INTERACTION OF PROSPIDIUM CHLORIDE WITH WATER IN METHANOL – RESULTS OF CALORIMETRIC AND NMR STUDIES

Biomacromolecules/Nanomaterials bioconjugate complexes have many applications in the interdisciplinary research fields. Accessible and easy synthesis methods of these complexes are the key roles for these applications. High quality water-soluble surface-charged quantum dots (QDs) were successfully prepared via surface modification by amphiphilic surfactants. The positively charged QDs can interact with deoxyribonucleic acid (DNA) molecules to form QDs/DNA bioconjugates via self-targeting electrostatic force. The stability of these QDs/DNA bioconjugates is influenced by ionic strength and concentration of negative or neutral surfactants in the solution. High ionic concentration or ca. 10(-3) mol/L surfactants can break the interaction between the QDs and DNA molecules (Lambda DNA/Hind III Marker segments) and controllably release DNA molecules from these bioconjugates. The conformation of DNA molecules has little change during the binding and releasing process. The condensation of lambda DNA molecules can be induced by positively charged QDs. High resolution transmission electron microscopy experiments have revealed the different stages of DNA condensation process, showing the fine structures of QDs/DNA bioconjugates at biomolecular scale. A long chain DNA molecule starts to self-enwind and condense to a porous globule when it is exposing to positively charged QDs but there is no direct interaction between QDs and DNA at early stages of condensation. After the DNA molecule becomes a compact globule, QDs stick onto its surface via electrostatic force. The coil conformation of the DNA molecules can be recovered from globule structure after DNA molecules are controllably released from bioconjugate complexes. These QDs/DNA bioconjugates have great potential applications for gene delivery and at the same time the fluorescence of QDs can be utilized to monitor the DNA releasing process.

ABSTRACTWe focus on lyotropic liquid crystals (LCs) in water system similar to living body, and have investigated the behavior of deoxyribonucleic acid (DNA) molecules in the DNA-doped lyotropic LC. As a result, the microscopic texture becomes disturbed and the domain breaks down by DNA doping. Therefore, DNA molecules can behave as impurities. Furthermore, in the ion density measurement, the ion current peaks appear by DNA doping, and thus, DNA molecules can behave as ion careers in the LC medium. On the other hand, DNA molecules form the aggregations in their high concentration.

28] Purification, specific fragmentation, and separation of large DNA molecules

On-chip concentration method for deoxyribonucleic acid (DNA) molecules is preconcentrating DNA molecules before analyses using nanometer-sized structures formed in a microchannel and is effective in improving the sensitivity in DNA analyses using microfluidic devices. Although accurate and predictive theoretical models of concentration profile and concentration factor in on-chip concentration can be used for designing nanostructures and optimizing conditions for concentration, there has been few studies on models. In our previous study, we presented a method of on-chip concentration of DNA molecules using a nanoslit, which is a smaller gap than the diameter of random-coiled DNA molecules. This method is based on the principle of an entropic trap, and we achieved DNA concentration by controlling the applied voltage. In this study, we developed theoretical models of concentration profile and concentration factor in on-chip concentration for DNA molecules using a nanoslit. We conducted concentration experiments of lambda DNA (λ DNA) using our fabricated chip device with a 25-nm nanoslit. The theoretical results of our models were in good agreement with these experimental results. Based on our theoretical models, we determined the optimal applied voltage to be 0.95 V for maximizing the concentration factor in λ DNA concentration by using our chip device.

29] Orthogonal-field-alternation gel electrophoresis

COLICIN factors E2 and E3 (Col E2 and Col E3) are stably maintained extrachromosomal genetic elements carried by Escherichia coli that have been identified as small circular deoxyribonucleic acid (DNA) molecules with the same molecular weights (5 × 106)1. Cells carrying one of these Col factors can produce a specific antibiotic protein2, colicin E2 or colicin E3 and also exhibit an “immunity” to the lethal action of the specific colicin it produces3. While the mechanisms of action of colicin E2 and E3 are quite different4–6, structural and immunological comparisons suggest the proteins are related2 as does the shared receptor sites for colicin adsorption7–9. The partial immunity that cells colicinogenic for Col E2 exhibit for colicin E310 suggests another possible relation may exist between the two colicin factors. In order to further understand the relationships of these two small colicin factors, an examination of the presence and location of homologous base sequences in their DNA molecules was undertaken. The experiments reported here include the electron microscopic examination of heteroduplex molecules formed by renaturing mixtures of denatured Col E2 and Col E3 DNA in formamide solutions11–14, as well as measurements of competitive annealing between both DNA molecules using DNA-DNA membrane filter hybridization techniques15.

Controlled deposition of single DNA molecules on bare gold electrodes

Dispersive transfer of the parental DNA molecule to the progeny of phage ∅X-174

We study the diffusion of T4 GT7 deoxyribonucleic acid (DNA) molecules confined in nanochannels with an effective size of 307 nm before and after knot formation. The measured DNA chain diffusivity is 0.0243 ± 0.0009 μm²/s for unknotted DNA molecules and 0.014 ± 0.001 μm²/s for the DNA molecules that contain knots with an estimated knot contour length of 9 ± 2 μm. The reduced diffusivity in the presence of large knots indicates that the DNA–wall friction, rather than the shortening of the nondraining molecule, dominates the friction of knotted DNA in the extended de Gennes regime of nanochannel confinement.

We have succeeded in attaching deoxyribo nucleic acid (DNA) molecules to a semiconducting Si substrate by adding MgCl2 to the DNA solution. The optimum concentration of MgCl2 solution to form the DNA network structure is 0.05 to 0.5 mM. Furthermore, it is found that DNA molecules attach to a hydrophilic SiO2 surface but not to a hydrophobic SiH surface. This result indicates that it is possible to fabricate micropatterning on a Si surface by using a DNA template and photolithography.

Deoxyribonucleic acid (DNA) molecules can be selectively adsorbed onto a SiO2 surface in SiO2/SiH pattern, fabricated using photolithography, by adding MgCl2 to a DNA solution. Since DNA molecules can be adsorbed onto a Si substrate through Mg2+, the adsorption of DNA molecules in a SiO2/SiH pattern is influenced by the concentration of MgCl2 and the difference in chemical property between a SiO2 surface and a SiH surface. The optimum concentration of MgCl2 at which DNA molecules are selectively adsorbed onto a SiO2 surface was 0.1 mM.

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.

Deoxyribonucleic acid (DNA) molecules were doped with Au atoms and their electrical transport properties were measured. The Au doping was carried out by incubating a mixture of HAuCl4·3H2O and DNA solutions. The binding of Au atoms to DNA bases was identified using Fourier transform infrared spectroscopy and X-ray photoemission spectroscopy. The Au-doped DNA molecules were deposited on nanoelectrodes and the presence of the molecules between the electrodes was determined by both scanning electron microscopy and atomic force microscopy. Measurement of the current-voltage characteristics showed that the Au-doped DNA molecules exhibited a higher conductivity than undoped DNA molecules. Detailed analysis of the chemical composition shows that there is a strong possibility of reliably controlling the conductivity of DNA molecules using this method.

In this experimental work the acute toxicity of a chemically modified derivative of the natural pigment chlorophyll a called monocationic chlorin e6, which is a promising photosensitizer (PS) for antimicrobial and antitumor photodynamic therapy, was studied using white rats. The advantages of the PS under investigation are an intense absorption in the long-wavelength region of the visible spectrum, a sufficiently high quantum yield of singlet oxygen generation, pronounced amphiphilic properties along with an appropriate solubility in water, and a high level of photocytotoxic- ity in relation to both malignant HeLa cells and antibiotic-resistant hospital strains of E. сoli bacteria., P. aerugenosa and others. It has been shown that the value of LD 50 of the considered PS can be calculated as the value of 100 mg/kg. In the reproduced experimental model of acute toxicity, pathomorphological changes in the vital organs of laboratory animals indicate a pronounced vasopathic effect of the drug with the development of cerebral edema and respiratory distress syndrome, which have become the main signs of thanatogenesis.

Chapter 2 - Imaging and force detection of single deoxyribonucleic acid molecules by atomic force microscopy