Dielectric control of counterion-induced single-chain folding transition of DNA

Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions

Condensation of DNA is vital for its biological functions and controlled nucleic acid assemblies. However, the mechanisms of DNA condensation are not fully understood due to the inability of experiments to access cation distributions and the complex interplay of energetic and entropic forces during assembly. By constructing free energy surfaces using exhaustive sampling and detailed analysis of cation distributions, we elucidate the mechanism of DNA condensation in different salt conditions and with different DNA sequences. We found that DNA condensation is facilitated by the correlated dynamics of the localized cations at the grooves of DNA helices. These dynamics are strongly dependent on the salt conditions and DNA sequences. In the presence of magnesium ions, major groove binding facilitates attraction. In contrast, in the presence of polyvalent cations, minor groove binding serves to create charge patterns, leading to condensation. Our findings present a novel advancement in the field and have broad implications for understanding and controlling nucleic acid complexes in vivo and in vitro.

Compaction of Calf Thymus DNA by a Potential One-Head-Two-Tail Surfactant: Properties of Nanomaterials and Biological Testing for Gene Delivery

A one-head-two-tail cationic surfactant, Dilauryldimethylammonium bromide (DDAB) has shown a great extent of calf thymus DNA (ct-DNA) compaction being adsorbed on the surfaces of negatively charged SiO2 nanoparticles (NPs). DDAB molecules show high adsorption efficiency and induce many positive surface charges per-unit surface area of the SiO2 NPs compared to cationic Gemini (12-6-12) and conventional (DTAB) surfactants in an aqueous medium at pH 7.4, as evident from zeta potential and EDAX data. Transmission electron microscopy and field emission scanning electron microscopy images, along with ethidium bromide exclusion assay and DLS data support the compaction of ct-DNA. Fluorescence microscopic images show that in the presence of SiO2 NPs, DDAB can perform 50% compaction of ct-DNA at a concentration ∼58% and ∼99% lower than that of 12-6-12 and DTAB, respectively. Better ct-DNA compaction by DDAB is evident compared to other Gemini surfactants (12-4-12 and 12-8-12) as well reported before. Time-correlated single photon counting fluorescence intensity decay measurements of a probe DAPI in ct-DNA have revealed the average lifetime value that is decreased by ∼61% at 2.5 μM of DDAB in the presence of SiO2 NPs as compared to a decrease by only ∼29% in its absence, supporting NPs-induced stronger surfactant binding with ct-DNA. Fluorescence lifetime data have also demonstrated the crowding effect of NPs. At 2.5 μM of DDAB, both fast and slow rotational relaxation components of DAPI contribute almost equally to depolarization with the absence of NPs; however, with the presence of NPs, ∼96% weightage of the anisotropy decay is for the fast component. The present DDAB-SiO2 NPs combination has proved to be an excellent gene delivery system based on the cell viability in the mouse mammary gland adenocarcinoma cells (4T1) and human embryonic kidney (HEK) 293 cell lines, and in vitro and in vivo studies.

A two-stage energy tuning strategy via salt and glycine programmed DNA-engineered crystals

To obtain high-quality DNA-engineered crystals at room temperature, a two-stage energy tuning strategy by first adding NaCl and then glycine (Gly) is proposed. The addition of Gly can exquisitely balance the attraction and repulsion energies for crystallization. The state transition induced by energy rather than temperature is significant for a biosystem.

DNA Condensation Triggered by the Synergistic Self-Assembly of Tetraphenylethylene-Viologen Aggregates and CT-DNA

Development of small organic chromophores as DNA condensing agents, which explore supramolecular interactions and absorbance or fluorescence-based tracking of condensation and gene delivery processes, is in the initial stages. Herein, we report the synthesis and electrostatic/groove binding interaction-directed synergistic self-assembly of the aggregates of two viologen-functionalized tetraphenylethylene (TPE-V) molecules with CT-DNA and subsequent concentration-dependent DNA condensation process. TPE-V molecules differ in their chemical structure according to the number of viologen units. Photophysical and morphological studies have revealed the interaction of the aggregates of TPE-V in Tris buffer with CT-DNA, which transforms the fibrous network structure of CT-DNA to partially condensed beads-on-a-string-like arrangement with TPE-V aggregates as beads via electrostatic and groove binding interactions. Upon further increasing the concentration of TPE-V, the "beads-on-a-string"-type assembly of TPE-V/CT-DNA complex changes to completely condensed compact structures with 40-50 nm in diameter through the effective charge neutralization process. Enhancement in the melting temperature of CT-DNA, quenching of the fluorescence emission of ethidium bromide/CT-DNA complex, and the formation of induced CD signal in the presence of TPE-V molecules support the observed morphological changes and thereby verify the DNA condensation abilities of TPE-V molecules. Decrease in the hydrodynamic size, increase in the zeta potential value with the addition of TPE-V molecules to CT-DNA, failure of TPE-V/cucurbit(8)uril complex to condense CT-DNA, and the enhanced DNA condensation ability of TPE-V2 with two viologen units compared to TPE-V1 with a single viologen unit confirm the importance of positively charged viologen units in the DNA condensation process. Initial cytotoxicity analysis on A549 cancer and WI-38 normal cells revealed that these DNA condensing agents are non-toxic in nature and hence could be utilized in further cellular delivery studies.

Electrochemical Studies of Cation Condensation-Induced Collapse of Surface-Bound DNA

In this paper, we demonstrate the ability to control and electrochemically monitor nucleic acid conformation by inducing collapse of short, surface-bound nucleotides (7-28 nucleotides). More specifically, we monitored changes in a 5'-electrode-bound DNA structure via changes in the faradaic current related to the reduction/oxidation of a 3'-terminal-appended redox molecule. Reversible DNA collapse was induced by cation condensation achieved by either reducing the dielectric permittivity of the interrogation solution or by the addition of multivalent cations such as the polyamine spermidine (3⁺). Additionally, we find that while the change in electrochemical signal associated with surface bound DNA collapse is dependent on nucleic acid length and surface packing density, the solution conditions (e.g., dielectric permittivity) required for collapse remain constant. As such, we find that collapse of the short DNA strands occurs when the effective charge of the DNA backbone is ∼73-89% neutralized by cations in solution/buffer, according to Manning's theory on cation condensation. This work provides new insight into the structure function relationship of surface-bound nucleic acids and how this is manifested in electrochemical signaling.

Like-charge polymer-membrane complexation mediated by multivalent cations: One-loop-dressed strong coupling theory

We probe the electrostatic mechanism driving adsorption of polyelectrolytes onto like-charged membranes upon the addition of tri- and tetravalent counterions to a bathing monovalent salt solution. We develop a one-loop-dressed strong coupling theory that treats the monovalent salt at the electrostatic one-loop level and the multivalent counterions within a strong-coupling approach. It is shown that the adhesive force of the multivalent counterions mediating the like-charge adsorption arises from their strong condensation at the charged membrane. The resulting interfacial counterion excess locally maximizes the screening ability of the electrolyte and minimizes the electrostatic polymer grand potential. This translates into an attractive force that pulls the polymer to the similarly charged membrane. We show that the high counterion valency enables this adsorption transition even at weakly charged membranes. Additionally, strongly charged membranes give rise to monovalent counterion-induced correlations and intensify the interfacial multivalent counterion condensation, strengthening the complexation of the polymer with the like-charged membrane, as well as triggering the orientational transition of the molecule prior to its adsorption. Finally, our theory provides two additional key features as evidenced by previous adsorption experiments: first, the critical counterion concentration for polymer adsorption decreases with the rise of the counterion valency and, second, the addition of monovalent salt enhances the screening of the membrane charges and suppresses monovalent counterion correlations close to the surface. This weakens the interfacial multivalent counterion condensation and results in the desorption of the polymer from the substrate.

ortho-Fluoroazobenzene derivatives as DNA intercalators for photocontrol of DNA and nucleosome binding by visible light

We report a high-affinity photoswitchable DNA binder, which displays different nucleosome-binding capacities upon visible-light irradiation. Both photochemical and DNA-recognition properties were examined by UV-Vis, HPLC, CD spectroscopy, NMR, FID assays, EMSA and DLS. Our probe sets the basis for developing new optoepigenetic tools for conditional modulation of nucleosomal DNA accessibility.

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

DNA conformation is strongly dependent on the valence of counterions in solution, and a valence of at least three is needed for DNA compaction. Recently, we directly demonstrated DNA compaction and its regulation, mediated by divalent cations, by lowering the pH of a solution. In the present study, we found that the critical electrophoretic mobility of DNA is promoted to around -1.0 × 10-4 cm² V-1 s-1 to incur DNA compaction or condensation in a tri- and tetravalent counterions solution, corresponding to an about 89% neutralized charge fraction of DNA. This is also valid for DNA compaction by divalent counterions in a low pH solution. It is notable that the critical charge neutralization of DNA for compaction is only about 1% higher than the saturated charge fraction of DNA in a mild divalent ion solution. We also found that DNA compaction by divalent cations at low pH is weakened and even decondensed with an increasing concentration of counterions.

The Mixing Counterion Effect on DNA Compaction and Charge Neutralization at Low Ionic Strength

DNA compaction and charge neutralization in a mixing counterion solution involves competitive and cooperative electrostatic binding, and sometimes counterion complexation. At normal ionic strength, it has been found that the charge neutralization of DNA by the multivalent counterion is suppressed when being added extra mono- and di-valent counterions. Here, we explore the effect mixing counterion on DNA compaction and charge neutralization under the condition of low ionic strength. Being quite different from normal ionic strength, the electrophoretic mobility of DNA in multivalent counterion solution (octalysine, spermine) increases the presence of mono- and di-valent cations, such as sodium and magnesium ions. It means that the charge neutralization of DNA by the multivalent counterion is promoted rather than suppressed when introducing extra mono- and di-valent counterions into solution. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates under the same condition by single molecular magnetic tweezers. This mixing effect can be attributed to the cooperative electrostatic binding of counterions to DNA when the concentration of counterions in solution is below a critical concentration.

In vitro transcription-translation using bacterial genome as a template to reconstitute intracellular profile

In vitro transcription–translation systems (TX–TL) can synthesize most of individual genes encoded in genomes by using strong promoters and translation initiation sequences. This fact raises a possibility that TX–TL using genome as a template can reconstitute the profile of RNA and proteins in living cells. By using cell extracts and genome prepared from different organisms, here we developed a system for in vitro genome transcription–translation (iGeTT) using bacterial genome and cell extracts, and surveyed de novo synthesis of RNA and proteins. Two-dimensional electrophoresis and nano LC–MS/MS showed that proteins were actually expressed by iGeTT. Quantitation of transcription levels of 50 genes for intracellular homeostasis revealed that the levels of RNA synthesis by iGeTT are highly correlated with those in growth phase cells. Furthermore, activity of iGeTT was influenced by transcription derived from genome structure and gene location in genome. These results suggest that intracellular profiles and characters of genome can be emulated by TX–TL using genome as a template.

Peptide nucleic acid-ionic self-complementary peptide conjugates: highly efficient DNA condensers with specific condensing mechanism

Peptide nucleic acid-ionic self-complementary peptide conjugates can induce efficient DNA condensation via base-pairing interaction and peptide association.

Single Molecular Demonstration of Modulating Charge Inversion of DNA

Charge inversion of DNA is a counterintuitive phenomenon in which the effective charge of DNA switches its sign from negative to positive in the presence of multivalent counterions. The underlying microscopic mechanism is still controversial whether it is driven by a specific chemical affinity or electrostatic ion correlation. It is well known that DNA shows no charge inversion in normal aqueous solution of trivalent counterions though they can induce the conformational compaction of DNA. However, in the same trivalent counterion condition, we demonstrate for the first time the occurrence of DNA charge inversion by decreasing the dielectric constant of solution to make the electrophoretic mobility of DNA increase from a negative value to a positive value. In contrast, the charge inversion of DNA induced by quadrivalent counterions can be canceled out by increasing the dielectric constant of solution. The physical modulation of DNA effective charge in two ways unambiguously demonstrates that charge inversion of DNA is a predominantly electrostatic phenomenon driven by the existence of a strongly correlated liquid (SCL) of counterions at the DNA surface. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates by single molecular MT.

Conformational changes of polyelectrolyte chains in solvent mixtures

We numerically investigate the behaviors of polyelectrolyte chains in solvent mixtures, taking into account the effects of the concentration inhomogeneity and the degree of the ionization. When changing the interaction parameters between the solvent components, we found a first order transition of the polymer conformation. In the mixing state far from the coexistence curve, the polymers behave as semi-flexible chains. In the phase-separated state, on the other hand, they show compact conformations included in the droplets. As the interaction parameters of the mixture are increased, an inhomogeneous concentration field develops around the polymer and induces critical Casimir attractive interactions among the monomers. The competition between the electrostatic interactions and the critical Casimir ones gives rise to drastic changes in the conformation.

Photochromic switching of the DNA helicity induced by azobenzene derivatives

The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (Azo-2N and Azo-3N) with double stranded DNA and demonstrate that the photoisomerization of Azo-3N leads to changes in DNA structure. In particular, we show that stabilization and destabilization of the B-DNA secondary structure can be photochemically induced in situ by light. This photo-triggered process is fully reversible and could be an alternative pathway to control a broad range of biological processes. Moreover, we found that the bicationic Azo-3N exhibited a higher DNA-binding constant than the monocationic Azo-2N pointing out that the number of positive charges along the photosensitive polyamines chain plays a pivotal role in stabilizing the photochrome-DNA complex.

Influence of asymmetric depletion of solvents on the electric double layer of charged objects in binary polar solvent mixtures

The ratio of the dipole moment to the volume of solvent is the key factor for asymmetric depletion of solvents.

Photosensitive polyamines for high-performance photocontrol of DNA higher-order structure

Polyamines are small, ubiquitous, positively charged molecules that play an essential role in numerous biological processes such as DNA packaging, gene regulation, neuron activity, and cell proliferation. Here, we synthesize the first series of photosensitive polyamines (PPAs) and demonstrate their ability to photoreversibly control nanoscale DNA higher-order structure with high efficiency. We show with fluorescence microscopy imaging that the efficiency of the PPAs as DNA-compacting agents is directly correlated to their molecular charge. Micromolar concentration of the most efficient molecule described here, a PPA containing three charges at neutral pH, compacts DNA molecules from a few kilobase pairs to a few hundred kilobase pairs, while subsequent 3 min UV illuminations at 365 nm triggers complete unfolding of DNA molecules. Additional application of blue light (440 nm for 3 min) induces the refolding of DNA into the compact state. Atomic force microscopy reveals that the compaction involves a global folding of the whole DNA molecule, whereas UV-induced unfolding is a modification initiated from the periphery of the compacted DNA, resulting in the occurrence of intermediate flower-like structures prior to the fully unfolded state.

Phenylene-ethynylene trication as an efficient fluorescent signal transducer in an aptasensor for potassium ion

A tricationic phenylene-ethynylene (N(3+)) fluorophore is investigated as a fluorescent transducer in homogeneous aptasensing system for potassium ion (K(+)) assay in aqueous media. The enhancement of the fluorescent signal of N(3+) by three K(+) aptamers consisting of 12, 15, and 21 nucleotides are observed and used for the determination of N(3+)-aptamer binding affinities. The binding affinities increase with the length of the aptameric oligonucleotides and are proven to be important to the sensitivity and selectivity of the aptasensors. The enhanced fluorescent signal of each N(3+)-aptamer solution is selectively quenched by K(+) due to the ability of K(+) in stabilizing the G-quadruplex structure of the aptamer. Among three aptamers, the 15-base aptamer provides optimal sensitivity and selectivity over other ions such as Li(+), Na(+), NH(4)(+), Mg(2+), Ca(2+) and Sr(2+). The sensing system shows the detection limit of 1 μM of K(+) in clean buffered solution and 30 μM of K(+) in the solution containing 4800-fold excess of Na(+), with wide linear dynamic ranges of micro- to millimolar concentration. This label-free fluorescence aptasensor is conveniently and effectively applicable for analysis of K(+) in urine samples.

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.

Electrostatic contribution to DNA condensation--application of 'energy minimization' in a simple model in the strong Coulomb coupling regime

The process of bending of straight DNA to a circular form in the presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in a strong Coulomb coupling environment, employing a previously developed energy minimization simulation technique. The inherent characteristics of the simulation technique allow the monitoring of the required electrostatic contribution to the bending. The curvature of the bending has been found to play a crucial role in facilitating the electrostatic attractive potential energy. The total electrostatic potential energy has been found to decrease with bending, which indicates that bending straight DNA to a circular form or to a toroidal form in the presence of neutralizing counterions is energetically favourable and is practically a spontaneous phenomenon.

A new view of the bacterial cytosol environment

The cytosol is the major environment in all bacterial cells. The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied. Using recent and detailed data on metabolite concentrations, we have created a molecular mechanical model of the prokaryotic cytosol environment of Escherichia coli, containing proteins, metabolites and monatomic ions. We use 200 ns molecular dynamics simulations to compute diffusion rates, the extent of contact between molecules and dielectric constants. Large metabolites spend ∼80% of their time in contact with other molecules while small metabolites vary with some only spending 20% of time in contact. Large non-covalently interacting metabolite structures mediated by hydrogen-bonds, ionic and π stacking interactions are common and often associate with proteins. Mg²⁺ ions were prominent in NIMS and almost absent free in solution. Κ⁺ is generally not involved in NIMSs and populates the solvent fairly uniformly, hence its important role as an osmolyte. In simulations containing ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions. Hence, it is likely that with larger proteins metabolites would diffuse even more slowly. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monatomic ion effects cancel. These findings suggest regions of influence specific to particular proteins affecting metabolite diffusion and electrostatics. Also some proteins may have a higher propensity for associations with metabolites owing to their larger electrostatic fields. We hope that future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dilute aqueous solution.

The cytosol is the major cellular environment housing the majority of cellular activity. Although the cytosol is an aqueous environment, it contains high concentrations of ions, metabolites, and proteins, making it very different from dilute aqueous solution, which is frequently used for in vitro biochemistry. Recent advances in metabolomics have provided detailed concentration data for metabolites in E.coli. We used this information to construct accurate atomistic models of the cytosol solution. We find that, unlike the situation in dilute solutions, most metabolites spend the majority of their time in contact with other metabolites, or in contact with proteins. Furthermore, we find large non-covalently interacting metabolite structures are common and often associated with proteins. The presence of proteins reduced metabolite diffusion owing to long lasting correlations of motion. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from proteins as metabolite and monatomic ion effects largely cancel. These findings suggest specific protein spheres of influence affecting metabolite diffusion and the electrostatic environment.

Physics of DNA: unravelling hidden abilities encoded in the structure of ‘the most important molecule’

A comprehensive article “Structure and Interactions of Biological Helices”, published in 2007 in Reviews of Modern Physics, overviewed various aspects of the effect of DNA structure on DNA–DNA interactions in solution and related phenomena, with a thorough analysis of the theory of these effects. Here, an updated qualitative account of this area is presented without any sophisticated ‘algebra’. It overviews the basic principles of the structure-specific interactions between double-stranded DNA and focuses on the physics behind several related properties encoded in the structure of DNA. Among them are (i) DNA condensation and aptitude to pack into small compartments of cells or viral capcids, (ii) the structure of DNA mesophases, and (iii) the ability of homologous genes to recognize each other prior to recombination from a distance. Highlighted are some of latest developments of the theory, including the shape of the ‘recognition well’. The article ends with a brief discussion of the first experimental evidence of the protein-free homology recognition in a ‘test tube’.

Counterion condensation and shape within Poisson-Boltzmann theory

An analytical approximation to the nonlinear Poisson-Boltzmann (PB) equation is applied to charged macromolecules that possess one-dimensional symmetry and can be modeled by a plane, infinite cylinder, or sphere. A functional substitution allows the nonlinear PB equation subject to linear boundary conditions to be transformed into an approximate linear (Debye-Hückel-type) equation subject to nonlinear boundary conditions. A simple analytical result for the surface potential of such polyelectrolytes follows, leading to expressions for the amount of condensed (or renormalized) charge and the electrostatic Helmholtz energy for polyelectrolytes. Analytical high-charge/low-salt and low-charge/high-salt limits are shown to be similar to results obtained by others based on PB or counterion condensation theory. Several important general observations concerning polyelectrolytes treated within the context of PB theory can be made including: (1) all charged surfaces display some counterion condensation for finite electrolyte concentration, (2) the effect of surface geometry is described primarily by the sum of the Debye constant and the mean curvature of the surface, (3) two surfaces with the same surface charge density and mean curvature condense approximately identical fractions of counterions, (4) the amount of condensation is not determined by a predefined "condensation distance" although such a distance can be determined uniquely from it, and (5) substantial condensation occurs if the Debye constant of the electrolyte is much less than the mean curvature of a highly charged polyelectrolyte.

Electrostatic exclusion of neutral solutes from condensed DNA and other charged phases

Motivated by experiments on condensed DNA phases in binary mixtures of water and a low-dielectric solute, we develop a theory for the electrostatic contribution to solute exclusion from a highly charged phase, within the continuum approximation of the medium. Because the electric field is maximum at the surface of each ion, the electrostatic energy is dominated by the Born energy; interactions between charges are of secondary importance. Neglecting interactions and considering only the competition between the Born energy and the free energy of mixing, we predict that low dielectric solutes are excluded from condensed DNA phases in water-cosolvent mixtures. This suggests that the traditional continuum electrostatic approach of modeling binary mixtures with a uniform dielectric constant needs to be modified. The linking of solute exclusion to solute dielectric properties also suggests a mechanism for predicting the electrostatic contribution to preferential hydration of polar and charged surfaces.

Interaction between 14mer DNA oligonucleotide and cationic surfactants of various chain lengths

In the recent genomic era, a novel gene silencing approach has been introduced based on the use of small synthetic oligonucleotides, such as antisense RNAs, siRNAs, to inhibit the expression of a specific target gene. Successful implementation of this methodology calls for the development of efficient systems to deliver small oligonucleotides into the cells using various natural and synthetic cationic agents. While extensive studies have focused on the interaction of various natural and synthetic cationic surfactants with long DNA, less attention has been paid to surfactant interaction with small oligonucleotides. In this study, the interaction between 14mer double stranded DNA and alkyltrimethylammonium bromides of C16 (cetyl, CTAB), C14 (tetradecyl, TTAB), and C12 (dodecyl, DTAB) chain lengths was investigated at different charge ratios by gel electrophoresis, ethidium bromide exclusion, circular dichroism, and UV melting. Our gel studies at 1 microM oligonucleotide concentration showed that CTAB, TTAB, and DTAB neutralize the oligonucleotides at a charge ratio (Z+/-) of 1, 14, and 50, respectively. At lower charge ratios, CTAB and TTAB interact with oligonucleotides, and the complexes show electrophoretic mobility shifts in the gel, while such mobility shifts were completely absent in the case of DTAB. UV melting experiments revealed that interaction with all three surfactants increased the thermostability of the oligonucleotide. The extent of thermal stabilization was highest in the case of CTAB, moderate in the case of TTAB, and extremely low in the case of DTAB. Oligonucleotides within fully neutralized complexes denatured at further higher temperatures, and again, stabilization was the highest in the case of CTAB followed by TTAB and DTAB, hence revealing that the oligonucleotides interacted more strongly with CTAB than with the other two surfactants. Ethidium bromide exclusion studies also supported our UV melting studies, confirming that CTAB binds most strongly to the oligonucleotide. CD titrations of oligonucleotides with increasing amounts of surfactants revealed common spectral patterns consisting of the progressive loss of CD signals for native helical DNA conformations. Overall, our results demonstrate that interaction between oligonucleotides and cationic surfactants, although qualitatively similar to long double stranded DNA, shows subtle differences that need to be understood to improve small oligonucleotide delivery into the cells by using common delivery agents that have been used to deliver long pieces of DNA.

Single-Chain Compaction of Long Duplex DNA by Cationic Nanoparticles: Modes of Interaction and Comparison with Chromatin

The compaction of long duplex DNA by cationic nanoparticles (NP) used as a primary model of histone core particles has been investigated. We have systematically studied the effect of salt concentration, particle size, and particle charge by means of single-molecule observations-fluorescence microscopy (FM) and transmission electron microscopy (TEM)-and molecular dynamics (MD) simulations. We have found that the large-scale DNA compaction is progressive and proceeds through the formation of beads-on-a-string structures of various morphologies. The DNA adsorbed amount per particle depends weakly on NP concentration but increases significantly with an increase in particle size and is optimal at an intermediate salt concentration. Three different complexation mechanisms have been identified depending on the correlation between DNA and NPs in terms of geometry, chain rigidity, and electrostatic interactions: free DNA adsorption onto NP surface, DNA wrapping around NP, and NP collection on DNA chain.

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.

Temperature effects on threshold counterion concentration to induce aggregation of fd virus

We seek to elucidate the dominant mechanism of attractive interaction between like-charged biopolymers by measuring the temperature dependence of the critical divalent counterion concentration (Cc) for the aggregation of fd viruses. A decrease in either temperature or the dieletric constant alone causes a decrease in Cc, providing evidence for the Wigner crystal model. Surprisingly, the effects of these two parameters can be combined so that Cc is expressed as a function of a single parameter: the Bjerrum length. Cc decreases exponentially as the Bjerrum length increases, suggesting that an energetic balance between the entropic effect of counterions and the counterion mediated attractive interaction gives rise to the onset of bundle formation.

Compaction of DNA on nanoscale three-dimensional templates

There exist several important in vivo examples, where a DNA chain is compacted on interacting with nanoscale objects such as proteins, thereby forming complexes with a well defined molecular architecture. One of the well known manifestations of such a natural organization of a semi-flexible DNA chain on nanoscale objects is hierarchical DNA molecule assembly into a chromosome, which is mediated by cationic histone proteins at the first stages of compaction. The biological importance of this and other natural nanostructural organizations of the DNA molecule has inspired many theoretical and numerical studies to gain physical insight into this problem. On the other hand, the experimental model systems containing DNA and nanoobjects, which are important to extend our knowledge beyond natural systems, were almost unavailable until the last decade. Accelerating progress in nanoscale chemistry and materials science has brought about various nanoscale three-dimensional structures such as dendrimers, nanoparticles, and nanotubes, and thus has provided a basis for the next important step in creating novel DNA-containing nanostructures, modelling of natural DNA compaction, and verification of accumulated theoretical predictions on the interaction between DNA and nanoscale templates. This review is written to highlight this early stage of nano-inspired progress and it is focused on physico-chemical and biophysical experimental investigations as well as theoretical and numerical studies dedicated to the compaction of DNA on nanoscale three-dimensional templates.