Measurement of net proton-hydroxyl permeability of large unilamellar liposomes with the fluorescent pH probe, 9-aminoacridine

The fluorescent probe 9-aminoacridine was used to measure the rate of decay of experimentally established pH gradients across liposome membranes. From the rate of decay, separate permeability coefficients for protons (PH) and hydroxyls (POH) were calculated and summed to yield the net proton-hydroxyl permeability (Pnet). The net permeability of protons and hydroxyls was found to be approximately 10(-4) cm/s, six orders of magnitude greater than that measured for sodium and pyrophosphate ions under similar conditions. This suggests that protons and/or hydroxyls cross lipid bilayers by a different mechanism than do other monovalent cations and anions. In addition, the measurements provide a standard for net proton-hydroxyl permeability in pure phospholipid bilayers for comparison with biological membranes.     

Carbon dioxide efflux accompanies release of fertilization acid from sea urchin eggs

“Fertilization acid” is released from sea urchin eggs upon fertilization and decreases the pH of the surrounding seawater. In bicarbonate-free artificial seawater flushed with nitrogen gas, the pH shift still occurs but returns to the original value in a few minutes, suggesting that the released acid is volatile. A likely candidate for a volatile acid is carbon dioxide released from the eggs. Therefore, the total CO₂ content of seawater was measured pre- and post-fertilization and was found to be correlated stoichiometrically with released proton equivalents, leading to the conclusion that fertilization acid is largely carbon dioxide. Manometric analysis of cell extracts and ashed eggs suggest that the carbon dioxide may be stored in the unfertilized egg as an inorganic carbonate.     

Properties, composition, and structure of stearic acid-stearate monolayers on alkaline earth solutions

Interactions between alkaline earth ions and the carboxylate ligand in a stearic acid surface film have been investigated by IR spectrophotometry and surface chemical procedures. The frequency and shape of the carboxylate absorption band and the effect of hydration and pH on band characteristics suggest that beryllium, magnesium, and calcium ions form calcium-type complexes with the stearate ligand while strontium and barium ions form both calcium-type complexes and more ionic barium-type complexes, which have lower carboxylate band maxima. Since IR band frequencies in anhydrous calcium-type complexes are directly proportional to the charge/(crystal radius) ratio, it is apparent that covalency decreases in the order: Be > Mg > Ca > Sr > Ba. The decreasing order of stability constants estimated from spectrophotometric titration data, Be > Ca > Mg > Sr > Ba, demonstrates that calcium behaves anomalously. This anomalous behavior is also apparent in the high solid-to-liquid phase transition temperature and small surface area of the calcium-carboxylate film compared to films composed of complexes with the other ions. A geometric factor related to the ionic radius and the radius of the carboxylate binding site formed by a calcium stearate lattice is proposed to explain the unique properties of calcium-carboxylate surface films. Although the beryllium complex has the highest carboxylate band frequency and stability constant, it gives an atypical "expanded" surface film. A hydrogen bonded lattice formed with a soluble beryllium monohydrate is suggested as an explanation for this film property.     

Self-assembly processes in the prebiotic environment

An important question guiding research on the origin of life concerns the environmental conditions where molecular systems with the properties of life first appeared on the early Earth. An appropriate site would require liquid water, a source of organic compounds, a source of energy to drive polymerization reactions and a process by which the compounds were sufficiently concentrated to undergo physical and chemical interactions. One such site is a geothermal setting, in which organic compounds interact with mineral surfaces to promote self-assembly and polymerization reactions. Here, we report an initial study of two geothermal sites where mixtures of representative organic solutes (amino acids, nucleobases, a fatty acid and glycerol) and phosphate were mixed with high-temperature water in clay-lined pools. Most of the added organics and phosphate were removed from solution with half-times measured in minutes to a few hours. Analysis of the clay, primarily smectite and kaolin, showed that the organics were adsorbed to the mineral surfaces at the acidic pH of the pools, but could subsequently be released in basic solutions. These results help to constrain the range of possible environments for the origin of life. A site conducive to self-assembly of organic solutes would be an aqueous environment relatively low in ionic solutes, at an intermediate temperature range and neutral pH ranges, in which cyclic concentration of the solutes can occur by transient dry intervals.     

Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules

Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore.     

Unexpected differences between D- and L- tyrosine lead to chiral enhancement in racemic mixtures.

We report here an unexpected difference in the solubilities of D- and L-tyrosine in water, which could be discerned by their rate of crystallization and the resulting concentrations of their saturated solutions. A supersaturated solution of 10 mM L-tyrosine at 20 degrees C crystallized much more slowly than that of D-tyrosine under the same conditions, and the saturated solution of L-tyrosine was more concentrated than that of D-tyrosine. Supersaturated solutions of 10 mM DL-tyrosine in water formed precipitates of predominantly D-tyrosine and DL-tyrosine, resulting in an excess of L-tyrosine in the saturated solution. The experimental setups were monitored independently by UV-absorption, radioactivity tracing, optical rotation and X-ray diffraction. The process of nucleation and crystallization of D- and L-tyrosine is characterized by an exceptionally high cooperativity. It is possible that minute energy differences between D- and L-tyrosine, originating from parity violation or other non-conservative chiral discriminatory rules, could account for the observations. The physical process that initiated chiral selection in biological systems remains a challenging problem in understanding the origin of life, and it is possible that chiral compounds were concentrated from supersaturated racemic mixtures by preferential crystallization.     

Production of RNA by a polymerase protein encapsulated within phospholipid vesicles

Catalyzed polymerization reactions represent a primary anabolic activity of all cells. It can be assumed that early cells carried out such reactions, in which macromolecular catalysts were encapsulated within some type of boundary membrane. In the experiments described here, we show that a template-independent RNA polymerase (polynucleotide phosphorylase) can be encapsulated in dimyristoyl phosphatidylcholine vesicles without substrate. When the substrate adenosine diphosphate (ADP) was provided externally, long-chain RNA polymers were synthesized within the vesicles. Substrate flux was maximized by maintaining the vesicles at the phase transition temperature of the component lipid. A protease was introduced externally as an additional control. Free enzyme was inactivated under identical conditions. RNA products were visualized in situ by ethidium bromide fluorescence. The products were harvested from the liposomes, radiolabeled, and analyzed by polyacrylamide gel electrophoresis. Encapsulated catalysts represent a model for primitive cellular systems in which an RNA polymerase was entrapped within a protected microenvironment.Abbreviations ADP adenosine diphosphate - DMPC dimyristoyl phosphatidylcholine - EDTA ethylenediaminetetraacetic acid - LUV large unilamellar vesicle - MLV multilamellar vesicle - PAGE polyacrylamide gel electrophoresis - PNPase or PNP polynucleotide phosphorylase - SUV small unilamellar vesicle Correspondence to.: A.C. Chakrabarti