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 PUC13 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 disorder-order transition. The result also indicates that the condensed particles are polymeric, but not randomly aggregative, further proving the toroidal structures are formed in certain regularities.     

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

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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.     

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.     

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.     

用红外光谱法对热固性酚醛树脂固化过程的研究

用红外光谱法研究了四种热固性酚醛树脂在固化过程中的化学变化。结果表明热固性酚醛树脂的固化过程,首先是羟甲基发生缩合反应,缩合反应形成醚键是主要的。热固性酚醛树脂在进一步固化时(150—200°)出现了羰基,它的出现不是亚甲基氧化所致,而是部分醚键断裂形成了醛羰基。对热固性酚醛树脂的固化过程的机理进行了讨论。     

TS-1分子筛骨架钛原子引入过程的研究

采用廉价的四丙基溴化铵（ＴＰＡＢｒ）为模板剂合成了ＴＳ１分子筛．在晶化过程中,运用ＸＲＤ,ＩＣＰ,ＩＲ,２９ＳｉＭＡＳＮＭＲ和ＵＶＶｉｓ光谱等表征手段,系统地研究了钛原子引入分子筛骨架的机制,观察到钛原子随分子筛的形成同步进入骨架的规律．另外,尽管在晶化初期固相中没有ＴｉＯ２结晶出现,但存在分散态的ＴｉＯｘ物种．随晶化时间的延长,液相中钛物种之间聚合的几率增加,使固相中ＴｉＯ２晶体不断形成．     

SYNTHESIS OF ETHYL PYRROLE-2-CARBOXYLATES: A REGIOSELECTIVE CYCLIZATION OF ENAMINONES UNDER KNORR-TYPE CONDITIONS

ABSTRACT

A regioselective formation of ethyl pyrrole-2-carboxylates 4 and 5 is effected by reductive condensation of enaminones 1a–f and ethyl 2-oximinoacetoacetate 2. The structures of the products have been delineated by spectroscopic methods.     

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.     

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。     

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.     

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.     

Polymer-monovalent salt-induced DNA compaction studied via single-molecule microfluidic trapping

Polymer-monovalent salt-induced single-molecule DNA compaction/condensation in a microfluidic stagnation point flow was studied by analyzing both DNA compaction images and time trajectories. For the whole DNA compaction process we observed three successive steps: Step I, a relaxation process of the stretched DNA that occurs slowly along the whole DNA chain, Step II, nucleus formation and growth, and Step III, corresponding to a rapid compaction of the chain. A memory effect was observed between Steps I and III, and a new (intruder-induced) nucleation mode was observed for the first time. This study extends the use of the microfluidic stagnation point flow, which we have previously used for sequence detection and to measure enzyme kinetics site-specifically.     

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.     

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.     

Structural investigations on the hydrolysis and condensation behavior of pure and chemically modified alkoxides. 2. Germanium alkoxides

Structural investigations on the hydrolysis and condensation behavior of germanium alkoxides were for the first time performed by means of X-ray absorption fine structure and Raman spectroscopy. The studies reveal that germanium alkoxides are monomeric in nature and undergo very fast hydrolysis and condensation reactions upon water addition. However, the chelation of germanium alkoxides by acetylacetone does not take place even 48 h after mixing, and any change in hydrolysis and condensation behavior is not observed after acetylacetone addition. When mixed with prehydrolyzed silicon alkoxide, the structures of germanium alkoxides are not modified. Both Si and Ge precursors are insensitive to the presence of each other in the reaction solution even after 48 h of aging. The addition of water to this mixture catalyzes the hydrolysis and condensation reactions very fast and leads to the formation of Ge-O-Ge (and consequently Si-O-Si) homocondensation products.     

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.     

ROLE OF COMPLEX FORMATION IN THE PHOTOSENSITIZED DEGRADATION OF DNA INDUCED BY N'-FORMYLKYNURENINE

Abstract— N'-Formylkynurenine derivatives efficiently bind to DNA or polynucleotides. Homopolynucleotides and DNA display marked differences in the binding process. Association constants are derived which indicate that the oxidized indole ring is more strongly bound to DNA than the unoxidized one. Irradiation of such complexes with wavelengths greater than 320 nm induces pyrimidine dimer formation as well as DNA chain breaks. Complex formation is shown to play an important role in these photosensitized reactions.
The photodynamic action of N'-formylkynurenine on DNA constituents is negligible at neutral pH but guanine and xanthine derivatives are sensitizable at higher pH. Thymine dimer splitting can occur in aggregated frozen aqueous solutions of N'-formylkynurenine and thymine dimer but this photosensitized splitting is negligible in liquid solutions at room temperature.     

INTERNALIZATION OF GAP JUNCTIONS BETWEEN NEURON AND GLIAL CELL AND FORMATION OF ANNULAR LAMELLAR BODIES IN CHINESE LEECH Whitmania pigra

This paper reveals the formation of annular lamellar body (ALB) in the ganglion of leech by means of in situ fixation and the lanthanum nitrate tracer technique. This formation involves both wrapping and internalization of the gap junctions between glial processes themselves, as well as between neuron and glial process. The results indicate that there is probably an active process of internalization of membrane structures involving gap junctions between neuron and glial cell in the central nervous system in leech. The functions of ALB are discussed.