Phase Behavior of Single DNA in Mixed Solvents

Structural stability of DNA origami nanostructures in organic solvents

DNA origami nanostructures have attracted significant attention as an innovative tool in a variety of research areas, spanning from nanophotonics to bottom-up nanofabrication. However, the use of DNA origami is often restricted by their rather limited structural stability in application-specific conditions. The structural integrity of DNA origami is known to be superstructure-dependent, and the integrity is influenced by various external factors, for example cation concentration, temperature, and presence of nucleases. Given the necessity to functionalize DNA origami also with non-water-soluble entities, it is important to acquire knowledge of the structural stability of DNA origami in various organic solvents. Therefore, we herein systematically investigate the post-folding DNA origami stability in a variety of polar, water-miscible solvents, including acetone, ethanol, DMF, and DMSO. Our results suggest that the structural integrity of DNA origami in organic solvents is both superstructure-dependent and dependent on the properties of the organic solvent. In addition, DNA origami are generally more resistant to added organic solvents in folding buffer compared to that in deionized water. DNA origami stability can be maintained in up to 25-40% DMF or DMSO and up to 70-90% acetone or ethanol, with the highest overall stability observed in acetone. By rationally selecting both the DNA origami design and the solvent, the DNA origami stability can be maintained in high concentrations of organic solvents, which paves the way for more extensive use of non-water-soluble compounds for DNA origami functionalization and complexation.

Force-induced unzipping of DNA in the presence of solvent molecules

The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.

DNA Hyperstructure

This study presents a new procedure to condense DNA molecules and precipitate them onto a glass slide. The resulting DNA molecules undergo autonomous self-assembly, creating closed superstructures on the micrometer scale, which are called DNA hyperstructures. These structures can be observed using low-magnification (4×) light microscopy. Precisely controlling the alcohol/glacial acetic acid ratio and DNA concentration during precipitation enabled the regulation of structure compaction on the slide. The alcohol/glacial acetic acid ratio is inversely proportional to the DNA concentration to achieve optimal compaction on the slide. Confocal microscopy fluorescence analysis of DNA extracts stained with DAPI shows that nucleic acids self-assemble to form structures during precipitation on the slide. This methodology is relevant since it facilitates the precipitation and visualization of DNA, regardless of its origin or molecular weight. To confirm its versatility, results with DNA extracted from human peripheral blood, the Lambda virus, and plasmid pBR322 are presented. The study examined the morphological features of DNA hyperstructures in both healthy individuals and those diagnosed with different medical conditions or illnesses, revealing distinct patterns specific to each case. This innovative technology has potential for disease detection in peripheral blood samples, ranging from cancer and Alzheimer's disease to determining the gender of the gestational product at an early stage.

The conformational phase diagram of charged polymers in the presence of attractive bridging crowders

Using extensive molecular dynamics simulations, we obtain the conformational phase diagram of a charged polymer in the presence of oppositely charged counterions and neutral attractive crowders for monovalent, divalent, and trivalent counterion valencies. We demonstrate that the charged polymer can exist in three phases: (1) an extended phase for low charge densities and weak polymer-crowder attractive interactions [Charged Extended (CE)]; (2) a collapsed phase for high charge densities and weak polymer-crowder attractive interactions, primarily driven by counterion condensation [Charged Collapsed due to Intra-polymer interactions [(CCI)]; and (3) a collapsed phase for strong polymer-crowder attractive interactions, irrespective of the charge density, driven by crowders acting as bridges or cross-links [Charged Collapsed due to Bridging interactions [(CCB)]. Importantly, simulations reveal that the interaction with crowders can induce collapse, despite the presence of strong repulsive electrostatic interactions, and can replace condensed counterions to facilitate a direct transition from the CCI and CE phases to the CCB phase.

Effects of Microfluidic Shear on the Plasmid DNA Structure: Implications for Polymeric Gene Delivery Vectors

Microfluidic manufacturing of advanced gene delivery vectors necessitates consideration of the effects of microfluidic shear forces on the structural integrity of plasmid DNA (pDNA). In this paper, we expose pDNA to variable shear forces in a two-phase, gas-liquid microfluidic reactor and apply gel electrophoresis to analyze the products of on-chip shear-induced degradation. The effects of shear rate, solvent environment, pDNA size, and copolymer complexation on shear-induced degradation are investigated. We find that small naked pDNA (pUC18, 2.7 kb) exhibits shear rate-dependent shear degradation in the microfluidic channels in a mixed organic solvent (dioxane/water/acetic acid; 90/10/<0.1 w/w/w), with the extents of both supercoil isoform relaxation and complete fragmentation increasing as the maximum shear rates increase from 4 × 105 to 2 × 106 s-1. However, over the same range of shear rates, the same pDNA sample shows no evidence of microfluidic shear-induced degradation in a pure aqueous environment. Quiescent control experiments in the same mixed organic solvent prove that a combination of solvent and shear forces is involved in the observed shear-induced degradation. Furthermore, we show that shear degradation effects in mixed organic solvents can be significantly attenuated by complexation of pDNA with the block copolymer polycaprolactone-block-poly(2-vinylpyridine) prior to exposure to microfluidic shear. Finally, we demonstrate that medium (pDSK519, 8.1 kb) and large (pRK290, 20 kb) naked pDNA are more sensitive to shear-induced microfluidic degradation in the mixed organic solvent environment than small pDNA, with both plasmids showing complete fragmentation even at the lowest shear rate, although we found no evidence of shear-induced damage in water for the largest investigated naked pDNA even at the highest flow rate. The resulting understanding of the interplay of the solvent and shear effects during microfluidic processing should inform microfluidic manufacturing routes to new gene therapy formulations.

Exploring the Structural Diversity of DNA Bottlebrush Polymers Using an Oligonucleotide Macromonomer Approach

Herein, we demonstrate that macromonomers consisting of organics-soluble, chemically protected oligonucleotides (protDNA) and poly(ethylene glycol) (PEG) chains can be converted into bottlebrush polymers of distinct architectures via ring-opening metathesis polymerization (ROMP). Using a custom norbornene-containing phosphoramidite, two types of macromonomers were obtained: a linear norbornene-protDNA-PEG structure and a Y-shaped structure where the polymerizable norbornene group is situated at the junction where protDNA and PEG meet. With this strategy, the PEG chains can be placed either near the backbone of the bottlebrush or on its periphery, and in principle anywhere between these two extremes by adjusting the norbornene location, which makes this strategy attractive for constructing architecturally sophisticated oligonucleotide-containing copolymers.

The effect of explicit polarity on the conformational behavior of a single polyelectrolyte chain

In this work using dissipative particle dynamics simulations with explicit treatment of polar species we demonstrate that the molecular nature of dielectric media has a significant impact on swelling and collapse of a polyelectrolyte chain in a dilute solution. We show that the small-scale effects related to the presence of polar species lead to the intensification of the electrostatic interactions when the charges are close to each other and/or their density is high enough. As a result, the electrostatic strength , usually regarded as the main parameter governing the polyelectrolyte chain collapse, does not have a universal meaning: the value of λ at which the coil-to-globule transition occurs is found to be dependent on the specific fixed value of the solvent bulk permittivity ε while varying the monomer unit charge Q and vice versa. This effect is observed even when the backbone and the counterions have the same polarity as the solvent beads, i.e. no dielectric mismatch is present. The reason for such behavior is rationalized in terms of the "effective" dielectric permittivity ε^eff which depends on the volume fraction φ of charged units inside the polymer chain volume; using ε^eff instead of ε collapses all data onto one master curve describing the chain shrinking with λ. Furthermore, it is shown that a polar chain adopts less swollen conformations in the polyelectrolyte regime and collapses more easily compared to a non-polar chain.

Kinetics of charged polymer collapse in poor solvents

Extensive molecular dynamics simulations, using simple charged polymer models, have been employed to probe the collapse kinetics of a single flexible polyelectrolyte (PE) chain under implicit poor solvent conditions. We investigate the role of the charged nature of PE chain (A), valency of counterions (Z) on the kinetics of such PE collapse. Our study shows that the collapse kinetics of charged polymers are significantly different from those of the neutral polymer and that the finite-size scaling behavior of PE collapse times does not follow the Rouse scaling as observed in the case of neutral polymers. The critical exponent for charged PE chains is found to be less than that of neutral polymers and also exhibits dependence on counterion valency. The coarsening of clusters along the PE chain suggests a multi-stage collapse and exhibits opposite behavior of exponents compared to neutral polymers: faster in the early stages and slower in the later stages of collapse.

Synthetic Approaches for Copolymers Containing Nucleic Acids and Analogues: Challenges and Opportunities

A deep integration of nucleic acids with other classes of materials have become the basis of many useful technologies. Among these biohybrids, nucleic acid-containing copolymers has seen rapid development in both chemistry and application. This review focuses on the various synthetic approaches to access nucleic acid-polymer biohybrids spanning post-polymerization conjugation, nucleic acids in polymerization, solid-phase synthesis, and nucleoside/nucleobase-functionalized polymers. We highlight the challenges associated with working with nucleic acids with each approach and the ingenuity of the solutions, with the hope of lowering the entry barrier and inpsiring further investigations in this exciting area.

Study of the polyribosyl-ribitol-phosphate precipitation mechanism by salts and organic solvents

Precipitation has been widely applied to purification and fractionation of biological macromolecules. Several physical-chemical factors contribute to the destabilization of those solutions, such as the nature of solvent employed, presence of salts, temperature, and concentration of the macromolecule. In the case of charged biopolymers, electrostatic forces are the major contributors to their stability in solution. However, the role of each variable and the exact mechanism of precipitation are not completely understood yet. The aim of this work was to study the precipitation of polyribosyl-ribitol-phosphate (PRP, a linear homogeneous anionic biopolymer) in presence of salts and non-solvents, in order to contribute to the elucidation of its precipitation mechanism. The solvents tested (acetone, ethanol, and isopropanol) presented distinct dielectric constants. The salts used (NH₄Cl, NaCl, KCl, MgCl₂, and CaCl₂) differ by their cations. For each salt concentration, the solvent fraction that induces precipitation was identified and the dielectric constant of the bulk solution was calculated. Precipitation always occurred at well-defined combinations of solvents and salts. At low concentration of monovalent salts, there was a linear correlation between the logarithm of the salt concentration and the inverse of the medium dielectric constant at a defined precipitation point. This is a strong indication that the stability of the solution depends almost exclusively on the balance of electrostatic forces. This behavior is compatible with the DLVO modeling of colloidal systems. When divalent salts were used, low concentrations of the counterion were sufficient to induce precipitation, due to a phenomenon called ionic condensation. Apparently, PRP precipitates when around 90% of its charges are neutralized, value that is similar to charge neutralization for DNA precipitation.

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

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

Solvent hydrophobicity induced complex coacervation of dsDNA and in situ formed zein nanoparticles

Zein, a predominantly hydrophobic protein, was sustained as a stable dispersion in ethanol-water (80 : 20, % (v/v)) binary solvent at room temperature (25 °C). Addition of aqueous dsDNA solution (1% (w/v)) to the above dispersion prepared with the protein concentration of C_zein = 0.01-0.5% (w/v) caused a concomitant change in ethanol content from 14-35% (v/v), which in turn generated zein nanoparticles in situ of size 80-120 nm increasing with water content. The subsequent associative interaction between DNA (polyanion; 2000 bps) and the positively charged zein nanoparticles, (at pH = 4) was driven by Coulombic forces, and by the solvent hydrophobicity due to the ethanol content of the binary solvent. Experimentally, two interesting regions of interaction were observed from turbidity, zeta potential, particle sizing, and viscosity data: (i) for C_zein < 0.2% (w/v), zein nanoparticles of size 80 nm bind to dsDNA (primary complex) causing its condensation (apparent hydrodynamic size decreased from ≈2100 to 560 nm), and (ii) for 0.2% < C_zein < 0.5% (w/v) larger nanoparticles (>80 nm) were selectively bound to primary complexes to form partially charge neutralized interpolymer soluble complexes (secondary complexes), followed by complex coacervation. During this process, there was depletion of water in the vicinity of the nucleic acid, which was replaced by hydration provided by the ethanol-water binary solvent. Equilibrium coacervate samples were probed for their microstructure by small angle neutron scattering, and for their viscoelastic properties by rheology. The interplay of solvent hydrophobicity, electrostatic interaction, and zein nanoparticle size dependent charge neutralization had a commensurate effect on this hitherto unexplored coacervation phenomenon.

Model studies of the effects of intracellular crowding on nucleic acid interactions

Molecular interactions and reactions in living cells occur with high concentrations of background molecules and ions. Many research studies have shown that intracellular molecules have characteristics different from those obtained using simple aqueous solutions. To better understand the behavior of biomolecules in intracellular environments, biophysical experiments were conducted under cell-mimicking conditions in a test tube. It has been shown that the molecular environments at the physiological level of macromolecular crowding, spatial confinement, water activity and dielectric constant, have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The experimental approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model experiments used to evaluate the influences of intracellular environment on nucleic acid interactions.

Polymer chain collapse induced by many-body dipole correlations

We present a simple analytical theory of a flexible polymer chain dissolved in a good solvent, carrying permanent freely oriented dipoles on the monomers. We take into account the dipole correlations within the random phase approximation (RPA), as well as a dielectric heterogeneity in the internal polymer volume relative to the bulk solution. We demonstrate that the dipole correlations of monomers can be taken into account as pairwise ones only when the polymer chain is in a coil conformation. In this case the dipole correlations manifest themselves through the Keesom interactions of the permanent dipoles. On the other hand, the dielectric heterogeneity effect (dielectric mismatch effect) leads to the effective interaction between the monomers of the polymeric coil. Both of these effects can be taken into account by renormalizing the second virial coefficient of the monomer-monomer volume interactions. We establish that in the case when the solvent dielectric permittivity exceeds the dielectric permittivity of the polymeric material, the dielectric mismatch effect competes with the dipole attractive interactions, leading to polymer coil expansion. In the opposite case, both the dielectric mismatch effect and the dipole attractive interaction lead to the polymer coil collapse. We analyse the coil-globule transition caused by the dipole correlations of monomers within the many-body theory. We demonstrate that accounting for the dipole correlations higher than the pairwise ones smooths this pure electrostatics driven coil-globule transition of the polymer chain.

Regimes of electrostatic collapse of a highly charged polyelectrolyte in a poor solvent

We perform extensive molecular dynamics simulations of a highly charged, collapsed, flexible polyelectrolyte chain in a poor solvent for the case when the electrostatic interactions, characterized by the reduced Bjerrum length l_B, are strong. We find the existence of several sub-regimes in the dependence of the gyration radius of the chain R_g on l_B characterized by R_g ∼ l. In contrast to a good solvent, the exponent γ for a poor solvent crucially depends on the size and valency of the counterions. To explain the different sub-regimes, we generalize the existing counterion fluctuation theory by including a more complete account of all possible volume interactions in the free energy of the polyelectrolyte chain. We also show that the presence of condensed counterions modifies the effective attraction among the chain monomers and modulates the sign of the second virial coefficient under poor solvent conditions.

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.

Mechanism of Chain Collapse of Strongly Charged Polyelectrolytes

We perform extensive molecular dynamics simulations of a charged polymer in a good solvent in the regime where the chain is collapsed. We analyze the dependence of the gyration radius R_{g} on the reduced Bjerrum length ℓ_{B} and find two different regimes. In the first one, called a weak electrostatic regime, R_{g}∼ℓ_{B}^{-1/2}, which is consistent only with the predictions of the counterion-fluctuation theory. In the second one, called a strong electrostatic regime, we find R_{g}∼ℓ_{B}^{-1/5}. To explain the novel regime we modify the counterion-fluctuation theory.

Lipoplex-Mediated Deintercalation of Doxorubicin from Calf Thymus DNA-Doxorubicin Complex

In this paper, we report the lipoplex-mediated deintercalation of anticancer drug doxorubicin (DOX) from the DOX-DNA complex under controlled experimental conditions. We used three zwitterionic liposomes, namely, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC), which are widely different in their phase transition temperatures to form a lipoplex with calf thymus DNA in the presence of Ca(2+) ions. The study revealed that DPPC being in sol-gel phase was more effective in releasing the drug from the DOX-DNA complex compared with liposomes that remain in liquid crystalline phase (DMPC and POPC). The higher extent of drug release in the case of DPPC liposomes was attributed to the stronger lipoplex formation with DNA as compared with that of other liposomes. Owing to the relatively smaller head group area, the DPPC liposomes in their sol-gel phase can absorb a larger number of Ca(2+) ions and hence offer a strong electrostatic interaction with DNA. This interaction was confirmed by time-resolved anisotropy and circular dichroism spectroscopy. Apart from the electrostatic interaction, the possible hydrophobic interaction between the liposomes and DNA was also taken into account for the observed deintercalation. The successful uptake of drug molecules by liposomes from the drug-DNA complex in the post-release period was also confirmed using confocal laser scanning microscopy (CLSM).

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.

Attractive ion-ion correlation forces and the dielectric approximation

We analyze the classical problem of the interaction between two charged surfaces separated by a solution containing neutralizing counter-ions. The focus is on obtaining a description where the solvent is treated explicitly rather than through a dielectric approximation as is conventionally done. We summarize the results of three papers where we have used a Stockmayer fluid model in Monte Carlo simulations. It is shown that the attractive ion-ion correlation mechanism is also operating when the solvent is described explicitly. There appears an oscillatory component to the force, but when this is accounted for, there is a semi-quantitative agreement between the continuum model and the model with explicit solvent. The properties of the continuum model can be reached in a molecular system by making the solvent molecules much smaller than the ions. It is demonstrated that having an explicit solvent model makes the analysis of force mechanisms more delicate due to the interplay between several different microscopic contributions to the force. Finally, it is argued that the agreement between the forces calculated using the continuum and the explicit solvent models, respectively, has as its basis the circumstance that the force between the surfaces is mainly caused by long-range ion-ion interactions, for which the dielectric approximation is most adequate. This argument applies equally well to an aqueous system as to the Stockmayer fluid.

The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents

Organic solvents and apolar media are used in the studies of nucleic acids to modify the conformation and function of nucleic acids, to improve solubility of hydrophobic ligands, to construct molecular scaffolds for organic synthesis, and to study molecular crowding effects. Understanding how organic solvents affect nucleic acid interactions and identifying the factors that dominate solvent effects are important for the creation of oligonucleotide-based technologies. This review describes the structural and catalytic properties of DNA and RNA oligonucleotides in organic solutions and in aqueous solutions with organic cosolvents. There are several possible mechanisms underlying the effects of organic solvents on nucleic acid interactions. The reported results emphasize the significance of the osmotic pressure effect and the dielectric constant effect in addition to specific interactions with nucleic acid strands. This review will serve as a guide for the selection of solvent systems based on the purpose of the nucleic acid-based experiments.

A Green Solvent Induced DNA Package

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

Effect of salts, solvents and buffer on miRNA detection using DNA silver nanocluster (DNA/AgNCs) probes

MicroRNAs (miRNAs) are small regulatory RNAs (size ~21 nt to ~25 nt) which regulate a variety of important cellular events in plants, animals and single cell eukaryotes. Especially because of their use in diagnostics of human diseases, efforts have been directed towards the invention of a rapid, simple and sequence selective detection method for miRNAs. Recently, we reported an innovative method for the determination of miRNA levels using the red fluorescent properties of DNA/silver nanoclusters (DNA/AgNCs). Our method is based on monitoring the emission drop of a DNA/AgNCs probe in the presence of its specific target miRNA. Accordingly, the accuracy and efficiency of the method relies on the sensitivity of hybridization between the probe and target. To gain specific and robust hybridization between probe and target, we investigated a range of diverse salts, organic solvents, and buffer to optimize target sensing conditions. Under the newly adjusted conditions, the target sensitivity and the formation of emissive DNA/AgNCs probes were significantly improved. Also, fortification of the Tris-acetate buffer with inorganic salts or organic solvents improved the sensitivity of the DNA/AgNC probes. On the basis of these optimizations, the versatility of the DNA/AgNCs-based miRNA detection method can be expanded.

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.

Dimerization of nucleic acid hairpins in the conditions caused by neutral cosolutes

Characterization of metal ion binding to RNA and DNA base pairs is important for understanding their energy contribution to the folding and conformational changes of nucleic acid structures. In this study, we examine the equilibrium shift from the hairpin toward the dimer formation, induced by nonspecifically bound metal ions. The hairpin dimerization is markedly enhanced in the presence of high background concentrations of poly(ethylene glycol) (PEG) and several small organic molecules. The simple volume exclusion effect and the base pair stability cannot entirely account for this increase. We find that the dielectric constant correlates well with the dimerization efficiency in the conditions caused by small alcohol molecules and amide compounds as well as PEG. The hairpin dimerization experiments reveal the potential of PEG for enhancing the binding affinity between nucleic acids and metal ions, by reducing the solution dielectric constant without decreasing the thermodynamic stability of nucleic acid structures. The results presented here contribute to the understanding of nucleic acid folding and its ability to switch between alternative conformations under the condition of limited cation availability and cellular physiology.

A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

We report a systematic study of the condensation of plasmid DNA by oligocations with variation of the charge, Z, from +3 to +31. The oligocations include a series of synthetic linear ε-oligo(L-lysines), (denoted εKn, n = 3–10, 31; n is the number of lysines with the ligand charge Z = n+1) and branched α-substituted homologues of εK10: εYK10, εLK10 (Z = +11); εRK10, εYRK10 and εLYRK10 (Z = +21). Data were obtained by light scattering, UV absorption monitored precipitation assay and isothermal titration calorimetry in a wide range concentrations of DNA and monovalent salt (KCl, CKCl). The dependence of EC50 (ligand concentration at the midpoint of DNA condensation) on C(KCl) shows the existence of a salt-independent regime at low C(KCl) and a salt-dependent regime with a steep rise of EC50 with increase of C(KCl). Increase of the ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher C(KCl). A novel and simple relationship describing the EC50 dependence on DNA concentration, charge of the ligand and the salt-dependent dissociation constant of the ligand–DNA complex is derived. For the ε-oligolysines εK6–εK10, the experimental dependencies of EC50 on C(KCl) and Z are well-described by an equation with a common set of parameters. Implications from our findings for understanding DNA condensation in chromatin are discussed.

The transition from a molecular to a continuum solvent in electrical double layers showing ion-ion correlation effects

We analyze, using Monte Carlo simulations, how a dielectric medium, modeled as a Stockmayer fluid, modulates the force between two similarly charged surfaces. A major objective is to provide a basis for understanding the strengths and weaknesses of the primitive model. The system studied has uniformly charged walls separated by counterions and solvent, where the latter is kept at constant chemical potential as the separation between the walls is varied. For two different types of Stockmayer fluids, one with a "low" (ε(r) ≃ 4.4) and one with a "high" (ε(r) ≃ 20) relative dielectric permittivity, the size of the solvent molecules is varied systematically. As the size of the solvent molecules becomes smaller one approaches the continuum limit, where the primitive model should give an increasingly more accurate representation. We find that having an explicit description of the solvent gives rise to an oscillatory component in the force between the surfaces. The wavelength of the oscillations reflects the diameter of the solvent molecules. The smaller the solvent molecules the smaller are the amplitudes of the oscillations. On integrating the force curves to yield interaction free energies the oscillatory features become less apparent. For the smallest solvent size studied the interaction curves show clear similarities with those obtained from the primitive model. The qualitative effect of the dielectric screening is recovered. It is found that the deviations from the mean field description also appear for the molecular solvent. All this suggests that there are no major deviations due to the neglect of many-body contributions in the solvent-averaged potential of the primitive model. This also holds for the incompressibility assumption implicitly applied when using the primitive model.

Kinetic study on the reentrant condensation of oligonucleotide in trivalent salt solution

The reentrant condensation of 21-bp oligonucleotide in the presence of spermidine was investigated by laser light scattering and capillary electrophoresis. 21-bp oligonucleotide showed a bimodal distribution in 1 × TE buffer, with the slow mode being the characteristic diffusion of polyelectrolyte in solution without enough salt. At the fixed spermidine concentration, the reentry of oligonucleotide underwent aggregation, phase separation, and disassociation in sequence with time, and the kinetics was extremely slow. For example, it took more than 1200 h (50 days) for the reentry to complete at 21 mM spermidine. Higher spermidine concentration led to faster kinetics. After reentry, the slow mode disappeared, and the charges of oligonucleotide were at least partially neutralized. No prominent charge inversion was observed. The kinetics of oligonucleotide reentry in the presence of spermidine gained insight in the interactions of polyelectrolyte in aqueous solution.

Characterizing DNA condensation and conformational changes in organic solvents

Organic solvents offer a new approach to formulate DNA into novel structures suitable for gene delivery. In this study, we examined the in situ behavior of DNA in N, N-dimethylformamide (DMF) at low concentration via laser light scattering (LLS), TEM, UV absorbance and Zeta potential analysis. Results revealed that, in DMF, a 21bp oligonucleotide remained intact, while calf thymus DNA and supercoiled plasmid DNA were condensed and denatured. During condensation and denaturation, the size was decreased by a factor of 8–10, with calf thymus DNA forming spherical globules while plasmid DNA exhibited a toroid-like conformation. In the condensed state, DNA molecules were still able to release the counterions to be negatively charged, indicating that the condensation was mainly driven by the excluded volume interactions. The condensation induced by DMF was reversible for plasmid DNA but not for calf thymus DNA. When plasmid DNA was removed from DMF and resuspended in an aqueous solution, the DNA was quickly regained a double stranded configuration. These findings provide further insight into the behavior and condensation mechanism of DNA in an organic solvent and may aid in developing more efficient non-viral gene delivery systems.

Determination of equilibrium association constants of ligand-DNA complexes by electrospray mass spectrometry

Electrospray mass spectrometry can be used to detect ligand-DNA noncovalent complexes formed in solution. This chapter describes how to determine equilibrium association constants of the complexes. Particular attention is devoted to describing how to tune an electrospray mass spectrometer using a 12-mer oligodeoxynucleotides duplex in order to perform these experiments. This protocol can then be applied to any nucleic acid structure that can be ionized with electrospray mass spectrometry.