Divalent cations are not required for the stability of the low-salt Z-DNA conformation in poly(dG-ethyl5dC)

It is demonstrated that poly(dG-ethyl5dC) adopts Z form in low-salt solution like poly(dG-methyl5dC). Its existence is, however, not contingent on the presence of divalent cations in the polynucleotide solution. The Z form is transformed into B form below room temperature. The arising B form cannot be transformed back into Z form by millimolar MgCl2 concentrations. On the contrary, the addition of MgCl2 at room temperature converts the low-salt Z form of poly(dG-ethyl5dC) into B form. It follows from the results that Z form is a stable DNA conformation not only at high but even at low ionic strengths.     

Divalent Cations are not Required for the Stability of the Low-Salt Z-DNA Conformation in Poly(dG-ethyl5 dC)

Abstract

It is demonstrated that poly(dG-ethyl⁵dC) adopts Z form in low-salt solution like poly(dGmethyl⁵dC). Its existence is, however, not contingent on the presence of divalent cations in the polynucleotide solution. The Z form is transformed into B form below room temperature. The arising B form cannot be transformed back into Z form by millimolar MgCl₂ concentrations. On the contrary, the addition of MgCl₂ at room temperature converts the low-salt Z form of poly(dG-ethyl⁵dC) into B form. It follows from the results that Z form is a stable DNA conformation not only at high but even at low ionic strengths.     

Histidine 190-D1 and glutamate 189-D1 provide structural stabilization in photosystem II

In photosynthesis, photosystem II (PSII) conducts the light-driven oxidation of water to oxygen. Tyrosine Z is Tyr 161 of the D1 polypeptide; Z acts as an intermediary electron carrier in water oxidation. In this report, EPR spectroscopy was used to study the effect of His 190 and Glu 189 on Z* yield and reduction kinetics. Neither mutation has a significant impact on the EPR line shape of Z*. At room temperature and pH 7.5, the E189Q-D1 mutation has a single turnover Z* yield that is 84% compared to wild-type. The H190Q-D1 mutation decreases the Z* yield at room temperature by a factor of 2.6 but has a more modest effect (factor of 1.6) at -10 degrees C. The temperature dependence is shown to be primarily reversible. Neither mutation has a dramatic effect on Z* decay kinetics. The Z* minus Z FT-IR spectrum, recorded at pH 7.5 on H190Q, reveals perturbations, including an increased spectral contribution from a PSII chlorophyll. The Z* minus Z FT-IR spectrum, recorded at pH 7.5 on E189Q, shows perturbations, including a decreased contribution from the carboxylate side chain of a glutamate or aspartate. Temperature-dependent changes in H190Q-D1 and E189Q-D1 Z. yield are attributed to a reversible conformational change, which alters the electron-transfer rate from Z to P(680)(+). On the basis of these results, we conclude that H190 and E189 play a role in the structural stabilization of PSII. We postulate that some or all of the phenotypic changes observed in H190Q and E189Q mutants may be caused by structural alterations in PSII.     

Immobilization of enzymes with polyaziridines.

A novel method of enzyme immobilization using a low molecular weight prepolymer of tri-functional aziridines which can immobilize enzymes both by covalent attachment and entrapment within a gel matrix is described. The enzymes are immobilized on a solid support and exhibit an excellent retention of enzymatic activity. The immobilization procedure is essentially a single step process which can be easily performed at room temperature or 4 degrees C in either aqueous solution or in an inert organic solvent. The polyaziridines used in the immobilization are nontoxic, available in bulk at low cost and completely miscible with water and many organic solvents, thus providing one of the most satisfactory methods of immobilization available.     

Low pH myoglobin photoproducts.

Recently, there has been interest in determining the conditions under which the iron-histidine bond ruptures in myoglobin at low pH, so that the effect of proximal heme ligation can be studied. A 220-cm-1 Raman mode, assigned to iron-histidine stretching, is clearly visible after photolysis of aqueous MbCO samples below pH4 at room temperature (Sage et al. Biochemistry. 30:1237-1247). In contrast, Iben et al. (Biophys. J. 59:908-919) do not observe this mode upon photolysis of a pH3 MbCO sample in a glycerol/water glass at low temperature. In order to account for both the low temperature and the room temperature experiments, Iben et al. suggest a scheme involving an unusual protonation state of the proximal histidine. Here, we discuss some inconsistencies in their explanation of the room temperature results and offer instead a simple modification of an earlier model. In addition, circular dichroism data are presented that indicate partial unfolding of MbCO in aqueous solution below pH4, and raise questions about the claim of Iben et al. that MbCO remains folded in 75% glycerol at pH3.     

The B----Z transition in two synthetic oligonucleotides: d(C-2-amino-ACGTG) and d(m5CGCAm5CGTGCG) studied by IR, NMR and CD spectroscopies.

The sequences CA'CGTG (where A' = 2-aminodeoxyadenosine) and m5CGCAm5CGTGCG are prepared and studied by IR, CD and 1H-NMR. Infrared spectra demonstrate the capacity of the modified hexamer and decamer to adopt a Z conformation. The influence of the NH2 substitution on the adenine or of the methylated terminal part of the decamer acting with the increase of the DNA concentration stabilizes the Z conformation at room temperature in low humidity films. Very weak proportion of Z conformation is detected in UV dilute solutions. In more concentrated NMR solutions, the Z proportion induced by high salt content is only 20-25%. The effects of the concentration and of the covalent modification of the bases are discussed.     

Atmospheric stability in cell culture vessels.

We have investigated that atmospheric stability in polystyrene and glass cell culture vessels by measuring the dissolved O2 and CO2 in the media of both seeded and unseeded culture vessels incubated at 37 degrees C. There was no diffusion of either O2 or CO2 through glass vessels. At low partial pressures of oxygen (PO2), oxygen diffused into the polystyrene flasks at a rate of 1 to 2 mmHg per 24 hr, and at high PO2, oxygen diffused slowly out of polystyrene flasks. CO2 diffused out of polystyrene flasks with a half-time of 260 hr resulting in a considerable elevation in pH. In seeded polystyrene flasks with the PO2 less than or equal to room air, cellular oxygen consumption was masked by the inward diffusion of oxygen. In addition, the fall in pH due to metabolic CO2 and organic acid production during cell growth in polystyrene flasks was buffered by the diffusion of CO2 out of the vessels.     

Molecular motions of polysaccharides in the solid state: dextran, pullulan and amylose.

Dextran, pullulan and amylose have been investigated by differential scanning calorimetry, thermogravimetric analysis, dynamic mechanical and dielectric spectroscopy over a wide range of temperatures and frequencies. No melting or glass transition is seen below the range of thermal degradation (about 300 degrees C) for either amylose or pullulan; only dextran shows a Tg at 223 degrees C (delta cp = 0.40 J/g deg). The viscoelastic spectrum of the 'dry' polysaccharides is characterized by a low temperature relaxation that occurs at -94, -73 and -59 degrees C, at 1 kHz, (activation energy 32, 39 and 52 kJ/mol) in dextran, pullulan and amylose respectively and is assigned to small entity local motions of the polysaccharide backbone. Absorbed water strongly modifies the relaxation spectrum, inducing a new relaxation below room temperature and dissipation regions associated with water loss above room temperature. The former appears at temperatures higher than the relaxation characteristic of the dry polymer and moves to lower temperature with increasing water content. In normal 'room humidity' conditions (about 10% absorbed water) the water-induced relaxation, attributed to the motion of complex polymer-water relaxing units, is the only observable feature in the dynamic mechanical and dielectric spectrum below room temperature.     

Two-dimensional 1H NMR study of d(br5C-G)3 in the Z-form. Self association and flexibility of the left-handed double helix

The Z conformation of the auto complementary hexanucleoside pentaphosphate d(br5C-G)3 in 1 M NaClO4 solution has been investigated by using 2D NMR techniques. NOESY experiments performed at different temperatures show that the oligonucleotide exhibits end-to-end associations at room temperature. The conformation of the hexanucleotide molecules is very similar to that found in the crystal which was described by Chevrier et al. (J. Mol. Biol., 1986, 188, 707-719) as a Z-I form. When the temperature is increased the aggregates are dissociated and a conformational change is observed which is interpreted as a Z-I in equilibrium Z-II transition.     

High Efficiency (>17%) Si‐Organic Hybrid Solar Cells by Simultaneous Structural,Electrical, and Interfacial Engineering via Low‐Temperature Processes

Highly efficient organic–inorganic hybrid solar cells of Si‐poly(3,4‐ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS) have been demonstrated by simultaneous structural, electrical, and interfacial engineering with low processing temperature. Si substrate has been sculpted into hierarchical structure to reduce light reflection loss and increase interfacial junction area at the same time. Regarding the electrical optimization, highly conductive organic PEDOT:PSS layer has been formulated with low sheet resistance. It is argued that the sheet resistance, rather than conductivity, is the primary parameter for the high efficiency hybrid cells, which leads to the optimization of thickness, i.e., thick enough to have low sheet resistance but transparent enough to pass the incident sunlight. Finally, siloxane oligomers have been inserted into top/bottom interfaces by contact‐printing at room ambient, which suppresses carrier recombination at interfaces and reduces contact resistance at bottom electrode. Contrary to high‐temperature doping (for the formation of front surface or back surface fields), wet solution processes or vacuum‐based deposition, the contact‐printing can be done at room ambient to reduce carrier recombination at the interfaces. The high efficiency obtained with low processing temperature can make this type of cells be a possible candidate for post‐Si photovoltaics.     

Nuclear Overhauser effects in linear peptides. A low-temperature 500 MHz study of Met-enkephalin

Met5-enkephalin was studied in 1 mM solutions in 2H2O at room temperature and in a cryoprotective mixture (DMSOd6/2H2O, mole fraction of DMSO 0.49) in the temperature range 265-298 K. Small positive effects were observed between the ortho and meta protons of Tyr in aqueous solution at room temperature. Intraresidue effects can be made strong and negative by increasing the viscosity of the medium with a combination of cryoprotective mixtures and low temperatures. The use of mixtures with properties very close to water is very promising for conformational studies of enkephalins and of other small linear peptides.     

Cyclic 3',5'-adenosine monophosphate level and adenylate cyclase activity in human blood platelets during storage in ACD solution.

The level of cyclic 3',5'-adenosine monophosphate (cAMP) in human platelets and the activity of platelet adenylate cyclase in response to prostaglandin E1 stimulation do not change during two days storage at room temperature in ACD solution. However, the level of cyclic AMP is lower in platelets stored in ACD solution than in platelets from blood anticoagulated by ethylenediamine tetra-acetic acid.     

Optical spectra of lactoperoxidase as a function of solvent

The iron of lactoperoxidase is predominantly high-spin at ambient temperature. Optical spectra of lactoperoxidase indicate that the iron changes from high-spin to low-spin in the temperature range from room temperature to 20 K. The transformation is independent of whether the enzyme is in glycerol/water or solid sugar glass. Addition of the inhibitor benzohydroxamic acid increases the amount of the low-spin form, and again the transformation is independent of whether the protein is in an aqueous solution or a nearly anhydrous sugar. In contrast to lactoperoxidase, horseradish peroxidase remains high-spin over the temperature excursion in both solvents and with addition of benzohydroxamic acid. We conclude that details of the heme pocket of lactoperoxidase allow ligation changes with temperature that are dependent upon the apoprotein but independent of solvent fluctuations. At low pH, lactoperoxidase shows a solvent-dependent transition; the high-spin form is predominant in anhydrous sugar glass, but in the presence of water, the low-spin form is also present in abundance. The active site of lactoperoxidase is not as tightly constrained at low pH as at neutrality, though the enzyme is active over a wide pH range.     

B,Z conformations and mechanism of the Z-B-coil transitions of the self-complementary deoxy-hexanucleotide d(C-G-m5C-G-C-G) by 1H-NMR and CD spectroscopy

The helical structures of d(C-G-m5C-G-C-G) were studied in aqueous solution at various salt concentrations and temperatures by CD and 1H-NMR spectroscopy. At room temperature only the B form is observed in 0.1 M NaCl whereas the B and Z forms are simultaneously present in 1.8 M NaCl. At high salt concentration (4 M NaCl) the Z form is largely predominant (greater than 95%). The Z form proton resonances were assigned by using the polarisation transfer method (between B and Z at 1.8 M NaCl) and by proton-proton decoupling (at high salt concentration). The Z-B-Coil transitions were studied as a function of temperature with the 1.8 M NaCl solution. At high temperature (95 degrees C) only the coil form (S) is present. Below 55 degrees C the coil proportion is negligible, and the B-Z exchange is slow. The disappearance of the coil gives rise at first to the B form and on lowering the temperature the Z proportion increases to the detriment of the B form. Proton linewidth, relaxation and polarisation transfer studies confirm the conclusion in the previous report on d(m5C-G-C-G-m5C-G) (Tran-Dinh et al Biochemistry 1984 in the press) that Z exchanges only with B whereas the latter also exchanges with S,Z in equilibrium B in equilibrium S. The present data show that even at high salt concentration where only the Z form of d(C-G-m5C-G-C-G) is observed the Z-S transition also passes through the B form as an intermediate stage. The B-Z transition takes place when the Watson-Crick hydrogen bonds are firmly maintained and is greatly favoured when there are three hydrogen bonds between the base-pairs.     

Photocyclization of a conformationally constrained 2-vinylbiphenyl.

The synthesis and photochemical behavior of a rigid analog of syn-2-vinylbiphenyl are reported. This analog undergoes quantitative conversion to a tetrahydrobenzanthracene derivative upon irradiation in fluid solution. Product formation is proposed to occur via photocyclization to yield an unstable intermediate followed by an intramolecular thermal hydrogen shift. The intermediate can be observed upon irradiation at low temperature either in a rigid glass or in liquid propane solution. The temperature dependence of its decay is indicative of a tunneling mechanism for the hydrogen shift process.     

Aqueous aldehyde (Faglu) methods for the fluorescence histochemical localization of catecholamines and for ultrastructural studies of central nervous tissue.

Aqueous solutions combining a high concentration of formaldehyde (4%) with low concentrations of glutaraldehyde (0.5--01%) have been used to simultaneously localize amines by the formation of fluorescent products and to fix central nervous tissue for electron microscopy. The fluorescence reaction is produced by the aldehyde mixture at room temperature and the fluorescence is stable when the tissue is maintained in aqueous solution. This means that nerve cell bodies and terminal fields which contain catecholamines can be located accurately in vibratome sections at the light microscope level and, after further processing, can be examined under the electron microscope. With 1% glutaraldehyde in the aldehyde mixture, ultrastructural details are well preserved; there is no significant distortion of any component of the tissue. If vibratome or cryostat sections are dried against glass slides, the intensity of the fluorescence reaction is enhanced and the sections can be permanently mounted.     

Amide isosteres of lexitropsins: synthesis, DNA binding characteristics and sequence selectivity of thioformyldistamycin.

The synthesis and properties of an amide isostere of the antibiotic distamycin, thioformyldistamycin 3 is described. Compound 3 exists predominantly in the E conformation of the thioamide group in freshly prepared DMSO solution but is converted into the Z form, predicted by molecular mechanics to be more stable, on standing for 24 h. The coalescence temperature in DMSO is 110 degrees C by 1H-NMR. The thioformyl moiety of 3 is resistant to both peptidase action and acid treatment. Complementary strand MPE footprinting on a EcoRI/Hind III restriction fragment of pBR322 DNA demonstrated that either E or Z forms of 3 give a single set of footprints very similar to that of the parent antibiotic with strongest protection at TAAG and TATTAT with moderately strong protection at ATTT and AAAA. The strength of binding of 3 and distamycin from delta Tm measurements to either poly.d(AT) or calf thymus DNA is comparable. Molecular modeling predicted a preferred conformation for 3 wherein the C = S bond has a torsional angle of 110 degrees with the pyrrole ring. The energy difference between this conformation and the E form is less than 1 kcal/mole. In contrast the E-form has an energy 17.3 kcal/mole greater than the Z and a value of 26.3 kcal/mole was calculated for the energy barrier between the two isomers.     

E.s.r. of spin-trapped radicals in gamma-irradiated polycrystalline DL-alanine. A quantitative determination of radical yield

The quantitative aspects of determining free radicals in polycrystalline amino acids gamma-irradiated at room temperature and subsequently dissolved in spin-trap solutions were investigated. The deamination radical in DL-alanine was used for detailed studies and 2-methyl-2-nitrosopropane (MNP) was employed as the spin-trap. The spin-trapping efficiency (the number of radicals spin-trapped in solution divided by the number of radicals initially present in the gamma-irradiated solid) was found to be in the range 1 to 10 per cent for aqueous solutions depending on the experimental conditions. The effects of dose, particle size, pH, spin-trap concentration, age of spin-trap solution, MNP monomer to dimer ratio and the presence of organic solvents were investigated. Several reactions were found to decrease the spin-trapping efficiency; radical-radical recombination, the competition between the spin-adduct and the spin-trap for radicals and the reaction of radicals with the MNP dimer. The reaction of intact DL-alanine molecules with deamination radicals to produce H-abstraction radicals which are not spin-trapped does not significantly lower the spin-trapping efficiency. The results obtained with compounds such as glycine, glycylglycine, L-valine and L-proline suggest that the low spin-trapping efficiency found for DL-alanine may be representative of polycrystalline amino acids.     

Degradation of 1,3-dichloropropene by a soil bacterial consortium and Rhodococcus sp. AS2C isolated from the consortium

A bacterial consortium capable of degrading the fumigant 1,3-D ((Z)- and (E)-1,3-dichloropropene) was enriched from an enhanced soil. This mixedculture degraded (Z)- and (E)-1,3-D only in the presence of a suitable biodegradable organic substrate, such as tryptone, tryptophan, or alanine. After 8 months of subculturing at 2- to 3-week intervals, a strain of Rhodococcus sp. (AS2C) that was capable of degrading 1,3-D cometabolically in the presenceof a suitable second substrate was isolated. (Z)-3-chloroallyl alcohol (3-CAA) and (Z)-3-chloroacrylic acid (3-CAAC), and (E)-3-CAA and (E)-3-CAAC were the metabolites of (Z)- and (E)-1,3-D, respectively. (E)-1,3-D was degraded faster than (Z)-1,3-D by the strain AS2C and the consortium. AS2C also degraded (E)-3-CAA faster than (Z)-3-CAA. Isomerization of (E)-1,3-D to (Z)-1,3-D orthe (Z) form to the (E) form did not occur.     

B,Z Conformations and Mechanism of the Z-B-Coil Transitions of the Self-Complementary Deoxy-hexanucleotide d(C-G-m5C-G-C-G) by 1H-NMR and CD Spectroscopy

Abstract

The helical structures of d(C-G-m⁵C-G-C-G) were studied in aqueous solution at various salt concentrations and temperatures by CD and ¹H-NMR spectroscopy. At room temperature only the B form is observed in 0.1 M NaCl whereas the B and Z forms are simultaneously present in 1.8 M NaCl. At high salt concentration (4 M NaCl) the Z form is largely predominant (> 95%). The Z form proton resonances were assigned by using the polarisation transfer method (between B and Z at 1.8 M NaCl) and by proton-proton decoupling (at high salt concentration).

The Z-B-Coil transitions were studied as a function of temperature with the 1.8 M NaCl solution. At high temperature (95°C) only the coil form (S) is present. Below 55°C the coil proportion is negligible, and the B-Z exchange is slow. The disappearance of the coil gives rise at first to the B form and on lowering the temperature the Z proportion increases to the detriment of the B form. Proton linewidth, relaxation and polarisation transfer studies confirm the conclusion in the previous report on d(m⁵C-G-C-G-m⁵C-G) (Tran-Dinh et al Biochemistry 1984 in the press) that Z exchanges only with B whereas the latter also exchanges with S,Z ? B ? S. The present data show that even at high salt concentration where only the Z form of d(C-G-m⁵C-G-C-G) is observed the Z-S transition also passes through the B form as an intermediate stage. The B-Z transition takes place when the Watson-Crick hydrogen bonds are firmly maintained and is greatly favoured when there are three hydrogen bonds between the base-pairs.