Search PubMed⌕ Search

Biomedical subjects

D W Deamer

Publications and source records attributed to D W Deamer.

At least 19 recordsLinked to original sources
PubMed2001

Eutectic phases in ice facilitate nonenzymatic nucleic acid synthesis.

Polymeric compounds similar to oligonucleotides are relevant to the origin of life and particularly to the concept of an RNA world. Although short oligomers of RNA can be synthesized nonenzymatically under laboratory conditions by second-order reactions in concentrated solutions, there is no consensus on how these polymers could have been synthesized de novo on the early Earth from dilute solutions of monomers. To address this question in the context of an RNA world, we have explored ice eutectic phases as a reaction medium. When an aqueous solution freezes, the solutes become concentrated in the spaces between the ice crystals. The increased concentration offsets the effect of the lower temperature and accelerates the reaction. Here we show that in the presence of metal ions in dilute solutions, frozen samples of phosphoimidazolide-activated uridine react within days at -18 degrees C to form oligouridylates up to 11 bases long. Product yields typically exceed 90%, and approximately 30% of the oligomers include one or more 3'-5' linkages. These conditions facilitate not only the notoriously difficult oligouridylate synthesis, but also the oligomerization of activated cytidylate, adenylate, and guanylate. To our knowledge, this represents the first report to indicate that ice matrices on the early Earth may have accelerated certain prebiotic polymerization reactions.

Biological Evolution↗
PubMed2000

Nanopores and nucleic acids: prospects for ultrarapid sequencing.

DNA and RNA molecules can be detected as they are driven through a nanopore by an applied electric field at rates ranging from several hundred microseconds to a few milliseconds per molecule. The nanopore can rapidly discriminate between pyrimidine and purine segments along a single-stranded nucleic acid molecule. Nanopore detection and characterization of single molecules represents a new method for directly reading information encoded in linear polymers. If single-nucleotide resolution can be achieved, it is possible that nucleic acid sequences can be determined at rates exceeding a thousand bases per second.

Bacterial Toxins↗
PubMed1999

Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules.

Single molecules of DNA or RNA can be detected as they are driven through an alpha-hemolysin channel by an applied electric field. During translocation, nucleotides within the polynucleotide must pass through the channel pore in sequential, single-file order because the limiting diameter of the pore can accommodate only one strand of DNA or RNA at a time. Here we demonstrate that this nanopore behaves as a detector that can rapidly discriminate between pyrimidine and purine segments along an RNA molecule. Nanopore detection and characterization of single molecules represent a new method for directly reading information encoded in linear polymers, and are critical first steps toward direct sequencing of individual DNA and RNA molecules.

Bacterial Toxins↗
PubMed1998

Permeation of halide anions through phospholipid bilayers occurs by the solubility-diffusion mechanism.

Two alternative mechanisms are frequently used to describe ionic permeation of lipid bilayers. In the first, ions partition into the hydrophobic phase and then diffuse across (the solubility-diffusion mechanism). The second mechanism assumes that ions traverse the bilayer through transient hydrophilic defects caused by thermal fluctuations (the pore mechanism). The theoretical predictions made by both models were tested for halide anions by measuring the permeability coefficients for chloride, bromide, and iodide as a function of bilayer thickness, ionic radius, and sign of charge. To vary the bilayer thickness systematically, liposomes were prepared from monounsaturated phosphatidylcholines (PC) with chain lengths between 16 and 24 carbon atoms. The fluorescent dye MQAE (N-(ethoxycarbonylmethyl)-6-methoxyquinolinium bromide) served as an indicator for halide concentration inside the liposomes and was used to follow the kinetics of halide flux across the bilayer membranes. The observed permeability coefficients ranged from 10(-9) to 10(-7) cm/s and increased as the bilayer thickness was reduced. Bromide was found to permeate approximately six times faster than chloride through bilayers of identical thickness, and iodide permeated three to four times faster than bromide. The dependence of the halide permeability coefficients on bilayer thickness and on ionic size were consistent with permeation of hydrated ions by a solubility-diffusion mechanism rather than through transient pores. Halide permeation therefore differs from that of a monovalent cation such as potassium, which has been accounted for by a combination of the two mechanisms depending on bilayer thickness.

Anions↗
PubMed1997

Biological potential of extraterrestrial materials. 2. Microbial and plant responses to nutrients in the Murchison carbonaceous meteorite.

Meteoritic materials are investigated as potential early planetary nutrients. Aqueous extracts of the Murchison C2 carbonaceous meteorite are utilized as a sole carbon source by microorganisms, as demonstrated by the genetically modified Pseudomonas fluorescence equipped with the lux gene. Nutrient effects are observed also with the soil microorganisms Nocardia asteroides and Arthrobacter pascens that reach populations up to 5 x 10(7) CFU/ml in meteorite extracts, similar to populations in terrestrial soil extracts. Plant tissue cultures of Asparagus officinalis and Solanum tuberosum (potato) exhibit enhanced pigmentation and some enhanced growth when meteorite extracts are added to partial nutrient media, but inhibited growth when added to full nutrient solution. The meteorite extracts lead to large increases in S, Ca, Mg, and Fe plant tissue contents as shown by X-ray fluorescence, while P, K, and Cl contents show mixed effects. In both microbiological and plant tissue experiments, the nutrient and inhibitory effects appear to be best balanced for growth at about 1:20 (extracted solid : H2O) ratios. The results suggest that solutions in cavities in meteorites can provide efficient concentrated biogenic and early nutrient environments, including high phosphate levels, which may be the limiting nutrient. The results also suggest that carbonaceous asteroid resources can sustain soil microbial activity and provide essential macronutrients for future space-based ecosystems.

Arthrobacter↗
PubMed1997

Redox chemistry at liquid/liquid interfaces.

The interface between two immiscible liquids with immobilized photosynthetic pigments can serve as the simplest model of a biological membrane convenient for the investigation of photoprocesses accompanied by spatial separation of charges. As it follows from thermodynamics, if the resolvation energies of substrates and products are very different, the interface between two immiscible liquids may act as a catalyst. Theoretical aspects of charge transfer reactions at oil/water interfaces are discussed. Conditions under which the free energy of activation of the interfacial reaction of electron transfer decreases are established. The activation energy of electron transfer depends on the charges of the reactants and dielectric permittivity of the non-aqueous phase. This can be useful when choosing a pair of immiscible solvents to decrease the activation energy of the reaction in question or to inhibit an undesired process. Experimental interfacial catalytic systems are discussed. Amphiphilic molecules such as chlorophyll or porphyrins were studied as catalysts of electron transfer reactions at the oil/water interface.

Benzene↗
PubMed1997

The first living systems: a bioenergetic perspective.

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.

Energy Metabolism↗
PubMed1996

Characterization of individual polynucleotide molecules using a membrane channel.

We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. The passage of each molecule is detected as a transient decrease of ionic current whose duration is proportional to polymer length. Channel blockades can therefore be used to measure polynucleotide length. With further improvements, the method could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA.

Base Sequence↗
PubMed1996

Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness.

Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and ionic solute permeation. These two mechanisms make distinctively different predictions about the permeability coefficient as a function of bilayer thickness. Whereas the solubility-diffusion mechanism predicts only a modest variation related to bilayer thickness, the pore model predicts an exponential relationship. To test these models, we measured the permeability of phospholipid bilayers to protons, potassium ions, water, urea, and glycerol. Bilayers were prepared as liposomes, and thickness was varied systematically by using unsaturated lipids with chain lengths ranging from 14 to 24 carbon atoms. The permeability coefficient of water and neutral polar solutes displayed a modest dependence on bilayer thickness, with an approximately linear fivefold decrease as the carbon number varied from 14 to 24 atoms. In contrast, the permeability to protons and potassium ions decreased sharply by two orders of magnitude between 14 and 18 carbon atoms, and leveled off, when the chain length was further extended to 24 carbon atoms. The results for water and the neutral permeating solutes are best explained by the solubility-diffusion mechanism. The results for protons and potassium ions in shorter-chain lipids are consistent with the transient pore model, but better fit the theoretical line predicted by the solubility-diffusion model at longer chain lengths.

Biophysical Phenomena↗
PubMed1996

Electrical double layers at the oil/water interface.

This review presents the historical development and current status of the theory of the electrical double layer at a liquid/liquid interface. It gives rigorous thermodynamic definitions of all basic concepts related to liquid interfaces and to the electrical double layer. The difference between the surface of a solid electrode and the interface of two immiscible electrolyte solutions (ITIES) is analyzed in connection to their electrical properties. The most important classical relationships for the electrical double layer are presented and critically discussed. The generalized adsorption isotherm is derived. After a short review of the classical Gouy-Chapman and Verwey-Niessen models, more recent developments of the double layer theory are presented. These include effects of variable dielectric permittivity, nonlocal electrostatics, hydration forces, the modified Poisson-Boltzmann equation and the ion-dipole plasma. The relative merits of different theories are estimated by comparing them with computer simulation of the ITIES and electrical double layer. Special attention is given to the structure of ITIES and its variation due to adsorption of ions and amphiphilic molecules.

Adsorption↗
PubMed1995

Energy conversion at liquid/liquid interfaces: artificial photosynthetic systems.

This chapter focuses on multielectron reactions in organized assemblies of molecules at the liquid/liquid interface. We describe the thermodynamic and kinetic parameters of such reactions, including the structure of the reaction centers, charge movement along the electron transfer pathways, and the role of electric double layers in artificial photosynthesis. Some examples of artificial photosynthesis at the oil/water interface are considered, including water photooxidation to the molecular oxygen, oxygen photoreduction, photosynthesis of amphiphilic compounds and proton evolution by photochemical processes.

Chlorophyll↗
PubMed1994

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.

Adenosine Diphosphate↗
PubMed1994

Permeation of membranes by the neutral form of amino acids and peptides: relevance to the origin of peptide translocation.

The flux of amino acids and other nutrient solutes such as phosphate across lipid bilayers (liposomes) is 10(5) slower than facilitated inward transport across biological membranes. This suggest that primitive cells lacking highly evolved transport systems would have difficulty transporting sufficient nutrients for cell growth to occur. There are two possible ways by which early life may have overcome this difficulty: (1) The membranes of the earliest cellular life-forms may have been intrinsically more permeable to solutes; or (2) some transport mechanism may have been available to facilitate transbilayer movement of solutes essential for cell survival and growth prior to the evolution of membrane transport proteins. Translocation of neutral species represents one such mechanism. The neutral forms of amino acids modified by methylation (creating protonated weak bases) permeate membranes up to 10(10) times faster than charged forms. This increased permeability when coupled to a transmembrane pH gradient can result in significantly increased rates of net unidirectional transport. Such pH gradients can be generated in vesicles used to model protocells that preceded and were presumably ancestral to early forms of life. This transport mechanism may still play a role in some protein translocation processes (e.g. for certain signal sequences, toxins and thylakoid proteins) in vivo.

Amino Acids↗
PubMed1994

Alpha-helical hydrophobic polypeptides form proton-selective channels in lipid bilayers.

Proton translocation is important in membrane-mediated processes such as ATP-dependent proton pumps, ATP synthesis, bacteriorhodopsin, and cytochrome oxidase function. The fundamental mechanism, however, is poorly understood. To test the theoretical possibility that bundles of hydrophobic alpha-helices could provide a low energy pathway for ion translocation through the lipid bilayer, polyamino acids were incorporated into extruded liposomes and planar lipid membranes, and proton translocation was measured. Liposomes with incorporated long-chain poly-L-alanine or poly-L-leucine were found to have proton permeability coefficients 5 to 7 times greater than control liposomes, whereas short-chain polyamino acids had relatively little effect. Potassium permeability was not increased markedly by any of the polyamino acids tested. Analytical thin layer chromatography measurements of lipid content and a fluorescamine assay for amino acids showed that there were approximately 135 polyleucine or 65 polyalanine molecules associated with each liposome. Fourier transform infrared spectroscopy indicated that a major fraction of the long-chain hydrophobic peptides existed in an alpha-helical conformation. Single-channel recording in both 0.1 N HCl and 0.1 M KCl was also used to determine whether proton-conducting channels formed in planar lipid membranes (phosphatidylcholine/phosphatidylethanolamine, 1:1). Poly-L-leucine and poly-L-alanine in HCl caused a 10- to 30-fold increase in frequency of conductive events compared to that seen in KCl or by the other polyamino acids in either solution. This finding correlates well with the liposome observations in which these two polyamino acids caused the largest increase in membrane proton permeability but had little effect on potassium permeability. Poly-L-leucine was considerably more conductive than poly-L-alanine due primarily to larger event amplitudes and, to a lesser extent, a higher event frequency. Poly-L-leucine caused two populations of conductive events, one in the 0.1-0.5 pA range, and one in the 1.0-5.0 pA range, whereas nearly all events caused by poly-L-alanine were in the 0.1-0.5 pA range at an applied voltage of +60 mV. The channel-like activity appeared to switch between conductive and nonconductive states, with most open-times in the range of 50-200 ms. We conclude that hydrophobic polyamino acids produce proton-conducting defects in lipid bilayers that may be used to model functional proton channels in biological membranes.

Alamethicin↗
PubMed1992

Permeability of lipid bilayers to amino acids and phosphate.

Permeability coefficients for amino acid classes, including neutral, polar, hydrophobic, and charged species, were measured and compared with values for other ionic solutes such as phosphate. The rates of efflux of glycine, lysine, phenylalanine, serine and tryptophan were determined after they were passively entrapped in large unilamellar vesicles (LUVs) composed of egg phosphatidylcholine (EPC) or dimyristoylphosphatidylcholine (DMPC). The following permeability coefficients were obtained for: glycine, 5.7 x 10(-12) cm s-1 (EPC), 2.0 x 10(-11) cm s-1 (DMPC); serine, 5.5 x 10(-12) cm s-1 (EPC), 1.6 x 10(-11) cm s-1 (DMPC); lysine, 5.1 x 10(-12) cm s-1 (EPC), 1.9 x 10(-11) cm s-1 (DMPC); tryptophan, 4.1 x 10(-10) cm s-1 (EPC); and phenylalanine, 2.5 x 10(-10) cm s-1 (EPC). Decreasing lipid chain length increased permeability slightly, while variations in pH had only minor effects on the permeability coefficients of the amino acids tested. Phosphate permeability was in the range of 10(-12)-10(-13) cm s-1 depending on the pH of the medium. The values for the polar and charged amino acids were surprisingly similar to those previously measured for monovalent cations such as sodium and potassium, which are in the range of 10(-12)-10(-13) cm s-1, depending on conditions and the lipid species used. This observation suggests that the permeation rates for the neutral, polar and charged amino acids are controlled by bilayer fluctuations and transient defects, rather than partition coefficients and Born energy barriers. The results are relevant to the permeation of certain peptides into lipid bilayers during protein translocation and membrane biogenesis.

Amino Acids↗
PubMed1992

Polycyclic aromatic hydrocarbons: primitive pigment systems in the prebiotic environment.

Polycyclic aromatic hydrocarbons (PAH) in the form of polymerized derivatives represent over 90% of the organic material of carbonaceous chondrites. It now appears likely that there was substantial survival of the organic content of meteoritic and cometary infall during late accretion, so that PAH would presumably be major components of the organic inventory present on the prebiotic Earth. An important question relative to chemical evolution and energy transduction is the nature of pigments which could be available to make light energy available to the earliest cellular forms of life. PAH and their derivatives all absorb light in the near UV and blue wavelengths, and are candidates for primitive pigments. We have explored this possibility in a model system consisting of mixtures of pyrene, fluoranthene and pyrene derivatives with hexadecane, dispersed in dilute salt solutions. Upon illumination, photochemical oxidation of the hexadecane occurs, with long-chain amphiphiles such as 2-hexadecanone and 2-hexadecanol as products. Because the reaction proceeds under strictly anaerobic conditions, the source of oxygen is apparently water. We also observed acid pH shifts during illumination. Photochemical production of hydrogen ion is significant, in that chemiosmotic proton gradients across membranes are used by all contemporary cells as a source of energy for ATP synthesis and nutrient transport. To test whether the protons could be used to transduce light energy into a useful form, PAH derivatives were included in lipid bilayer membranes (liposomes). Upon illumination, protons (or acidic products) were produced and accumulated inside the vesicles, so that substantial pH gradients were established across the membranes, acid inside. We conclude that PAH dissolved in aliphatic hydrocarbons absorb light energy and use it to oxidize the hydrocarbon to long-chain amphiphilic molecules. The oxidation is accompanied by release of protons. If PAH derivatives are included in the bilayer membrane of lipid vesicles, protons accumulate within the membrane-bounded volumes to form proton gradients. This system provides a useful model of a primitive photochemical reaction in which light energy is transduced into potentially useable forms.

Alkanes↗