Proton magnetic resonance studies of ribonucleic acid complexes. I. Complexes of biological bases and oligonucleotides with RNA. II. Template recognition and the degeneracy of the genetic code

Part I. Complexes of Biological Bases and Oligonucleotides with RNA

The physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.

Previous work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T₁ measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.

The interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with uridylyl (3' → 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.

The effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D₂0 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.

Part II. Template Recognition and the Degeneracy of the Genetic Code

The interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20°C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.

Due to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the "tautomeric doublet" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.

Magnetic Cross-Linked Enzyme Aggregates (mCLEAs) of Candida antarctica Lipase: An Efficient and Stable Biocatalyst for Biodiesel Synthesis

Enzyme-catalyzed production of biodiesel is the object of extensive research due to the global shortage of fossil fuels and increased environmental concerns. Herein we report the preparation and main characteristics of a novel biocatalyst consisting of Cross-Linked Enzyme Aggregates (CLEAs) of Candida antarctica lipase B (CALB) which are covalently bound to magnetic nanoparticles, and tackle its use for the synthesis of biodiesel from non-edible vegetable and waste frying oils. For this purpose, insolubilized CALB was covalently cross-linked to magnetic nanoparticles of magnetite which the surface was functionalized with –NH2 groups. The resulting biocatalyst combines the relevant catalytic properties of CLEAs (as great stability and feasibility for their reutilization) and the magnetic character, and thus the final product (mCLEAs) are superparamagnetic particles of a robust catalyst which is more stable than the free enzyme, easily recoverable from the reaction medium and reusable for new catalytic cycles. We have studied the main properties of this biocatalyst and we have assessed its utility to catalyze transesterification reactions to obtain biodiesel from non-edible vegetable oils including unrefined soybean, jatropha and cameline, as well as waste frying oil. Using 1% mCLEAs (w/w of oil) conversions near 80% were routinely obtained at 30°C after 24 h of reaction, this value rising to 92% after 72 h. Moreover, the magnetic biocatalyst can be easily recovered from the reaction mixture and reused for at least ten consecutive cycles of 24 h without apparent loss of activity. The obtained results suggest that mCLEAs prepared from CALB can become a powerful biocatalyst for application at industrial scale with better performance than those currently available.

Spin-related phenomena in magnetic and spin-orbit couppled bose-einstein condensates

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Magnetic field modulated direct overwrite with pulsed laser irradiation for TbFeCo magneto-optical disks

WE have designed a dual-beam magneto-optical (MO) storage system to test the dynamic storage properties of MO disks. The characteristics of this dual-beam system are demonstrated. Magnetic field modulated direct overwrite, which is a promising technique for highspeed MO storage, is realized on TbFeCo MO disks with this dual-beam MO system. The effect of light intensity, magnetic field intensity, and linear velocity of the disk and the modulating frequency variation on carrier-to-noise ratio is investigated. (C) 1997 Society of Photo-Optical Instrumentation Engineers.

Electric and magnetic losses and gains in determining the sign of refractive index

Within the framework of classic electromagnetic theories, we have studied the sign of refractive index of optical medias with the emphases on the roles of the electric and magnetic losses and gains. Starting from the Maxwell equations for an isotropic and homogeneous media, we have derived the general form of the complex refractive index and its relation with the complex electric permittivity and magnetic permeability, i.e. n = root epsilon mu, in which the intrinsic electric and magnetic losses and gains are included as the imaginary parts of the complex permittivity and permeability, respectively, as epsilon = epsilon(r) + i(epsilon i) and mu = mu(r) + i mu(i). The electric and magnetic losses are present in all passive materials, which correspond, respectively, to the positive imaginary permittivity and permeability epsilon(i) > 0 and mu(i) > 0. The electric and magnetic gains are present in materials where external pumping sources enable the light to be amplified instead of attenuated, which correspond, respectively, to the negative imaginary permittivity and permeability epsilon(i) < 0 and mu(i) < 0. We have analyzed and determined uniquely the sign of the refractive index, for all possible combinations of the four parameters epsilon(r), mu(r), epsilon(i), and mu(i), in light of the relativistic causality. A causal solution requires that the wave impedance be positive Re {Z} > 0. We illustrate the results for all cases in tables of the sign of refractive index. One of the most important messages from the sign tables is that, apart from the well-known case where simultaneously epsilon < 0 and mu < 0, there are other possibilities for the refractive index to be negative n < 0, for example, for epsilon(r) < 0, mu(r) > 0, epsilon(i) > 0, and mu(i) > 0, the refractive index is negative n < 0 provided mu(i)/epsilon(i) > mu(r)/vertical bar epsilon(r)vertical bar. (c) 2006 Elsevier B.V. All rights reserved.

Nonlinear magnetic vortex dynamics in a circular nanodot excited by spin-polarized current

We investigate analytically and numerically nonlinear vortex spin torque oscillator dynamics in a circular magnetic nanodot induced by a spin-polarized current perpendicular to the dot plane. We use a generalized nonlinear Thiele equation including spin-torque term by Slonczewski for describing the nanosize vortex core transient and steady orbit motions and analyze nonlinear contributions to all forces in this equation. Blue shift of the nano-oscillator frequency increasing the current is explained by a combination of the exchange, magnetostatic, and Zeeman energy contributions to the frequency nonlinear coefficient. Applicability and limitations of the standard nonlinear nano-oscillator model are discussed.