolytes from conductivity and turbidity measurements

The interactions between oppositely charged surfactant/polymer mixtures have been studied using conductivity and turbidity measurements. The dependence of aggregation phenomenon on the chain length and head group modifications of conventional cationic surfactants, i.e., hexadecyl- (HTAB), tetradecyl- (TTAB), and dodecyltrimethylammonium bromides (DTAB) and dimeric cationic surfactants, i.e., decyl- (DeDGB) and dodecyldimethylgemini bromides (DDGB), is investigated. It was observed that cationic surfactants induce cooperative binding with anionic polyelectrolytes at critical aggregation concentration (cac). The cac values are considerably lower than the critical micelle concentration (cmc) values for the same surfactant. After the complete complexation, free micelles are formed at the apparent critical micelle concentration (acmc), which is slightly higher in aqueous polyelectrolyte than in pure water. Among the conventional and dimeric cationic surfactants, DTAB and DeDGB, respectively, have been found to have least interactions with oppositely charged polyelectrolytes.     

Positive ion electrospray ionization mass spectrometry of double-stranded DNA/drug complexes.

Positive ion electrospray ionization mass spectra of 16 base-pair double-stranded (ds)DNA have been obtained with essentially no ions from single-stranded DNA present. Single-stranded DNA was minimized by: (1) careful choice of DNA sequences; (2) the use of a relatively high salt concentration (0.1 M ammonium acetate, pH 8.5), and, (3) a low desolvation temperature (40 degrees C). Similarly, ESI-MS complexes of dsDNA with cisplatin, daunomycin and distamycin were obtained that contained only negligible amounts of single-stranded DNA. The complexes with daunomycin and distamycin were more stable to strand separation in the gas phase than dsDNA alone. This is in agreement with solution studies and with other recent gas phase results. These data contrast with many earlier ESI-MS studies of dsDNA and DNA/drug complexes in which ions from ssDNA are also normally observed.     

Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces

The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.     

A novel fluorescent biosensor for sequence-specific recognition of double-stranded DNA with the platform of graphene oxide

A fluorescent biosensor for sequence-specific recognition of double-stranded DNA (dsDNA) was developed based upon the DNA hybridization between dye-labeled single-stranded DNA (ssDNA) and double-stranded DNA. The fluorescence of FAM-labeled single-stranded DNA was quenched when it adsorbed on the surface of graphene oxide (GO). Upon addition of the target dsDNA, a homopyrimidine·homopurine part of dsDNA on the Simian virus 40 (SV40) (4424-4440, gp6), hybridization occurred between the dye-labeled DNA and the target dsDNA, which induced the dye-labeled DNA desorbed from the surface of GO, and turned on the fluorescence of the dye. Under the optimum conditions, the enhanced fluorescence intensity was proportional to the concentration of target dsDNA in the range 40.0-260 nM, and the detection limit was found to be 14.3 nM alongside the good sequence selectivity.     

Spectroscopic and electrochemical studies on the interaction between luteolin and DNA

Journal of Solid State Electrochemistry - The interactions of luteolin (LUT) with DNA, including double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA), were investigated in detail by...     

Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): a molecular simulation study

The packing structures of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) thiolates on implicit gold surfaces were studied in explicit aqueous solutions of 1M NaCl using molecular dynamics simulations. The simulations were based on individual DNA chains placed in hexagonal simulation boxes of different sizes, representing various packing densities. The total potential energy per DNA chain was compared. The optimal packing structures were determined based on the minimal potential energy within the limits of the conditions that were evaluated in this study. The optimal packing density of ssDNA was found to be 0.19 DNA chains/nm(2), which is consistent with that determined experimentally. Furthermore, the optimal packing density of dsDNA was shown to be approximately 58% of the packing density for ssDNA, indicating that the packing of ssDNA should be approximately 58% of its optimal packing in order to achieve the best hybridization.     

Surface complexation of DNA with a cationic surfactant

We have studied the surface complexation of DNA with a cationic surfactant (DTAB) using a combination of methods: dynamic surface tension, ellipsometry and Brewster angle microscopy. Below the surfactant critical aggregation concentration (cac), complexation occurs only at the surface, and the results are consistent with neutralization of the surfactant charges by the free polymer ions. Above the cac, surfactant starts to bind cooperatively to DNA in the bulk, and adsorption of the preformed hydrophobic surfactant DNA aggregate is now possible, leading to thick surface layers. At still higher concentrations of surfactant (still below saturation of binding in the bulk), there is decrease in adsorption due to competition with bulk aggregates. Finally, as surfactant concentration is increased still further, bulk aggregates become less soluble and large amounts are adsorbed, forming a surface layer, which is solid-like and brittle.     

Characterization of single- and double-stranded DNA on gold surfaces

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.     

DNA‐Surfactant Interactions. Compaction,Condensation, Decompaction and Phase Separation

Recent investigations of the interaction between DNA and alkyltrimethylammonium bromides of various chain lengths are reviewed. Several techniques have been used such as phase map determinations, fluorescence microscopy, and electron microscopy. Dissociation of the DNA‐surfactant complexes, by the addition of anionic surfactant, has received special attention. Precipitation maps for DNA‐cationic surfactant systems were evaluated by turbidimetry for different salt concentrations, temperatures and surfactant chain lengths. Single‐stranded DNA molecules precipitate at lower surfactant concentrations than double‐helix ones. It was also observed that these systems precipitate for very low concentrations of both DNA and surfactant, and that the extension of the two‐phase region increases for longer chain surfactants; these observations correlate well with fluorescence microscopy results, monitoring the system at a single molecule level. Dissociation of the DNA‐cationic surfactant complexes and a concomitant release of DNA was achieved by addition of anionic surfactants. The unfolding of DNA molecules, previously compacted with cationic surfactant, was shown to be strongly dependent on the anionic surfactant chain length; lower amounts of a longer chain surfactant were needed to release DNA into solution. On the other hand, no dependence on the hydrophobicity of the compacting agent was observed. The structures of the aggregates formed by the two surfactants, after the interaction with DNA, were imaged by cryogenic transmission electron microscopy. It is possible to predict the structure of the aggregates formed by the surfactants, like vesicles, from the phase behaviour of the mixed surfactant systems. The compaction of a medium size polyanion with shorter polycations was furthermore studied by means of Monte Carlo simulations. The polyanion chain suffers a sudden collapse as a function of the condensing agent concentration and of the number of charges on the molecules. Further increase of the concentration gives an increase of the degree of compaction. The compaction was found to be associated with the polycations promoting bridging between different sites of the polyanion. When the total charge of the polycations was lower than that of the polyanion, a significant translational motion of the compacting agent along the polyanion was observed, producing only a small‐degree of intrachain segregation. However, complete charge neutralization was not a prerequisite to achieve compacted forms.     

Conformational change detection of DNA with the fluorogenic reagent of o-phthalaldehyde-beta-mercaptoethanol

o-Phthalaldehyde-beta-mercaptoethanol (OPAME) as a fluorogenic reagent has been found wide applications in the detection of amino acids based on its reaction with primary amino groups. In this contribution, we report our new findings concerning the reactions of OPAME with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), respectively. It has been found that ssDNA can react with OPAME easily as a result of giving rise to strong fluorescence emissions, while dsDNA, prepared by hybridizing ssDNA with its complementary target prior to the reaction, displays inert chemical activity and gives out weak fluorescence emission. Mechanism investigations have shown that the reaction activity between OPAME and DNA depends on the amino groups that are related to the conformation of uncoiled and exposed extent of DNA structure, and thus the inert chemical activity of dsDNA results from screening of the dsDNA bases in the interior of the double strands. Therefore, we could design a way to detect conformation change of DNA with OPAME and further develop a novel, simple label-free sequence detection method for complementary and single-base mismatched ssDNA in the hybridization of DNA.     

Immobilization of single-stranded deoxyribonucleic acid on gold electrode with self-assembled aminoethanethiol monolayer for DNA electrochemical sensor applications

A synthesized 24-mer single-stranded deoxyribonucleic acid (ssDNA) was covalently immobilized onto a self-assembled aminoethanethiol monolayer modified gold electrode, using water-soluble 1-ethyl-3(3-dimethylaminopropyl)-carbodiimide (EDC). The covalently immobilized ssDNAs were hybridized with complementary ssDNA (cDNA) or yAL(3) gene in solution, forming double-stranded DNAs (dsDNA). Meanwhile, daunomycin as an electrochemical active intercalator in the hybridization buffer solution was intercalated into the dsDNA to form a dsDNA/daunomycin system on the gold electrode surface, which was used for DNA electrochemical sensor. The cathodic waves of daunomycin bound to the double-stranded DNA (dsDNA) by linear sweep voltammetry were utilized to detect the cDNA. The cathodic peak current (i(pc)) of duanomycin was linearly related to the concentrations of cDNA between 0.1 mug ml(-1) and 0.1 ng ml(-1). The detection limit was about 30 pg ml(-1).     

A simple fluorometric assay for DNA exonuclease activity based on graphene oxide

A new assay platform for DNA exonuclease activity is developed based on the preferential binding of single-stranded DNA (ssDNA) over double-stranded DNA (dsDNA) to graphene oxide. This approach allows a simple and quantitative activity measurement in a short time at low cost.     

Comparative study on the interaction of DNA with three different kinds of surfactants and the formation of multilayer films

The interactions between double-stranded DNA (dsDNA) and three different kinds of surfactants, i.e., cationic, anionic, and nonionic surfactants, were investigated by cyclic voltammetry, electrochemical impedance spectroscopy and UV-vis spectroscopy. Multilayer films composed of DNA and surfactants were prepared at gold electrode by electrostatic or hydrophobic interactions. It was found that the cationic surfactant, CTAB, can bind to DNA by electrostatic interaction, and the electron transfer resistance of CTAB-DNA complex film increases first and then decreases with CTAB concentration. The anionic surfactant, LAS, can bind to DNA but by hydrophobic interaction, and the electron transfer resistance of the complex film keeps decreasing with LAS concentration. Nonionic surfactants can also directly bind to DNA by hydrophobic interaction. All the three different kinds of surfactants can form multilayer films with DNA on the electrode surface. The chemical structure of DNA keeps unchanged during interacting with these surfactants. The binding modes of DNA with these three different kinds of surfactants were also deduced.