Studies of dinucleoside monophosphates and monomer-polynucleotide interactions by proton magnetic resonance

The nature of the intra- and intermolecular base-stacking interactions involving several dinucleoside monophosphates in aqueous solution have been investigated by proton magnetic resonance spectrosocopy, and this method has been applied to a study of the interaction of polyuridylic acid with purine and adenosine monomers.

The pmr spectra of adenylyl (3' → 5') cytidine (ApC) and cytidylyl (3' → 5') adenosine (CpA) have been studied as a function of concentration and temperature. The results of these studies indicate that the intramolecular base-stacking interactions between the adenine and cytosine bases of these dinucleoside monophosphates are rather strong, and that the stacking tendencies are comparable for the two sequence isomers. The chemical shifts of the cytosine H₅ and adenine H₂ protons, and their variations with temperature, were shown to be consistent with stacked conformations in which both bases of the dinucleoside monophosphates are preferentially oriented in the anti conformation as in similar dApdC, and dCpdA (dA = deoxyadenosine; dC = deoxycytidine) segments in double helical DNA. The intramolecular stacking interaction was found to have a pronounced effect on the conformations of the ribose moieties, and these conformational changes are discussed. The concentration studies indicate extensive self-association of these dinucleoside monophosphates, and analysis of the concentration data facilitated determination of the dimerization constant for the association process as well as the nature of the intermolecular complexes.

The dependence of the ribose conformation upon the extent of intramolecular base-stacking was used to demonstrate that the base-base interaction in cytidylyl (3' → 5') cytidine (CpC) is rather strong, while there appears to be little interaction between the two uracil bases of uridylyl (3' → 5') uridine (UpU).

Studies of the binding of purine to several ribose and deoxyribose dinucleoside monophosphates show that the mode of interaction is base-stacking, and evidence for the formation of a purine-dinucleoside monophosphate intercalated complex is presented. The purine proton resonances are markedly broadened in this complex, and estimates of the purine linewidths in the complex and the equilibrium constant for purine intercalation are obtained.

A study of the interaction of unsubstitued purine with polyuridylic acid at 29°C by pmr indicated that purine binds to the uracil bases of the polymer by base-stacking. The severe broadening of the purine proton resonances observed provides strong evidence for the intercalation of purine between adjacent uracil bases of poly U. This interaction does not result in a more rigid or ordered structure for the polymer.

Investigation of the interaction between adenosine and polyuridylic acid revealed two modes of interaction between the monomer and the polymer, depending on the temperature. At temperatures above 26°C or so, monomeric adenosine binds to poly U by noncooperative A-U base stacking. Below this temperature, a rigid triple-stranded 1A:2U complex is formed, presumably via cooperative hydrogen-bonding as has previously been reported.

These results clearly illustrate the importance of base-stacking in non-specific interactions between bases, nucleosides and nucleotides, and also reveal the important role of the base-stacking interactions in cooperatively for med structures involving specific base-pairing where both types of interaction are possible.

I. Proton magnetic resonance of polynucleotides and transfer RNA. II. Electron spin relaxation studies of manganese (II) complexes in acetonitrile

Part I. Proton Magnetic Resonance of Polynucleotides and Transfer RNA.

Proton magnetic resonance was used to follow the temperature dependent intramolecular stacking of the bases in the polynucleotides of adenine and cytosine. Analysis of the results on the basis of a two state stacked-unstacked model yielded values of -4.5 kcal/mole and -9.5 kcal/mole for the enthalpies of stacking in polyadenylic and polycytidylic acid, respectively.

The interaction of purine with these molecules was also studied by pmr. Analysis of these results and the comparison of the thermal unstacking of polynucleotides and short chain nucleotides indicates that the bases contained in stacks within the long chain poly nucleotides are, on the average, closer together than the bases contained in stacks in the short chain nucleotides.

Temperature and purine studies were also carried out with an aqueous solution of formylmethionine transfer ribonucleic acid. Comparison of these results with the results of similar experiments with the homopolynucleotides of adenine, cytosine and uracil indicate that the purine is probably intercalating into loop regions of the molecule.

The solvent denaturation of phenylalanine transfer ribonucleic acid was followed by pmr. In a solvent mixture containing 83 volume per cent dimethylsulf oxide and 17 per cent deuterium oxide, the tRNA molecule is rendered quite flexible. It is possible to resolve resonances of protons on the common bases and on certain modified bases.

Part II. Electron Spin Relaxation Studies of Manganese (II) Complexes in Acetonitrile.

The electron paramagnetic resonance spectra of three Mn⁺² complexes, [Mn(CH₃CN)₆]⁺², [MnCl₄]^-2, and [MnBr₄]^-2, in acetonitrile were studied in detail. The objective of this study was to relate changes in the effective spin Hamiltonian parameters and the resonance line widths to the structure of these molecular complexes as well as to dynamical processes in solution.

Of the three systems studied, the results obtained from the [Mn(CH₃CN)₆]⁺² system were the most straight-forward to interpret. Resonance broadening attributable to manganese spin-spin dipolar interactions was observed as the manganese concentration was increased.

In the [MnCl₄]^-2 system, solvent fluctuations and dynamical ion-pairing appear to be significant in determining electron spin relaxation.

In the [MnBr₄]^-2 system, solvent fluctuations, ion-pairing, and Br- ligand exchange provide the principal means of electron spin relaxation. It was also found that the spin relaxation in this system is dependent upon the field strength and is directly related to the manganese concentration. A relaxation theory based on a two state collisional model was developed to account for the observed behavior.

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.

Tuning of the electronic characteristics of ZnO nanowire field effect transistors by proton irradiation.

We demonstrated a controllable tuning of the electronic characteristics of ZnO nanowire field effect transistors (FETs) using a high-energy proton beam. After a short proton irradiation time, the threshold voltage shifted to the negative gate bias direction with an increase in the electrical conductance, whereas the threshold voltage shifted to the positive gate bias direction with a decrease in the electrical conductance after a long proton irradiation time. The electrical characteristics of two different types of ZnO nanowires FET device structures in which the ZnO nanowires are placed on the substrate or suspended above the substrate and photoluminescence (PL) studies of the ZnO nanowires provide substantial evidence that the experimental observations result from the irradiation-induced charges in the bulk SiO(2) and at the SiO(2)/ZnO nanowire interface, which can be explained by a surface-band-bending model in terms of gate electric field modulation. Our study on the proton-irradiation-mediated functionalization can be potentially interesting not only for understanding the proton irradiation effects on nanoscale devices, but also for creating the property-tailored nanoscale devices.

Properties of the proton-evoked currents and their modulation by Ca2+ and Zn2+ in the acutely dissociated hippocampus CA1 neurons

The characterization of acid-sensing ion channel (ASIC)-like currents has been reported in hippocampal neurons in primary culture. However, it is suggested that the profile of expression of ASICs changes in culture. In this study, we investigated the properties of proton-activated current and its modulation by extracellular Ca2+ and Zn2+ in neurons acutely dissociated from the rat hippocampal CA1 using conventional whole-cell patch-clamp recording. A rapidly decaying inward current and membrane depolarization was induced by exogenous application of acidic solution. The current was sensitive to the extracellular proton with a response threshold of pH 7.0-6.8 and the pH(50) Of 6.1, the reversal potential close to the Na+ equilibrium potential. It had a characteristic of acid-sensing ion channels (ASICs) as demonstrated by its sensitivity to amiloride (IC50 = 19.6 +/- 2.1 muM). Either low [Ca2+](0) or high [Zn2+](0) increased the amplitude of the current. All these characteristics are consistent with a current mediated through a mixture of homomeric ASIC1a and heteromeric ASIC1a + 2a channels and closely replicate many of the characteristics that have been previously reported for hippocampal neurons cultured for a week or more, indicating that culture artifacts do not necessarily flaw the properties of ASICs. Interestingly, we found that high [Zn2+] (>10(-4) M) slowed the decay time constant of the ASIC-like current significantly in both acutely dissociated and cultured hippocampal neurons. In addition, the facilitating effects of low [Ca2+](0) and high [Zn2+](0) on the ASIC-like current were not additive. Since tissue acidosis, extracellular Zn elevation and/or Ca2+ reduction occur concurrently under some physiological and/or pathological conditions, the present observations suggest that hippocampal ASICs may offer a novel pharmacological target for therapeutic invention. (C) 2004 Elsevier B.V. All rights reserved.

UV photoconductivity characteristics of ZnO nanowire field effect transistor treated by proton irradiation

We investigated the UV photoconductivity characteristics of ZnO nanowire field effect transistors (FETs) irradiated by proton beams. After proton beam irradiation (using a beam energy of 10 MeV and a fluence of 10 12 cm -2), the drain current and carrier density in the ZnO nanowire FETs decreased, and the threshold voltage shifted to the positive gate bias direction due to the creation of interface traps at the SiO 2/ZnO nanowire interface by the proton beam. The interface traps produced a higher surface barrier potential and a larger depletion region at the ZnO nanowire surface, affecting the photoconductivity and its decay time. The UV photoconductivity of the proton-irradiated ZnO nanowire FETs was higher and more prolonged than that of the pristine ZnO nanowire FETs. The results extend our understanding of the UV photoconductivity characteristics of ZnO nanowire devices and other materials when irradiated with highly energetic particles. © 2012 Elsevier B.V. All rights reserved.

Proton irradiation-induced defects in undoped GaSb studied by positron lifetime spectroscopy and photoluminescence

Undoped GaSb was irradiated by 2.6 MeV protons. The irradiation-induced defects were studied by positron lifetime spectroscopy (PLS) and photoluminescence (PL). Positron lifetime measurements showed that vacancy-type defects were introduced after irradiation, and divacancies were formed at higher irradiation dose. Annealing experiments revealed there were different annealing steps between the as grown and proton-irradiated samples, the reason for which was tentatively attributed to the formation of divacancies in the proton-irradiated samples during annealing. All the vacancy defects could be annealed out at around 500 degrees C. The PL intensity quickly fell down after proton irradiation and decreased with increasing irradiation dose, indicating that irradiation induced non-irradiative recombination centers, whose candidates were assigned to the vacancy defects induced by proton irradiation.

Enhanced Proton Conduction in Polymer Electrolyte Membranes as Synthesized by Polymerization of Protic Ionic Liquid-Based Microemulsions

Proton-conducting membranes were prepared by polymerization of microemulsions consisting of surfactant-stabilized protic ionic liquid (PIL) nanodomains dispersed in a polymerizable oil, a mixture of styrene and acrylonitrile. The obtained PIL-based polymer composite membranes are transparent and flexible even though the resulting vinyl polymers are immiscible with PIL cores. This type of composite membranes have quite a good thermal stability, chemical stability, tunability, and good mechanical properties. Under nonhumidifying conditions, PIL-based membranes show a conductivity up to the order of 1 x 10(-1) S/cm at 160 degrees C, due to the well-connected PIL nanochannels preserved in the membrane. This type of polymer conducting membranes have potential application in high-temperature polymer electrolyte membrane fuel cells.

The effect of proton radiation on a superlumine scent diode (SLD)

The effect of proton radiation on a superluminescent diode (SLD) was studied, and the radiation damage from different energies was compared. The results reveal that the optical power degradation is greater from 350 KeV protons than from 1 MeV protons. Analysis of SLD characteristics after irradiation shows that the main effect of radiation is damage within the active region. At the same time, the results also show that quantum-well (QW) SLDs are far less sensitive to radiation than double-heterojunction (DH) SLDs. (C) 2007 Elsevier B.V. All rights reserved.

The new exploration for proton-implanted silicon: the conversion of a surface-region-purification-induced p-n junction into a p-i-n electrical structure approaching silicon on insulator

A surface-region-purification-induced p-n junction, a puzzle discovered at Brookhaven National Laboratory, in a silicon-on-defect-layer (SODL) material has been explored by carrying out various annealing conditions and subsequent measurements on electrical properties. The origin of the pn junction has been experimentally investigated. Furthermore, the p-n junction has been transformed into a p-i-n electrical structure by adding a high temperature annealing process to the previously used SODL procedure, making the SODL material approach silicon on insulator (SOI). The control of the initial oxygen amount in the silicon material is suggested to be critical for the experimental results.