First-order phase transition in large single duplex DNA induced by a nonionic surfactant

ct-DNA compaction by nanoparticles formed by silica and gemini surfactants having hydroxyl group substituted spacers: In vitro, in vivo, and ex vivo gene uptake to cancer cells

Hybrid nanoparticles formed by Silica (SiO2) coated with cationic gemini surfactants with variable hydroxyl group substituted spacers, 12-4(OH)-12,2Br- and 12-4(OH)2-12,2Br- have shown a great extent of compaction of calf thymus DNA (ct-DNA) compared to conventional counterpart cationic surfactant, dodecyl trimethylammonium bromide (DTAB). Study shows not only the hydrophobicity of the spacer but also the hydrogen bonding interactions between the hydroxyl group substituted spacer and DNA have a great role in DNA compaction. 12-4(OH)2-12,2Br- is more efficient in compacting ct-DNA compared to 12-4(OH)-12,2Br- due to the stronger binding of the former with ct-DNA than the latter. While 12-4(OH)-12,2Br- makes 50 % ct-DNA compaction at its 0.63 μM concentration in the presence of SiO2 nanoparticles, the same % of compaction can be achieved at a concentration as low as 0.25 μM of 12-4(OH)2-12,2Br-. However, DTAB makes 50 % ct-DNA compaction at a concentration as high as 7.00 μM under the same condition. Therefore, the present systems address the very common challenge, i.e., cytotoxicity due to cationic surfactants. The system of 12-4(OH)2-12,2Br- coated SiO2 nanoparticles displays the maximum cell viability (≥90 %), causing the least cell death in the mouse fibroblast cells (NIH3T3) cell lines compared to the cell viability of ≤80 % for DTAB. 12-4(OH)2-12,2Br- coated SiO2 nanoparticles system has presented excellent in vitro cellular uptake of genes on mouse mammary gland adenocarcinoma (4T1) cells after incubating for 3 h and 6 h. In vivo study shows that 12-4(OH)2-12,2Br- coated SiO2 nanoparticles system takes the highest amount of ct-DNA in cells and tumors in a time-dependent manner. The ex vivo studies using different organs of the mice demonstrate that the tumor sites in the breast of the mice are most affected by these formulations. Cytotoxicity assays and cellular uptake studies suggest that the present systems can be used for potential applications for gene delivery and oncological therapies.

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.

Field Hypothesis on the Self-regulation of Gene Expression

The mechanism of the self-regulation of gene expression in living cells is generally explained by considering complicated networks of key-lock relationships, and in fact there is a large body of evidence on a hugenumber of key-lock relationships. However, in the present article we stress that with the network hypothesis alone it is impossible to fully explain the mechanism of self-regulation in life. Recently, it has been established that individual giant DNA molecules, larger than several tens of kilo base pairs, undergo a large discrete transition in their higher-order structure. It has become clear that nonspecific weak interactions with various chemicals, suchas polyamines, small salts, ATP and RNA, cause on/off switching in the higher-order structure of DNA. Thus, the field parameters of the cellular environment should play important roles in the mechanism of self-regulation, in addition to networks of key and locks. This conformational transition induced by field parameters may be related to rigid on/off regulation, whereas key-lock relationships may be involved in a more flexible control of gene expression.

An investigation on interaction between 14mer DNA oligonucleotide and CTAB by fluorescence and fluorescence resonance energy transfer studies

Possible interaction mechanisms between oligonucleotide (DNA) of 14 base pairs with cetyl trimethyl ammonium bromide (CTAB) were postulated based on fluorescence and fluorescence resonance energy transfer (FRET) studies. Detailed FRET investigations were carried out by fluorometric titrations of the surfactant with various oligonucleotide duplexes with 5'-tagged fluorescein (donor) (D(D)), 5'-tagged TAMRA (acceptor) (D(A)) and both (D(DA)). In general, fluorescence spectra of the duplexes (D(D), D(A) and D(DA)) revealed a reduction in the fluorescence intensities of 5'-fluorescein as well as 5'-TAMRA and thereafter an attainment of saturation with increase in the surfactant concentration. The observed changes in the oligonucleotide fluorescence intensities for the duplexes under investigation could be attributed to the microenvironmental changes during the oligonucleotide-CTAB interaction. Considering together, it appeared that the interaction is a three-stage process, wherein the initial addition of surfactant caused neutralization of the 14mer at Z(+/-)(1) = 0.8, which is manifested by a slight reduction in fluorescence intensity. Further, addition of the surfactant molecules sharply reduced the fluorescence intensity of the oligonucleotide depicting oligonucleotide induced self-assembly until the second break point (Z(+/-)(2) = 1.7). From the second break point, a striking resonance energy transfer was observed from donor to acceptor, which revealed shortening of distance between 5' ends of the oligonucleotides that attained a saturation at Z(+/-)(3) = 2.5. Similar three-stage interaction of oligonucleotide with the surfactant has also been observed through fluorometric titrations in the presence of NaCl. However, in the presence of the salt, neutralization of oligonucleotide, surfactant aggregation and FRET occurred at higher charge ratios due to the screening effect of Na+ ions followed by an increase in critical association concentration (CAC) of the surfactant. Overall, investigations probe possible structural changes in the 14mer oligonucleotide-CTAB complex upon increase in the surfactant concentration.

Control of the compaction/unfolding transition of genomic DNA by the addition/disruption of lipid assemblies

We studied the interaction between individual long genomic DNA molecules and cationic lipid assemblies. The assembly of cationic lipid molecules into small unilamellar vesicles (SUVs) of about 50 nm diameter led to the compaction of DNA whereas the addition of a neutral surfactant resulted in the disruption of SUVs and the unfolding of DNA. This reversible process does not require any chemical reaction or change in the ionic strength of the solution. It was applied to switch DNA repeatedly between a compact and an unfolded conformation in a dynamic manner.

Interaction between DNA and cationic surfactants: effect of DNA conformation and surfactant headgroup

The interactions between DNA and a number of different cationic surfactants, differing in headgroup polarity, were investigated by electric conductivity measurements and fluorescence microscopy. It was observed that, the critical association concentration (cac), characterizing the onset of surfactant binding to DNA, does not vary significantly with the architecture of the headgroup. However, comparing with the critical micelle concentration (cmc) in the absence of DNA, it can be inferred that the micelles of a surfactant with a simple quaternary ammonium headgroup are much more stabilized by the presence of DNA than those of surfactants with hydroxylated head-groups. In line with previous studies of polymer-surfactant association, the cac does not vary significantly with either the DNA concentration or its chain length. On the other hand, a novel observation is that the cac is much lower when DNA is denaturated and in the single-stranded conformation, than for the double-helix DNA. This is contrary to expectation for a simple electrostatically driven association. Thus previous studies of polyelectrolyte-surfactant systems have shown that the cac decreases strongly with increasing linear charge density of the polyion. Since double-stranded DNA (dsDNA) has twice as large linear charge density as single-stranded DNA (ssDNA), the stronger binding in the latter case indicates an important role of nonelectrostatic effects. Both a higher flexibility of ssDNA and a higher hydrophobicity due to the exposed bases are found to play a role, with the hydrophobic interaction argued to be more important. The significance of hydrophobic DNA-surfactant interaction is in line with other observations. The significance of nonelectrostatic effects is also indicated in significant differences in cac between different surfactants for ssDNA but not for dsDNA. For lower concentrations of DNA, the conductivity measurements presented an "anomalous" feature, i.e., a second inflection point for surfactant concentrations below the cac; this feature was not displayed at higher concentrations of DNA. The effect is attributed to the presence of a mixture of ss- and dsDNA molecules. Thus the stability of dsDNA is dependent on a certain ion atmosphere; at lower ion concentrations the electrostatic repulsions between the DNA strands become too strong compared to the attractive interactions, and there is a dissociation into the individual strands. Fluorescence microscopy studies, performed at much lower DNA concentrations, demonstrated a transformation of dsDNA from an extended "coil" state to a compact "globule" condition, with a broad concentration region of coexistence of coils and globules. The onset of DNA compaction coincides roughly with the cac values obtained from conductivity measurements. This is in line with the observed independence of cac on the DNA concentration, together with the assumption that the onset of binding corresponds to an initiation of DNA compaction. No major changes in either the onset of compaction or complete compaction were observed as the surfactant headgroup was made more polar.

Weak Interaction Induces an ON/OFF Switch, whereas Strong Interaction Causes Gradual Change: Folding Transition of a Long Duplex DNA Chain by Poly-l-lysine

A large-scale conformational change in genomic DNA is an essential feature of gene activation in living cells. Considerable effort has been applied to explain the mechanism in terms of key-lock interaction between sequence-specific regulatory proteins and DNA, in addition to the modification of DNA and histones such as methylation and acetylation. However, it is still unclear whether these mechanisms can explain the ON/OFF switching of a large number of genes that accompanies differentiation, carcinogenesis, etc. In this study, using single-molecule observation of DNA molecules by fluorescence microscopy with the addition of poly-L-lysine with different numbers of monomer units (n = 3, 5, 9, and 92), we found that an ON/OFF discrete transition in the higher-order structure of long duplex DNA is induced by short poly-L-lysine, whereas a continuous gradual change is induced by long poly-L-lysine. On the other hand, polycations with a lower positive charge have less potential to induce DNA compaction. Such a drastic difference in the conformational transition of a giant DNA between short and large oligomers is discussed in relation to the mechanisms of gene regulation in a living cell.

How are small ions involved in the compaction of DNA molecules?

DNA is a genetic material found in all life on Earth. DNA is composed of four types of nucleotide subunits, and forms a double-helical one-dimensional polyelectrolyte chain. If we focus on the microscopic molecular structure, DNA is a rigid rod-like molecule. On the other hand, with coarse graining, a long-chain DNA exhibits fluctuating behavior over the whole molecule due to thermal fluctuation. Owe to its semiflexible nature, individual giant DNA molecule undergoes a large discrete transition in the higher-order structure. In this folding transition into a compact state, small ions in the solution have a critical effect, since DNA is highly charged. In the present article, we interpret the characteristic features of DNA compaction while paying special attention to the role of small ions, in relation to a variety of single-chain morphologies generated as a result of compaction.

DNA Condensation Induced by Cationic Surfactant: A Viscosimetry and Dynamic Light Scattering Study

The compaction of DNA induced by two simple amphiphiles, cetyltrimethylammonium bromide [CTAB] and dodecyldimethylamine oxide [DDAO], has been investigated by means of combined viscosity and dynamic light scattering measurements, to demonstrate the formation of soluble DNA/surfactant complexes, undergoing a coil-globule transition, upon the increase of the amphiphile concentration. In both of the two systems investigated, the complexation process reaches a maximum for a value of the surfactant to DNA phosphate groups molar ratio of about X = 1. Below this critical concentration, the coil and the globule state coexist in the solution, as clearly shown by the bimodal size distribution obtained from the light scattering intensity correlation functions. Some suggestions are given to support a molecular mechanism responsible for the complex formation, both in the case of a cationic surfactant (CTAB) and of a pH-dependent neutral or cationic amphiphile (DDAO), where the hydrophobic interactions play an important role.

Proton concentration (pH) switches the higher-order structure of DNA in the presence of spermine

Single-chain observations on the conformational change of giant DNA (T4 DNA) molecules were performed using fluorescence microscopy at different values of pH in the presence of spermine. Individual DNA molecules undergo a large discrete change, or all-or-none transition, in conformation from a folded compact state to an unfolded coil state with an increase in pH. This abrupt unfolding of DNA with an increase in pH is attributed to a decrease in the concentration of the tetravalent form in spermine [SPM(4+)]. We propose a scheme for the folding transition of single DNAs, where the manner of spermine binding changes dramatically from weak loose binding in the elongated coil state to strong tight binding in the folded compact state. We discuss the hierarchical nature of the transition, i.e. cooperative continuous change on the ensemble vs. all-or-none switching on individual DNAs.

Binding of molecules to DNA and other semiflexible polymers

A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers (e.g., DNA) represent an intermediate case between flexible polymers and stiff, rodlike ones, whose association with small molecules was previously studied. The chains are not flexible enough to actively participate in the self-assembly, yet their fluctuations induce long-range attractive interactions between bound molecules. In cases where the binding significantly affects the local chain stiffness, those interactions lead to a very sharp, cooperative association. This scenario is of relevance to the association of DNA with surfactants and compact proteins such as RecA. External tension exerted on the chain is found to significantly modify the binding by suppressing the fluctuation-induced interaction.

DNA conformational dynamics in the presence of catanionic mixtures

DNA conformational behavior in the presence of non-stoichiometric mixtures of two oppositely charged surfactants, cetyltrimethylammonium bromide and sodium octyl sulfate, was directly visualized in an aqueous solution with the use of a fluorescence microscopy technique. It was found that in the presence of cationic-rich catanionic mixtures, DNA molecules exhibit a conformational transition from elongated coil to compact globule states. Moreover, if the catanionic mixtures form positively charged vesicles, DNA is adsorbed onto the surface of the vesicles in a collapsed globular form. When anionic-rich catanionic mixtures are present in the solution, no change in the DNA conformational behavior was detected. Cryogenic transmission electron microscopy, as well as measurements of translational diffusion coefficients of individual DNA chains, supported our optical microscopy observations.

Folding and unfolding of a giant duplex-DNA in a mixed solution with polycations, polyanions and crowding neutral polymers

To understand the conformational behavior of a giant duplex-DNA chain in a mixed solution with various biopolymers with different state of ionization, the higher-order structure of the DNA chain was analyzed with a fluorescence microscope in the presence of polycations (poly-arginine), polyanions (poly-glutamic acid), and neutral polymers (poly-ethylene glycol) as a model for cellular environment. Concentrated medium with neutral polymer induced the discrete folding transition of the DNA. At the threshold condition for the transition, addition of small amounts of either the polycation or the polyanion caused marked structural changes in the folded DNAs. Based on thermodynamic considerations on the experimental results, profile of free energy of a single giant DNA chain was depicted with respect to the size, or the expansion factor alpha, in the three-dimensional structure of the DNA. The effect of the neural crowding polymer on the degree of folding of a single giant DNA chain is discussed in a semi-quantitative manner.