Sequence-dependent gating of an ion channel by DNA hairpin molecules

DNA hairpins produce ionic current signatures when captured by the alpha-hemolysin nano-scale pore under conditions of single molecule electrophoresis. Gating patterns produced by individual DNA hairpins when captured can be used to distinguish differences of a single base pair or even a single nucleotide [Vercoutere,W.A. et al. (2003) Nucleic Acids Res., 31, 1311–1318]. Here we investigate the mechanism(s) that may account for the ionic current gating signatures. The ionic current resistance profile of conductance states produced by DNA hairpin molecules with 3–12 bp stems showed a plateau in resistance between 10 and 12 bp, suggesting that hairpins with 10–12 bp stems span the pore vestibule. DNA hairpins with 9–12 bp stems produced gating signatures with the same relative conductance states. Systematic comparison of the conductance state dwell times and apparent activation energies for a series of 9–10 bp DNA hairpins suggest that the 3′ and 5′ ends interact at or near the limiting aperture within the vestibule of the alpha-hemolysin pore. The model presented may be useful in predicting and interpreting DNA detection using nanopore detectors. In addition, this well-defined molecular system may prove useful for investigating models of ligand-gated channels in biological membranes.     

Polycyclic aromatic hydrocarbons as plausible prebiotic membrane components

Aromatic molecules delivered to the young Earth during the heavy bombardment phase in the early history of our solar system were likely to be among the most abundant and stable organic compounds available. The Aromatic World hypothesis suggests that aromatic molecules might function as container elements, energy transduction elements and templating genetic components for early life forms. To investigate the possible role of aromatic molecules as container elements, we incorporated different polycyclic aromatic hydrocarbons (PAH) in the membranes of fatty acid vesicles. The goal was to determine whether PAH could function as a stabilizing agent, similar to the role that cholesterol plays in membranes today. We studied vesicle size distribution, critical vesicle concentration and permeability of the bilayers using C(6)-C(10) fatty acids mixed with amphiphilic PAH derivatives such as 1-hydroxypyrene, 9-anthracene carboxylic acid and 1,4 chrysene quinone. Dynamic Light Scattering (DLS) spectroscopy was used to measure the size distribution of vesicles and incorporation of PAH species was established by phase-contrast and epifluorescence microscopy. We employed conductimetric titration to determine the minimal concentration at which fatty acids could form stable vesicles in the presence of PAHs. We found that oxidized PAH derivatives can be incorporated into decanoic acid (DA) vesicle bilayers in mole ratios up to 1:10 (PAH:DA). Vesicle size distribution and critical vesicle concentration were largely unaffected by PAH incorporation, but 1-hydroxypyrene and 9-anthracene carboxylic acid lowered the permeability of fatty acid bilayers to small solutes up to 4-fold. These data represent the first indication of a cholesterol-like stabilizing effect of oxidized PAH derivatives in a simulated prebiotic membrane.     

Amphiphilic components of the murchison carbonaceous chondrite: Surface properties and membrane formation

We have investigated physicochemical properties of amphiphilic compounds in carbonaceous meteorites. The primary aim was to determine whether such materials represent plausible sources of lipid-like compounds that could have been involved as membrane components in primitive cells. Samples of the Murchison CM2 chondrite were extracted with chloroform-methanol, and the chloroform-soluble material was separated by two-dimensional thin layer chromatography. Fluorescnece, iodine stains and charring were used to identify major components on the plates. These were than scraped and eluted as specific fractions which were investigated by fluorescence and absorption spectra, surface chemical methods, gas chromatography-mass spectrometry, and electron microscopy. Fraction 5 was strongly fluorescent, and contained pyrene and fluoranthene, the major polycyclic aromatic hydrocarbons of the Murchison chondrite. This fraction was also present in extracts from the Murray and Mighei CM2 chondrites. Fraction 3 was surface active, forming apparent monomolecular films at air-water interfaces. Surface force measurements suggested that fraction 3 contained acidic groups. Fraction 1 was also surface active, and certain components could self-assemble into membranous vesicles which encapsulated polar solutes. The observations reported here demonstrate that organic compounds plausibly available on the primitive Earth through meteoritic infall are surface active, and have the ability to self-assemble into membranes.     

The chemical logic of a minimum protocell

Traditional schemes for the origin of cellular life on earth generally suppose that the chance assembly of polymer synthesis systems was the initial event, followed by incorporation into a membrane-enclosed volume to form the earliest cells. Here we discuss an alternative system consisting of replicating membrane vesicles, which we define as minimum protocells. These consist of vesicular bilayer membranes that self-assemble from relatively rare organic amphiphiles present in the prebiotic environment. If some of the amphiphiles are primitive pigment molecules asymmetrically oriented in the bilayer, light energy can be captured in the form of electrochemical ion gradients. This energy could then be used to convert relatively common precursor molecules into membrane amphiphiles, thereby providing an initial photosynthetic growth process, as well as an appropriate microenvironment for incorporation and evolution of polymer synthesis systems.     

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.     

Oxidative stress impairs the function of sarcoplasmic reticulum by oxidation of sulfhydryl groups in the Ca2+-ATPase

Sarcoplasmic reticulum (SR) microsomes were oxidized by exposure to peroxydisulfate, hydrogen peroxide, or iron/ascorbate or by extended storage. The decline in Ca2+-ATPase activity, Ca2+ transport, and the increase in Ca2+ permeability which occurred under these conditions did not appear to result from lipid oxidation because these functional changes were not correlated with the amount of thiobarbituric acid-reactive lipid. Consistent with this interpretation, lipid antioxidants did not prevent the decline in SR function. This suggests that inhibition was independent of lipid oxidation. Instead, oxidation directly inhibited the Ca2+-ATPase. The decline in enzyme activity may be due to oxidation of SH groups, as suggested by the ability of reducing agents to prevent inhibition, the decline in sulfhydryl content of oxidized SR, and the ability of sulfhydryl-binding agents to inhibit Ca2+-ATPase. Inhibition was not primarily due to crosslinking of the Ca2+-ATPase, because sodium dodecyl sulfate-polyacrylamide gels of normal and oxidized SR showed that the area of the Ca2+-ATPase band was not correlated with the Ca2+-ATPase activity. Inhibition of the Ca2+-ATPase by oxidative stress is relevant to models of cellular dysfunction in which toxicity is caused by a rise in intracellular calcium.