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.     

Emergence of multiple tori structures in a single polyelectrolyte chain

We investigated the collapsed structure of a weakly charged wormlike chain under a moderate concentration of 1:1 electrolyte solution. By assuming a torus as a grand state, we found that the size of a torus is determined by the balance between surface energy and electrostatic energy, which leads to a finite torus thickness almost independent of the chain contour length. Owing to this unique characteristic, a long charged wormlike chain forms multiple tori structure as a collapsed product, which is never seen with a neutral wormlike chain. These features were confirmed by a Monte Carlo simulation.     

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

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

Butterfly structure: signature of vibrational flopping in dissociative acetylene

We report experimental evidence for molecular deformation due to a vibrationally active transition state of multiply charged acetylene molecules under the impact of low energy Ar8+ projectiles. "Butterflylike" structures are observed in the experimental coincidence spectra between hydrogen and carbon ionic fragments. Such structures can be generated by numerical simulations and are found to originate from the bending motion of the dissociating molecule. Angular distributions for dissociation products from triply charged C2H2 ion are reported.     

Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

Electric and hydrodynamic stretching of DNA-polymer conjugates in free-solution electrophoresis

The conjugation of an uncharged polymer to DNA fragments makes it possible to separate DNA by free-solution electrophoresis. This end-labeled free-solution electrophoresis method has been shown to successfully separate ssDNA with single monomer resolution up to about 110 bases. It is the aim of this paper to investigate in more detail the coupled hydrodynamic and electrophoretic deformation of the ssDNA-label conjugate at fields below 400 V/cm. Our model is an extension of the theoretical approach originally developed by Stigter and Bustamante [Biophys. J. 75, 1197 (1998)] to investigate the problems of a tethered chain stretching in a hydrodynamic flow and of the electrophoretic stretch of a tethered polyelectrolyte. These two separate models are now used together since the charged DNA is "tethered" to the uncharged polymer (and vice versa), and the resulting self-consistent model is used to predict the deformation and the electrophoretic velocity for the hybrid molecule. Our theoretical and experimental results are in good qualitative agreement.     

On/off switching on polymer conformation

The manner of folding transition from elongated coil to compact globule of single polymer chain is discussed. Based on theoretical consideration, it is argued the semi-flexible polymer chain exhibits large discrete transition on the level of individual single chains, whereas the transition looks continuous, or cooperative, on the ensemble of chains. As the experimental verification, in the present article thermodynamic and kinetic aspects of folding transition of single giant DNA molecules are described. It is shown that rich variety of nano-ordered structures are obtained from single DNA molecules through suitable setup of the experimental conditions. The stability of such nano-structures generated from single polymer chain is discussed in relation to the ordered compact structure with large number of chains in semi-dilute and concentrated polymer solutions.     

Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution

We probe the urea-denaturation mechanism using molecular dynamics simulations of an elementary "folding" event, namely, the formation of end-to-end contact in the linear hydrocarbon chain (HC) CH(3)(CH(2))(18)CH(3). Electrostatic effects are examined using a model HC in which one end of the chain is positively charged (+0.2e) and the other contains a negative charge (-0.2e). For these systems multiple transitions between "folded" (conformations in which the chain ends are in contact) and "unfolded" (end-to-end contact is broken) can be observed during 4 ns molecular dynamics simulations. In water and 6 M aqueous urea solution HC and the charged HC fluctuate between collapsed globular conformations and a set of expanded structures. The collapsed conformation adopted by the HC in water is slightly destablized in 6 M urea. In contrast, the end-to-end contact is disrupted in the charged HC only in aqueous urea solution. Despite the presence of a large hydrophobic patch, on length scales on the order of approximately 8-10 A "denaturation" (transition to the expanded unfolded state) occurs by a direct interaction of urea with charges on the chain ends. The contiguous patch of hydrophobic moieties leads to "mild dewetting", which becomes more pronounced in the charged HC in 6 M aqueous urea solution. Our simulations establish that the urea denaturation mechanism is most likely electrostatic in origin.     

Feeling Inter‐ or Intramolecular Interactions with the Polymer Chain as Probe: Recent Progress in SMFS Studies on Macromolecular Interactions

Single‐molecule force spectroscopy (SMFS) opens new avenues for elucidating the structures and functions of large coiled molecules such as synthetic and biopolymers at the single‐molecule level. In addition, some of the features in the force–extension curves (i.e. force spectra) are closely related to primary/secondary structures of the molecules being stretched. For example, the long force plateau in the DNA stretching curve is related to the double‐helix structure. These features can be regarded as the force fingerprints of individual macromolecules. These force fingerprints can therefore be used as indicators/criteria of single‐molecule manipulation during the measurement of some unknown intra‐ or intermolecular interactions. By comparing the force spectra of a single polymer chain before and after interaction with other molecules, the mode/strength of such molecular interactions can be derived. This Review focuses on recent advances in AFM‐based SMFS studies on molecular interactions in both synthetic and biopolymer systems using a single macromolecular chain as probe, including interactions between nucleic acids and proteins, mechanochemistry of covalent bonds, conformation‐regulated enzymatic reactions, adsorption and desorption of biopolymers on a flat surface or from the nanopore of a carbon nanotube, and polymer interactions in the condensed state.     

UV degradation of deoxyribonucleic acid

The effects of UV synchrotron radiation on deoxyribonucleic acid (DNA) cast films have been systematically investigated by vacuum ultraviolet and infrared spectrophotometry as a function of irradiation time. Cast DNA films exposed at 140 nm (8.85 eV) for different irradiation times, revealed consistent changes in their VUV spectra which indicate a decrease of thymine groups and an increase of π → π* transition spectral signature associated with the CO group of the open sugar chain. This result was corroborated by a decrease in CO stretching vibration at 1061 cm⁻¹ observed in the infrared spectra. Both these results are consistent with the creation of single strand breaks in the deoxyribose component of DNA molecule and a decrease in the phosphate groups. It was also shown that UV radiation is effective in damaging the thymine groups involved in Hoogsteen base pairing with adenine. The analysis of the infrared data suggests that the usual spectroscopic fingerprints of DNA denaturation are not necessarily a reliable measure of DNA damage.     

Controlling the intrachain segregation on a single DNA molecule

Intrachain segregation in single DNA molecules induced by quaternary ammonium dications was studied. By means of fluorescent and electron microscopy, it was found that variations in the chemical structure of condensing agents provide one with the opportunity to control the average amount of intrachain segregation centers on the DNA single chain. The manner of interaction between the diammonium molecules was considered to be the key factor for controlling the morphology of the partially collapsed DNA molecules.     

Effect of Turbulent Flow on Coil‐Globule Transition of λ‐DNA

Summary: The addition of spermidine (SPD) into turbulent flow as a condensing agent showed the abrupt change of turbulent drag reducing (DR) efficiency of λ‐DNA in turbulent flow for the first time. The resultant asymptote DR efficiency explains the origin of those changes, which can be conclusively verified via the electrophoresis experiment. Despite the different fluid conditions, with and without condensing agent, all λ‐DNA molecules possessed the same half‐cut dimension, implying that the discrete change of DNA conformation can dramatically alter the flow characteristics.

Coil‐globule transition of DNA by spermidine.     

Mechanistic insight into the structure and dynamics of entangled and hydrated λ-phage DNA

Intrinsic dynamics of DNA plays a crucial role in DNA-protein interactions and has been emphasized as a possible key component for in vivo chromatin organization. We have prepared an entangled DNA microtube above the overlap concentration by exploiting the complementary cohesive ends of λ-phage DNA, which is confirmed by atomic force microscopy and agarose gel electrophoresis. Photon correlation spectroscopy further confirmed that the entangled solutions are found to exhibit the classical hydrodynamics of a single chain segment on length scales smaller than the hydrodynamic length scale of single λ-phage DNA molecule. We also observed that in 41.6% (gm water/gm DNA) hydrated state, λ-phage DNA exhibits a dynamic transition temperature (T(dt)) at 187 K and a crossover temperature (T(c)) at 246 K. Computational insight reveals that the observed structure and dynamics of entangled λ-phage DNA are distinctively different from the behavior of the corresponding unentangled DNA with open cohesive ends, which is reminiscent with our experimental observation.     

Folding transition of a single semiflexible polyelectrolyte chain through toroidal bundling of loop structures

We consider how the DNA coil-globule transition progresses via the formation of a toroidal ring structure. We formulate a theoretical model of this transition as a phenomenon in which an unstable single loop generated as a result of thermal fluctuation is stabilized through association with other loops along a polyelectrolyte chain. An essential property of the chain under consideration is that it follows a wormlike chain model. A toroidal bundle of loop structures is characterized by a radius and a winding number. The statistical properties of such a chain are discussed in terms of the free energy as a function of the fraction of unfolded segments. We also present an actual experimental observation of the coil-globule transition of single giant DNA molecules, T4 DNA (165.5 kbp), with spermidine (3+), where intrachain phase segregation appears at a NaCl concentration of more than 10 mM. Both the theory and experiments lead to two important points. First, the transition from a partially folded state to a completely folded state has the characteristics of a continuous transition, while the transition from an unfolded state to a folded state has the characteristics of a first-order phase transition. Second, the appearance of a partially folded structure requires a folded structure to be less densely packed than in the fully folded compact state.     

Stoichiometric polyelectrolyte complexes as comb copolymers

The collapse behavior of a single comblike copolymer chain has been studied by Monte Carlo simulations. It has been supposed that the solvent is good for the side chains but the solvent quality for the backbone chain changes. It has been shown that depending on the structural parameters of the comb copolymer (the lengths of the backbone and side chains, grafting density of the side chains) various thermodynamically stable morphologies of the collapsed backbone chain can be realized. In addition to ordinary spherical globule we have observed elongated structures as well as necklace-like conformations. The proposed model can be used to describe conformational behavior of stoichiometric complexes between block copolymers with a polyelectrolyte short block and oppositely charged linear homopolymers.     

Rolling circle enzymatic replication of a complex multi-crossover DNA nanostructure

Nature has evolved replicable biological molecules, such as DNA, as genetic information carriers. The replication process is tightly controlled by complicated cellular machinery. It is interesting to ask if artificial DNA nano-objects with a complex secondary structure can be replicated in the same way as simple DNA double helices. Here we demonstrate that paranemic crossover DNA, a structurally complicated multi-crossover DNA molecule, can be replicated successfully using Rolling Circle Amplification (RCA). The amplification efficiency is moderate with high fidelity, confirmed by native PAGE, thermal transition study, and Ferguson analysis. The structural details of the DNA structure after the full replication circle are verified by hydroxyl radical autofootprinting. We conclude that RCA can serve as a reliable method to replicate complex DNA structures. We also discuss the possibility of using viruses and bacteria to clone artificial DNA nano-objects. The findings that single stranded paranemic crossover DNA molecules can be replicated by DNA polymerase will not only be useful in nanotechnology but also may have implications for the possible existence of such complicated DNA structures in nature.     

DNA and surfactants in bulk and at interfaces

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

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

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

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

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

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

MORPHOLOGY EVOLUTION IN PTFE AS A FUNCTION OF MELT TIME AND TEMPERATURE Ⅰ. HIGH MOLECULAR WEIGHT SINGLE- AND MULTI-MOLECULE FOLDED CHAIN SINGLE CRYSTALS AND BAND STRUCTURES

The effect of sintering dispersed dispersion and nano-emulsion particles of high molecular weight polytetrafluoroethylene (PTFE) on a substrate as a function of "melt" time and temperature is described. Folded chain single crystals parallel to the substrate and as ribbons on-edge (with double striations), as well as bands, are produced for longer sintering times; particle merger and diffusion of individual molecules, crystallizing as folded chain, single (or few) molecule,single crystals when "trapped" on the substrate by cooling occur for shorter sintering times. It is suggested the observed structures develop with sintering time, in a mesomorphic melt. The structure of the nascent particles is also discussed.     

Rings-on-a-string chain structure in DNA

Using fluorescence microscopy (FM), which permits the observation of single molecules, we found that a pearling structure is generated on a single long DNA molecule upon the addition of a gemini (dimeric) surfactant. This pearling structure was further investigated by performing atomic force microscopy measurements on the same DNA molecules as observed by FM. These observations revealed that the pearling structure is composed of many rings that are interconnected by elongated coil parts along a single DNA molecule, i.e., rings-on-a-string structure. The mechanism of the formation of such an intrachain segregated structure in terms of microphase separation on a single polyelectrolyte chain is discussed.