FORMATION STUDY OF TOROIDAL CONDENSATION OF DNA

A detailed study of the formation of toroidal condensation produced from the 2700 base pair fragments of plasmid PUCI3 DNA, induced by metal ions, is introduced. We have extracted several typical intermediate structures based on investigation by electron microscopy, and compared their size distributions. The observations suggest that the formation process of DNA condensation is the process of folding and arranging DNA chains and that of disorderorder transition. The result also indicates that the condensed particles are polymeric, but not randomly aggregative, further proving thetoroidal structures are formed in certain regularities.     

Atomic force microscopy observation of the condensates of the spermidine-DNA complexes

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Helical Toroids Self-Assembled from a Binary System of Polypeptide Homopolymer and its Block Copolymer

Toroids and helices are fundamental geometrical structures in nature. Polymers can self-assemble into various nanostructures, including both toroids and helices; however, nanostructures combining toroidal and helical morphologies (that is, helical toroids) are rarely observed. A binary system is reported containing polypeptide homopolymer and its block copolymer, which can hierarchically self-assemble into uniform helical nanotoroids in solution. The formation of the helical toroids is a successive two-step process. First, the homopolymers aggregate into fibrils and convolve into toroids, thereby resembling the toroidal condensation of deoxyribonucleic acid (DNA) chains. Second, the block copolymers self-assemble on the homopolymer toroids and result in helical surface patterns. Additionally, the chirality of the surface helical patterns can be varied by the chirality of the polypeptide block copolymers.     

Helical Toroids Self‐Assembled from a Binary System of Polypeptide Homopolymer and its Block Copolymer

Toroids and helices are fundamental geometrical structures in nature. Polymers can self‐assemble into various nanostructures, including both toroids and helices; however, nanostructures combining toroidal and helical morphologies (that is, helical toroids) are rarely observed. A binary system is reported containing polypeptide homopolymer and its block copolymer, which can hierarchically self‐assemble into uniform helical nanotoroids in solution. The formation of the helical toroids is a successive two‐step process. First, the homopolymers aggregate into fibrils and convolve into toroids, thereby resembling the toroidal condensation of deoxyribonucleic acid (DNA) chains. Second, the block copolymers self‐assemble on the homopolymer toroids and result in helical surface patterns. Additionally, the chirality of the surface helical patterns can be varied by the chirality of the polypeptide block copolymers.     

Tailor-made poly(amidoamine)s for controlled complexation and condensation of DNA

A set of polymer carriers for DNA delivery was synthesized by combining monodisperse, sequence-defined poly(amidoamine) (PAA) segments with poly(ethylene oxide) (PEO) blocks. The precise definition of the PAA segments provides the possibility of correlating the chemical structure (monomer sequence) with the resulting biological properties. Three different PAA-PEO conjugates were synthesized by solid-phase supported synthesis, and the cationic nature of the PAA segments was systematically varied. This allows for the tailoring of interactions with double-stranded plasmid DNA (dsDNA). The potential of the PAA-PEO conjugates as non-viral vectors for gene delivery is demonstrated by investigating the dsDNA complexation and condensation properties. Depending on the applied carrier, a transition in polyplex (polymer-DNA ion complex) structures is observed. This reaches from extended ring-like structures to highly compact toroidal structures, where supercoiling of the DNA is induced. An aggregation model is proposed that is based on structural investigations of the polyplexes with atomic force microscopy (AFM) and dynamic light scattering (DLS). While the cationic PAA segment mediates primarily the contact of the carrier to the dsDNA, the PEO block stabilizes the polyplex and generates a "stealth" aggregate, as was suggested by Zeta potentials that were close to zero. The controlled aggregation leads to stable, single-plasmid complexes, and stabilizes the DNA structure itself. This is shown by ethidium bromide intercalation assays and DNase digestion assays. The presented PAA-PEO systems allow for the formation of well-defined single-plasmid polyplexes, preventing hard DNA compression and strongly polydisperse polyplexes. Moreover carrier polymers and the resulting polyplexes exhibit no cytotoxicity, as was shown by viability tests; this makes the carriers potentially suitable for in vivo delivery applications.     

Langevin dynamics of semiflexible polyelectrolytes: rod-toroid-globule-coil structures and counterion distribution

We have investigated the nature of counterion condensation on uniformly charged semiflexible polyelectrolyte chains and the concomitant configurations by monitoring the role of chain stiffness, chain length, counterion valency, and the strength of electrostatic interaction. The counterion condensation is seen to follow the adsorption process and the effective polymer charge increases with chain stiffness. Size and shape, as calculated through the radius of gyration, effective persistence length, and hydrodynamic radius, are studied. Stable coil-like, globular, folded-chain, toroidal, and rodlike configurations are possible at suitable combinations of values of chain stiffness, chain length, electrostatic interaction strength, and the valency of counterion. For high strengths of electrostatic interactions, sufficiently stiff polyelectrolytes form toroids in the presence of multivalent counterions, whereas flexible polyelectrolytes form disordered globules. The kinetic features of the nucleation and growth of toroids are monitored. Several metastable structures are found to frustrate the formation of toroids. The generic pathway involves the nucleation of one primary loop somewhere along the chain contour, followed by a growth process where the rest of the chain is folded continuously on top of the primary loop. The dependence of the average radii of toroids on the chain length is found to be roughly linear, in disagreement with existing scaling arguments.     

Low-energy states of a semiflexible polymer chain with attraction and the whip-toroid transitions

We establish a general model for the whip-toroid transitions of a semiflexible homopolymer chain using the path integral method and the O3 nonlinear sigma model on a line segment with the local inextensibility constraint. We exactly solve the energy levels of classical solutions and show that some of its classical configurations exhibit toroidal forms, and the system has phase transitions from a whip to toroidal states with a conformation parameter c = (W2l)(L2pi)2. We also discuss the stability of the toroid states and propose the low-energy effective Green's function. Finally, with the finite size effect on the toroid states, predicted toroidal properties are successfully compared to experimental results of DNA condensation.     

Dissipative particle dynamics simulations of toroidal structure formations of amphiphilic triblock copolymers

In this paper, the dynamic assembly of toroidal micelle structures of amphiphilic triblock copolymers in dilute solution has been investigated using dissipative particle dynamics simulations. The amphiphilic molecule is represented by a coarse-grained model, which contains hydrophilic and hydrophobic particles. Some microstructures of complex morphology having toroidal micelles have been observed in the simulations; the toroidal micelle formation is in accordance with the theoretical prediction of the toroidal structure in cylindrical micelle suspensions by Pochan et al. (Science 2004, 306, 94). These findings are very interesting, and these complex morphologies enrich our knowledge of the potential products obtained from the self-assembly of block copolymers.     

DNA liquid crystalline blue phases. Electron microscopy evidence and biological implications

The isotropic-liquid crystalline transition of concentrated DNA solutions is investigated using freeze-fracture electron microscopy in order to understand the first steps of the DNA condensation process. Between the isotropic liquid and the cholesteric mesophase, we report the existence of double twist DNA bundles and describe their long range ordering into 3D networks. This organization corresponds to the formation of 'blue phases' already observed in thermotropic liquid crystals, but never reported in lyotropic systems. In addition, the size of the DNA molecule, about ten times that of most thermotropic materials, allows here the molecular resolution imaging of blue phase structures. Since such structures recall chromatin organization of some Procaryotes and lower Eucaryotes, we suspect that they may be widespread and of potential interest in the regulation of chromatin functions.     

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.     

DNA condensation induced by a cationic polymer studied by atomic force microscopy and electrophoresis assay

We synthesized a cationic polymer, poly(PEGMA)-4N, which has brush-like chains and four positively charged amino groups at the end of the molecules. DNA condensation induced by poly(PEGMA)-4N was investigated through electrophoresis assay by its ability to retard DNA mobility and to inhibit HindIII enzyme cleavage. The detailed structures of DNA condensates induced by poly(PEGMA)-4N were observed through atomic force microscopy (AFM). Interactions between polymers and DNA are mainly attributed into depletion effect and electrostatic interaction. Positively charged amino groups in poly(PEGMA)-4N interact with DNA through electrostatic interaction, and depletion effect also takes effect because poly(PEGMA)-4N is a flexible polymer. Comparing the contributions that the two interactions gave in DNA condensation process, we found that depletion effect played a major role compared with electrostatic interaction.     

Cornucopian cylindrical aggregate morphologies from self-assembly of amphiphilic triblock copolymer in selective media

We have investigated, both experimentally and theoretically, the aggregation of ABA amphiphilic triblock copolymers in dilute solution. We observed a number of complex architectures having toroidal and network structures, including some novel ones. The computational analyses of these systems offer some insight into the origins of the self-assembly of these amphiphiles. The results we obtained using real-space self-consistent field theory reveal that the formation of network and toroidal structures from the block copolymers occurs as the result of the breaking of "inhomogeneous vesicles"; the observed polymorphism results from the existence of multiple metastable states.     

Visualization of complexes of Hoechst 33258 and DNA duplexes in solution by atomic force microscopy

Tertiary structure changes in DNA duplexes, induced by Hoechst 33258 binding, have been examined by the use of atomic force microscopy. Besides minor groove binding, which is an established mode of binding for this drug, Hoechst 33258 has now been found to show another binding mode, which causes an unwinding of the duplex. When the drug concentration is as high as 0.5 microg/ml, the Hoechst 33258 molecule seems to function as a clamp for two DNA chains and forms a condensate. The condensate was found to have a toroidal shape. By surveying more than 100 microscopic images of such condensates formed in I microg/ml drug solution, a mechanism of toroidal condensate formation has been proposed.     

Block copolymers confined in a nanopore: pathfinding in a curving and frustrating flatland

We have studied structure formation in a confined block copolymer melt by means of dynamic density functional theory. The confinement is two dimensional, and the confined geometry is that of a cylindrical nanopore. Although the results of this study are general, our coarse-grained molecular model is inspired by an experimental lamella-forming polysterene-polybutadiene diblock copolymer system [K. Shin et al., Science 306, 76 (2004)], in which an exotic toroidal structure was observed upon confinement in alumina nanopores. Our computational study shows that a zoo of exotic structures can be formed, although the majority, including the catenoid, helix, and double helix that were also found in Monte Carlo nanopore studies, are metastable states. We introduce a general classification scheme and consider the role of kinetics and elongational pressure on stability and formation pathway of both equilibrium and metastable structures in detail. We find that helicity and threefold connections mediate structural transitions on a larger scale. Moreover, by matching the remaining parameter in our mesoscopic method, the Flory-Huggins parameter chi, to the experimental system, we obtain a structure that resembles the experimental toroidal structure in great detail. Here, the most important factor seems to be the roughness of the pore, i.e., small variations of the pore radius on a scale that is larger than the characteristic size in the system.     

DNA体外缩合的研究进展

DNA缩合不仅是自然界常见的生理现象,也是非病毒载体介导基因转染的关键步骤。了解DNA体外缩合的性质与特征,将有助于设计出高效的非病毒转基因载体。本文综述了近十几年来以多价阳离子为缩合剂诱发的DNA体外缩合的研究进展,着重介绍了缩合的机理、过程、影响缩合的因素以及应用于转基因的最新成果。     

Kinetics and Mechanism of the Condensation of Pyridoxal with Amino Acids

The kinetics and mechanism of the condensation of amino acids with pyridoxal were studied in relation to the amino acid structure, solvent, pH, and temperature. A spectrophotometric study revealed several kinetically discernible reaction steps. The condensation rate as a function of pH passes through a maximum, which is caused by formation of two intermediates of different structures. The final products of the condensation and subsequent hydrolysis are pyridoxamine and α-keto acids. The reaction mechanism was suggested.     

MgCl2 Enhances Cluster Formation by Nanoscale Toroidal DNA Condensates

Multivalent cations can cause DNA to condense from its extended state in solution into high-density toroid-shaped particles. Developing methods to control the size and size distribution of DNA toroids is an important goal for the development of artificial gene delivery systems. Here we demonstrate that changes in salt conditions, prior to condensation by multivalent cations, can significantly affect DNA condensation. Specifically, millimolar concentrations of MgCl₂ are shown to cause the formation of toroid clusters, whereas NaCl at the same ionic strength does not.     

Construction and DNA Condensation of Cyclodextrin‐Coated Gold Nanoparticles with Anthryl Grafts

The condensation of DNA in a controlled manner is one of the key steps in gene delivery and gene therapy. For this purpose, a water‐soluble supramolecular nanostructure is constructed by coating 14 β‐cyclodextrins onto the surface of a gold nanoparticle, followed by the noncovalent association of different amounts of anthryl‐modified adamantanes with coated β‐cyclodextrins. The strong binding of β‐cyclodextrins with anthryl adamantanes (K_S=8.61×10⁴ M ^?1) efficiently stabilizes the supramolecular nanostructure. Spectrophotometric fluorescence spectra and microscopic studies demonstrated that, with many anthryl grafts that can intercalate in the outer space of the DNA double helix, this supramolecular nanostructure showed good condensation abilities to calf thymus DNA. Significantly, the condensation efficiency of supramolecular nanostructure towards DNA could be conveniently controlled by adjusting the ratio between gold nanoparticles and anthryl adamantane grafts, leading to the formation of DNA condensates of a size that are suitable for the endocytosis of hepatoma cells, which will make it potentially applicable in many fields of medicinal science and biotechnology.     

Photocontrolled Dopamine Polymerization on DNA Origami with Nanometer Resolution

Temporal and spatial control over polydopamine formation on the nanoscale can be achieved by installing an irradiation‐sensitive polymerization system on DNA origami. Precisely distributed G‐quadruplex structures on the DNA template serve as anchors for embedding the photosensitizer protoporphyrin IX, which—upon irradiation with visible light—induces the multistep oxidation of dopamine to polydopamine, producing polymeric structures on designated areas within the origami framework. The photochemical polymerization process allows exclusive control over polydopamine layer formation through the simple on/off switching of the light source. The obtained polymer–DNA hybrid material shows significantly enhanced stability, paving the way for biomedical and chemical applications that are typically not possible owing to the sensitivity of DNA.     

Efficient Oligomerization of Aromatic Amino Acids Induced by Gaps in Four-Helix Bundles of DNA or RNA

The formation of peptides from amino acids is one of the processes associated with life. Because of the dominant role of translation in extant biology, peptide-forming processes that are RNA induced are of particular interest. We have previously reported the formation of phosphoramidate-linked peptido RNAs as the products of spontaneous condensation reactions between ribonucleotides and free amino acids in aqueous solution. We now asked whether four-helix bundle (4HB) DNA or RNA folding motifs with a single- or double-nucleotide gap next to a 5’-phosphate can act as reaction sites for phosphoramidate formation. For glycine, this was found to be the case, whereas phenylalanine and tryptophan showed accelerated formation of peptides without a covalent link to the nucleic acid. Free peptides with up to 11 tryptophan or phenylalanine residues were found in precipitates forming in the presence of gap-containing DNA or RNA 4HBs. Control experiments using motifs with just a nick or primer alone did not have the same effect. Because folded structures with a gap in a double helix are likely products of hybridization of strands formed in statistically controlled oligomerization reactions, our results are interesting in the context of prebiotic scenarios. Independent of a putative role in evolution, our findings suggest that for some aromatic amino acids an RNA-induced pathway for oligomerization exists that does not have a discernable link to translation.