Studies with dithizone--XII. Formation of thiadiazolines by condensation with aldehydes and ketones

The red colour that develops when mineral acids are added to solutions of dithizone (I; 3-mercapto-1,5-diphenylformazan) in certain samples of dioxan is mainly due to the formation of 2-methyl-3-phenyl-5-phenylazo-1,3,4-thiadiazoline (II) derived in part from adventitious traces of 2-methyldioxalane. A purple compound of molecular formula C(13)H(10)N(4)S is also formed from (I) by an independent and slower reaction. The thiadiazoline (II) is readily prepared from (I) and acetaldehyde, but analogous compounds from formaldehyde benzaldehyde, acetone and ethyl methyl ketone are obtained in better yield by starting from diphenylthiocarbazide. Di-p-tolyldithizone gives similar reactions. Reduction of the thiadiazoline (II) [which has spectra very closely resembling those of 1:1 complexes of (I) with arylmercury (II) cations] with ammonium hydrogen sulphide in ethanol yields diphenylthiocarbazide by opening of the hetero-ring and elimination of an alkyl residue from the intermediate 3-alkylmercapto-1,5-diphenylformazan. Other examples of nucleophilic displacements from the formazan group by SH(-) have been investigated.     

Photoreversible DNA condensation using light-responsive surfactants

A means to control DNA compaction with light illumination has been developed using the interaction of DNA with a photoresponsive cationic surfactant. The surfactant undergoes a reversible photoisomerization upon exposure to visible (trans isomer, more hydrophobic) or UV (cis isomer, more hydrophilic) light. As a result, surfactant binding to DNA and the resulting DNA condensation can be tuned with light. Dynamic light scattering (DLS) measurements were used to follow lambda-DNA compaction from the elongated-coil to the compact globular form as a function of surfactant addition and light illumination. The results reveal that compaction occurs at a surfactant-to-DNA base pair ratio of approximately 7 under visible light, while no compaction is observed up to a ratio of 31 under UV light. Upon compaction, the measured diffusion coefficient increases from a value of 0.6 x 10(-8) cm2/s (elongated coil with an end-to-end distance of 1.27 microm) to a value of 1.7 x 10(-8) cm2/s (compact globule with a hydrodynamic radius of 120 nm). Moreover, the light-scattering results demonstrate that the compaction process is completely photoreversible. Fluorescence microscopy with T4-DNA was used to further confirm the light-scattering results, allowing single-molecule detection of the light-controlled coil-to-globule transition. These structural studies were combined with absorbance and fluorescence spectroscopy of crystal violet in order to elucidate the binding mechanism of the photosurfactant to DNA. The results indicate that both electrostatic and hydrophobic forces are important in the compaction process. Finally, a DNA-photosurfactant-water phase diagram was constructed to examine the effects of both DNA and surfactant concentration on DNA compaction. The results reveal that precipitation, which occurs during the latter stages of condensation, can also be reversibly controlled with light illumination. The combined results clearly show the ability to control the interaction between DNA and the complexing agent and, therefore, DNA condensation with light.     

Structural study of DNA condensation induced by novel phosphorylcholine-based copolymers for gene delivery and relevance to DNA protection

Poly[2-(dimethylamino)ethyl methacrylate-b-2-methacryloyloxyethyl phosphorylcholine] (DMA-MPC) is currently under investigation as a new vector candidate for gene therapy. The DMA block has been previously demonstrated to condense DNA effectively. The MPC block contains a phosphorylcholine (PC) headgroup, which can be found naturally in the outside of the cell membrane. This PC-based polymer is extremely hydrophilic and acts as a biocompatible steric stabilizer. In this study, we assess in detail the morphologies of DNA complexes obtained using the diblock copolymer series DMA(x)MPC30 (where the mean degree of polymerization of the MPC block was fixed at 30 and the DMA block length was systematically varied) using transmission electron microscopy (TEM) and liquid atomic force microscopy (AFM). Both techniques indicate more compact complex morphologies (more efficient condensation) as the length of the cationic DMA block increases. However, the detailed morphologies of the DMA(x)MPC30-DNA complexes observed by TEM in vacuo and by AFM in aqueous medium are different. This phenomena is believed to be related to the highly hydrophilic nature of the MPC block. TEM studies revealed that the morphology of the complexes changes from loosely condensed structures to highly condensed rods, toroids, and oval-shaped particles as the DMA moiety increases. In contrast, morphological changes from plectonemic loops to flower-like and rectangular block-like structures, with an increase in highly condensed central regions, are observed by in situ AFM studies. The relative population of each structure is clearly dependent on the polymer molecular composition. Enzymatic degradation assays revealed that only the DMA homopolymer provided effective DNA protection against DNase I degradation, while other highly condensed copolymer complexes, as judged from TEM and gel electrophoresis, only partially protected the DNA. However, AFM images indicated that the same highly condensed complexes have less condensed regions, which we believe to be the initiation sites for enzymatic attack. This indicates that the open structures observed by AFM of the DNA complexation by the DMA(x)MPC30 copolymer series are closer to in vivo morphology when compared to TEM.     

Design and synthesis of catenated rings based on toroidal DNA structures

Strand proximity and self-crossing that occur intrinsically in the relaxed forms of toroidal DNA are utilized unprecedentedly in our investigations for creating catenated DNA rings. In addition, our current studies show that the geometrical shapes of our newly obtained catenated DNA circles as well as their topological arrangements are vividly visible under atomic force microscopic examination.     

Surface-directed and ethanol-induced DNA condensation on mica

The adsorption of lambda-phage DNA onto mica was investigated with atomic force microscopy. We found that the morphologies depended on the solvent conditions in the sample preparation procedure. Flat-lying networks of hybridized single-stranded DNA were obtained if ultrapure water was used. If buffered conditions are maintained during the whole of the preparation procedure, single double-stranded DNA molecules are adsorbed. The adsorbed double-stranded DNA molecules subsequently can be condensed in situ on the surface by a brief rinse with anhydrous ethanol in the presence of divalent magnesium cations. The majority of these surface-directed and ethanol-induced condensed structures are toroids, but a small fraction of rods also has been observed. Analysis of the height and lateral dimensions shows that the toroids are single-molecular and disk-like with a height of one to two DNA diameters. The thin toroid morphology appears to be a general phenomenon of surface-directed condensation, irrespective of the nature of the condensing ligands and the specific surface interaction.     

DNA condensation induced by cationic surfactant: a viscosimetry and dynamic light scattering study

The compaction of DNA induced by two simple amphiphiles, cetyltrimethylammonium bromide [CTAB] and dodecyldimethylamine oxide [DDAO], has been investigated by means of combined viscosity and dynamic light scattering measurements, to demonstrate the formation of soluble DNA/surfactant complexes, undergoing a coil-globule transition, upon the increase of the amphiphile concentration. In both of the two systems investigated, the complexation process reaches a maximum for a value of the surfactant to DNA phosphate groups molar ratio of about X = 1. Below this critical concentration, the coil and the globule state coexist in the solution, as clearly shown by the bimodal size distribution obtained from the light scattering intensity correlation functions. Some suggestions are given to support a molecular mechanism responsible for the complex formation, both in the case of a cationic surfactant (CTAB) and of a pH-dependent neutral or cationic amphiphile (DDAO), where the hydrophobic interactions play an important role.     

Reversible condensation of DNA using a redox-active surfactant

We report characterization of aqueous solutions of dilute Lambda phage DNA containing the redox-active surfactant (11-ferrocenylundecyl)trimethylammonium bromide (FTMA) as a function of the oxidation state of the FTMA. FTMA undergoes a reversible one-electron oxidation from a reduced state that forms micelles in aqueous solution to an oxidized state (containing the ferrocenium cation) that does not self-associate in solution. This investigation sought to test the hypothesis that FTMA can be used to achieve reversible control over the conformation of DNA-surfactant complexes in solution. Whereas DNA adopts extended coil conformations in aqueous solutions, our measurements revealed that addition of reduced FTMA (2-5 microM) to aqueous solutions of DNA (5 microM in nucleotide units) resulted in coexistence of extended coils and compact globules in solution. At higher concentrations of reduced FTMA (up to 30 microM), the DNA was present as compact globules only. In contrast, oxidized FTMA had no measurable effect on the conformation of DNA, allowing DNA to maintain an extended coil state up to a concentration of 75 microM oxidized FTMA. We further demonstrate that it is possible to chemically or electrochemically transform the oxidation state of FTMA in preformed complexes of FTMA and DNA, thus achieving in situ control over the conformations of the DNA in solution. These results provide guidance for the design of surfactant systems that permit active control of DNA-surfactant interactions.     

Formation of columns of anomalous water by condensation in quartz capillaries

It is shown that these columns are formed in the kinetic mode from unsaturated water vapor. The condensation coefficient for an anomalous column is much less than for ordinary water. The growth rate is dependent on the equilibration time for the concentration of the anomalous component in the column. The diffusion coefficient for the anomalous component in water is less than the self-diffusion coefficient of water by nearly an order of magnitude; this and the low volatility are to be ascribed to large molecular size. It is supposed that the molecules of the anomalous component are strong groups of H₂O molecules that are only slowly converted to monomers.     

Formation of a surface covalent organic framework based on polyester condensation

The reaction between 1,3,5-tris(4-hydroxyphenyl)benzene and benzene-1,3,5-tricarbonyl trichloride leads to polyester condensation and formation of a novel COF on an Au(111) surface. The characterization performed in situ by means of variable temperature STM and XPS reveals the formation of an array of hexagonal cavities with ca. 2 nm size.     

Formation,structure and heterocyclization of aminoguanidine and ethyl acetoacetate condensation products

Condensation of aminoguanidine hydrochloride and ethyl acetoacetate results in 2,3-diamino-6-methylpyrimidin-4(3H)-one, 5-hydroxy-1-carboxamidino-3-methylpyrazole or ethyl N-[(5-hydroxy-3-methylpyrazol-1-yl)imidoyl]aminocrotonoate depending on the type of the base. Formation of pyrazole derivatives occurs in the case of dequaternized substrate imine-group protonating by the acids formed as a result of ion exchange reaction. Chelate fragment of amidinohydroxypyrazole structure provides stabilization of this compound and stipulates its inertness towared the heterocycle closure.     

Thermodynamics of DNA condensation caused by mn2+ binding

Interaction between Mn2+ ion and the two forms of DNA duplex (supercoiled and linearized pUC119 DNA) in solution has been examined by isothermal titration calorimetry. Although DNA condensation reaction heat was observed at 323 K, this was not the case at 298 K. DNA condensation was entropically driven and supercoiled DNA was found to be more susceptive. The enthalpy of DNA condensation is estimated 0.42 kJ/mol for both DNA forms. Conversely, the entropy of DNA condensation was 0.13 kJ/mol K for supercoiled DNA, and 0.12 kJ/mol K for linearized DNA. The difference of entropy is attributable to their DNA conformation.     

The condensation of diphenylphosphinic azide with substituted acetonitriles - Formation of phosphorylated tetrazolines

The condensation between diphenylphosphinic azide and several substituted phenylacetonitriles was investigated. Rather than a substituted aminotriazole, a phosphorylated tetrazoline (IX) was isolated from several reactions. In addition, a phosphorylated nitrile (X) and a phosphorylated eniminonitrile (XI) were found. N-Acylation of IX, followed by warming, lead to a phosphorylated oxadiazoline (XX). Structural assignments are based on UV, IR, and NMR spectral data and chemical degradative evidence. A brief analysis of the results is presented.     

Formation of oxaphospholane derivatives during the condensation of phosphonic acid esters with formaldehyde

Conclusions The condensation of esters of 2,2-dicarbethoxy-2-cyano-2-carbethoxy-, and 2-acetyl-2-carbethoxyethylphosphonic acids with formaldehyde (paraform) proceeds with the formation of oxaphospholane derivatives.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1180–1181, May, 1970.     

Synthesis of DNA conjugates by solid-phase fragment condensation via aldehyde-nucleophile coupling

Oligodeoxyribonucleotides were synthesized that contain a novel nucleoside, 2′-O-(2,3-dihydroxypropyl)cytidine. Its 2′-diol group was blocked by an allyloxycarbonyl protecting group. Selective deprotection of diol group(s) of the support-immobilized blocked oligodeoxyribonucleotide by Pd(0) followed by periodate oxidation resulted in generation of the 2′-aldehyde group(s) on solid-phase. The modified oligonucleotides were used to prepare a number of conjugates with acridine, biotin and N-modified laminin peptides by oxime, hydrazone and hydrazine formation. The method may be applicable to the synthesis of oligonucleotide-peptide conjugates.     

Chirality of toroidal molecular graphs

Symmetry properties of a class of toroidal molecular graphs, arising as covers of certain bipartite cubic Cayley graphs of dihedral groups, are studied. Although these symmetries make all vertices and all edges indistinguishable, they imply intrinsic chirality.     

A study of condensation of trithiane hexaoxide with formaldehyde

The title reaction catalyzed by NaOH in aqueous media was studied. The oligomeric products formed are characterized in terms of their yield, structure, etc. The effects of reaction parameters and media are also discussed. The reaction mechanism is proposed. © 1993 John Wiley & Sons, Inc.