I. The structure and properties of closed circular duplex DNA. II. Chemically interacting systems at equilibrium in a buoyant density gradient

I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. The buoyant densities and sedimentation velocities of both intact (I) and singly nicked (II) SV 40 DNAs were measured as a function of free dye concentration. The buoyant density data were used to determine the binding isotherms over a dye concentration range extending from 0 to 600 µg/m1 in 5.8 M CsCl. At high dye concentrations all of the binding sites in II, but not in I, are saturated. At free dye concentrations less than 5.4 µg/ml, I has a greater affinity for dye than II. At a critical amount of dye bound I and II have equal affinities, and at higher dye concentration I has a lower affinity than II. The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions.

The free energy of superhelix formation is calculated as a function of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. The free energy estimates are used to calculate the pitch and radius of the superhelix as a function of the number of superhelical turns. The pitch and radius of the native I superhelix are 430 Å and 135 Å, respectively.

A buoyant density method for the isolation and detection of closed circular DNA is described. The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length.

II. The general theory is presented for the sedimentation equilibrium of a macromolecule in a concentrated binary solvent in the presence of an additional reacting small molecule. Equations are derived for the calculation of the buoyant density of the complex and for the determination of the binding isotherm of the reagent to the macrospecies. The standard buoyant density, a thermodynamic function, is defined and the density gradients which characterize the four component system are derived. The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and silver to DNA.

Dynamic storage performance of two cyanine dye films and optimization design for a recordable compact disk

The optical constants of two cyanine dye films that we prepared were measured with a RAP-1-type (RAP is rotating analyzer and polarizer) spectroscopic ellipsometer. Toward making a simplified model for the wafers of a recordable compact disk (CD-R), we give their optimization designs developed with the cyanine dye films. in addition, the dynamic storage performances of two sample disks were tested by our dynamic storage testing system. Measurement results of the sample disks were obtained to test and verify our film designs. (C) 2000 Optical Society of America. OCIS codes: 160.4890, 160.4760, 210.4810.

Optical recording properties of metal-azo dye as recording medium with super-resolution near-field structure

A novel metallized azo dye has been synthesized. The absorption spectra of the thin film and thermal characteristic are measured. Static optical recording properties with and without the Bi mask layer super-resolution near-field structure (Super-RENS) of the metal-azo dye are investigated. The results show that the metal-azo dye film has a broad absorbance band in the region of 450-650 nm and the maximum absorbance wavelength is located at 603 nm. It is also found that the new metallized azo dye occupies excellent thermal stability, initiatory decomposition temperature is at 270 degrees C and the mass loss is about 48% in a narrow temperature region (15 degrees C). The complex refractive index N (N = n + ik) is measured. High refractive index (n = 2.45) and low extinction coefficient (k = 0.2) at the recording wavelength 650nm are attained. Static optical recording tests with and without Super-RENS are carried out using a 650nm semiconductor diode laser with recording power of 7mW and laser pulse duration of 200ns. The AFM images show that the diameter of recording mark on the dye film with the Bi mask layer is reduced about 42%, compared to that of recorded mark on the dye film without Super-RENS. It is indicated that Bi can well performed as a mask layer of the dye recording layer and the metallized azo dye can be a promising candidate for recording media with the super-resolution near-field structure.

Synthesis, optical and thermal characterization of novel thiazolyl heterocyclic azo dye

Thiazolyl heterocyclic azo dye and its metal (Ni2+, Co2+)-azo complexes were synthesized. Their structures were confirmed by elemental analysis, UV-VIS absorption spectra, FT-IR, H-1 NMR and MALDI-MS. The thermal properties of metal complexes were studied by DSC-TGA. The optical constants (complex refractive index N=n + ik) and thickness of the complex thin films on polished single-crystal silicon substrates were investigated on a scanning ellipsometer. Results indicate that thiazolyl metal-azo complexes possess good optical and thermal properties. They would be a promising recording medium candidate for NVD with the Super-resolution near field structure (Super-RENS) technology. (c) 2007 Elsevier B.V. All rights reserved.

Optical properties of dye-doped zirconia films by spectroscopic ellipsometry

The optical properties of zirconia films doped with rhodamine 6G and oxazine 725 by the sol-gel process were investigated using spectroscopic ellipsometry (SE). Accurate refractive index n and the extinction coefficient k were determined using a three-oscillator classical Lorentz model in the wavelength range of 300-800 nm. The derived refractive index of dye-doped films exhibited anomalous dispersion in the absorption region. Wavelength tunable output lasing action yellow and near-infrared wavelength region was achieved by DFB configuration using zirconia films doped with R6G and oxazine 725. (c) 2006 Elsevier B.V. All rights reserved.